Contacts of the helix formed by residues 110 - 134 (chain N) in PDB entry 1KYO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 110 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105N SER* 3.3 24.3 + - - +
106N TYR 4.4 0.2 - - - -
107N ARG 3.0 6.7 + - - +
109N PRO* 1.3 89.9 - - + +
111N VAL* 1.3 62.7 + - - +
112N THR* 3.4 1.8 - - - -
113N LEU* 3.0 42.8 - - + +
114N TRP* 3.1 8.8 + - - +
200N ALA 5.5 2.9 - - - +
201N LEU 6.1 0.2 - - - +
204N HIS* 3.3 30.0 + - + +
205N GLY 2.7 35.3 + - - +
206N SER 3.8 5.9 + - - -
207N SER* 4.2 24.1 + - - +
314N ARG* 3.0 36.2 - - - +
522N HEC 4.9 7.9 - - - -
52R GLU* 4.8 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N TYR 3.4 20.0 - - - +
107N ARG 3.8 8.5 - - - +
108N SER 4.2 10.1 - - - +
109N PRO 3.2 4.1 + - - +
110N ARG* 1.3 73.7 - - - +
112N THR* 1.3 55.3 - - + +
114N TRP* 3.0 4.9 + - - +
115N ASN* 2.6 57.2 + - - +
303N LEU 5.9 0.2 - - - +
306N PRO* 3.9 24.9 - - + -
307N PHE* 5.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 5.0 5.2 - - + +
9C TYR* 4.1 17.0 + - - -
109N PRO 3.9 16.8 - - - +
110N ARG* 4.8 0.4 - - - -
111N VAL* 1.3 74.4 - - + +
113N LEU* 1.3 57.8 + - + +
115N ASN* 3.1 10.5 + - - +
116N VAL* 2.9 36.3 + - - +
200N ALA* 4.1 15.3 - - + +
203N ILE* 6.1 4.9 - - + -
204N HIS* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N ARG* 3.0 34.5 + - + +
111N VAL 3.0 0.4 - - - -
112N THR* 1.3 82.1 + - + +
114N TRP* 1.3 59.8 + - - +
116N VAL* 3.3 1.8 + - - +
117N GLY 3.0 17.3 + - - -
197N HIS* 3.2 58.7 + - + +
200N ALA* 4.0 15.2 - - + +
201N LEU* 3.8 27.6 - - + +
522N HEC 3.4 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 114 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N MET* 4.1 24.2 - - + -
100N GLY* 4.6 3.6 - - - -
101N LEU* 4.4 24.2 - - + -
106N TYR* 3.4 39.9 - + + +
110N ARG 3.1 7.9 + - - +
111N VAL 3.0 7.4 + - - +
113N LEU* 1.3 81.4 - - - +
115N ASN* 1.3 70.0 + - - +
117N GLY* 3.1 3.3 + - - +
118N VAL* 2.9 39.4 + - + +
302N LEU* 2.9 46.8 + - + -
303N LEU* 4.9 0.2 - - - -
305N LEU* 4.9 9.2 - - + +
306N PRO* 4.5 10.4 - - + +
522N HEC 3.6 55.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N VAL* 2.6 44.0 + - - +
112N THR* 3.7 8.2 - - - +
114N TRP* 1.3 80.2 - - - +
116N VAL* 1.3 65.0 + - + +
118N VAL* 3.2 10.9 + - - +
119N ILE* 3.3 19.9 + - + +
303N LEU* 3.3 35.8 - - + +
307N PHE* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.7 26.7 - - + +
112N THR* 2.9 25.5 + - - +
113N LEU* 3.6 6.1 - - - +
115N ASN* 1.3 75.7 - - + +
117N GLY* 1.3 64.9 + - - +
119N ILE* 2.9 23.9 + - + +
120N ILE* 3.0 17.6 + - + +
193N MET* 3.6 33.0 - - - +
196N MET* 4.4 7.2 - - + +
197N HIS* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113N LEU 3.0 12.8 + - - -
114N TRP 3.1 4.9 + - - -
116N VAL* 1.3 77.7 - - - +
118N VAL* 1.3 60.5 + - - +
120N ILE* 3.2 6.5 + - - +
121N PHE 3.0 10.6 + - - -
197N HIS* 3.9 5.3 + - - -
522N HEC 3.0 51.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N TRP* 2.9 35.0 + - - +
115N ASN 3.6 7.0 - - - +
116N VAL 3.1 0.4 - - - -
117N GLY* 1.3 72.8 - - - +
119N ILE* 1.3 67.9 + - + +
121N PHE* 3.2 9.3 + - + +
122N THR* 3.1 27.1 + - - +
299N ILE* 4.5 20.9 - - + +
300N LEU* 5.5 3.4 - - + -
302N LEU* 4.3 14.8 - - + -
303N LEU* 3.8 33.9 - - + -
522N HEC 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N ASN* 3.3 14.1 + - + +
116N VAL* 2.9 15.0 + - + +
118N VAL* 1.3 77.6 - - + +
120N ILE* 1.3 60.1 + - - +
122N THR* 3.0 10.6 + - - -
123N LEU* 2.8 47.8 + - + +
193N MET* 4.3 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N MET* 4.8 2.2 - - + -
116N VAL* 3.4 12.6 - - + +
117N GLY* 3.2 10.3 + - - +
119N ILE* 1.3 76.9 - - - +
121N PHE* 1.3 50.5 + - - +
123N LEU* 3.8 7.8 - - - -
124N THR* 2.7 51.1 + - - +
190N ILE* 4.2 12.1 - - + -
193N MET* 3.6 41.1 - - + +
194N VAL* 4.0 13.0 - - + +
197N HIS* 4.0 20.0 - - + -
522N HEC 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N PHE* 4.8 5.4 - + - -
93N MET* 3.8 26.9 - - + -
94N PHE* 4.1 20.2 - + - -
97N MET* 3.8 30.3 - - + -
117N GLY 3.0 12.7 + - - +
118N VAL* 3.4 12.3 - - + +
119N ILE 3.1 0.2 - - - -
120N ILE* 1.3 76.4 - - - +
122N THR* 1.3 62.4 + - - +
124N THR* 3.7 0.9 - - - -
125N ILE* 3.1 58.4 + - + +
278N PHE* 3.8 31.6 - + - -
299N ILE* 4.3 23.1 - - + -
302N LEU* 4.8 7.9 - - + -
522N HEC 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N VAL* 3.1 12.5 + - - +
119N ILE* 3.0 10.8 + - - -
121N PHE* 1.3 79.6 - - - +
123N LEU* 1.3 63.5 + - + +
125N ILE* 3.6 5.5 + - - +
126N ALA* 3.2 21.6 + - + +
296N PHE* 6.5 1.8 - - + -
299N ILE* 4.0 24.6 - - + +
300N LEU* 5.9 1.9 - - - +
525N SMA 3.6 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N ILE* 2.8 39.9 + - + +
120N ILE* 3.8 5.4 - - - +
122N THR* 1.3 77.3 - - + +
124N THR* 1.3 59.7 - - - +
126N ALA* 3.1 9.8 + - + +
127N THR* 2.8 31.9 + - - -
186N VAL* 3.8 23.0 - - + +
189N ILE* 4.4 15.9 - - + -
190N ILE* 4.1 14.8 - - + -
193N MET* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89N PHE* 4.5 24.7 - - + -
90N PHE* 3.9 21.1 - - + -
93N MET* 3.9 22.0 - - + +
120N ILE* 2.7 39.3 + - - +
121N PHE 3.7 3.1 - - - -
123N LEU* 1.3 68.8 - - - +
125N ILE* 1.3 60.7 + - - +
127N THR* 3.2 1.4 + - - -
128N ALA* 2.9 29.8 + - - +
190N ILE* 3.9 18.1 - - + +
521N HEC 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N PHE* 3.8 25.6 - - + -
121N PHE* 3.1 54.3 + - + +
122N THR* 3.8 5.2 - - - +
124N THR* 1.3 75.3 - - - +
126N ALA* 1.3 62.3 + - - +
128N ALA* 3.5 2.6 + - - +
129N PHE* 3.1 22.5 + - - +
274N TYR* 6.0 0.2 - - - -
275N LEU* 4.1 16.7 - - + +
278N PHE* 4.6 8.3 - - + -
299N ILE* 4.4 14.6 - - + -
525N SMA 3.4 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N THR* 3.2 14.5 + - + +
123N LEU* 3.1 16.7 + - + +
125N ILE* 1.3 74.5 - - - +
127N THR* 1.3 66.2 + - - +
129N PHE* 3.2 7.4 + - - +
130N LEU* 2.9 33.6 + - + +
186N VAL* 5.5 2.9 - - + -
525N SMA 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123N LEU 2.8 18.4 + - - -
124N THR* 3.5 6.1 - - - -
126N ALA* 1.3 71.6 - - - +
128N ALA* 1.3 58.7 + - - +
130N LEU* 3.1 10.7 + - - +
131N GLY 3.0 11.1 + - - -
183N HIS* 2.8 35.3 + - - +
186N VAL* 3.3 12.9 - - + +
187N PRO* 3.6 33.4 - - + -
190N ILE* 3.2 18.4 - - + +
521N HEC 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N PHE* 3.9 27.6 - - + -
124N THR 2.9 16.5 + - - +
125N ILE 3.6 5.6 - - - +
127N THR* 1.3 75.6 - - - +
129N PHE* 1.3 56.3 + - - +
131N GLY 3.3 1.2 + - - -
132N TYR* 3.0 25.5 + - - +
274N TYR* 4.2 14.6 - - + +
521N HEC 3.5 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125N ILE 3.1 17.4 + - - +
126N ALA 3.8 5.4 - - - -
128N ALA* 1.3 73.3 - - - +
130N LEU* 1.3 75.8 + - + +
132N TYR* 3.5 8.9 + + + +
133N CYS* 3.1 47.1 + - - -
143N GLY* 3.7 11.0 - - - -
144N ALA* 4.0 8.1 - - - -
147N ILE* 3.3 44.0 - - + -
148N THR* 5.0 2.0 - - + -
179N PHE* 4.6 11.0 - + - -
272N GLU* 5.0 10.5 - - - +
275N LEU* 5.3 3.8 - - + +
525N SMA 3.5 57.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126N ALA* 2.9 22.4 + - + +
127N THR* 3.4 7.2 - - - +
129N PHE* 1.3 85.1 - - + +
131N GLY* 1.3 62.1 + - - +
133N CYS* 3.3 18.8 + - - +
134N CYS* 3.6 11.4 - - - -
179N PHE* 3.5 44.9 - - + +
182N LEU* 3.9 23.6 - - + -
183N HIS* 3.8 14.6 - - + +
186N VAL* 4.0 20.6 - - + -
525N SMA 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N THR 3.0 10.5 + - - -
128N ALA 3.7 1.3 - - - -
129N PHE 3.3 0.2 - - - -
130N LEU* 1.3 74.0 - - - +
132N TYR* 1.3 63.7 + - - +
133N CYS 3.1 2.5 - - - -
134N CYS* 3.1 15.4 + - - +
135N VAL 4.1 1.2 + - - -
183N HIS* 3.2 33.4 + - - -
521N HEC 3.4 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N ALA 3.0 17.6 + - - +
129N PHE* 3.8 8.3 - + + +
130N LEU 3.4 0.2 - - - -
131N GLY* 1.3 76.2 - - - +
133N CYS* 1.3 61.0 + - - +
134N CYS 3.4 0.2 + - - -
135N VAL* 3.7 7.8 + - - +
139N MET* 3.2 44.6 - - + +
140N SER* 2.8 27.6 + - - -
143N GLY* 5.8 3.4 - - - -
253N HIS* 4.0 15.7 + - - +
256N ASN* 3.8 19.6 - - + +
270N VAL 5.3 1.6 + - - -
272N GLU* 3.3 50.6 + - + +
274N TYR* 5.2 0.9 - - - +
521N HEC 3.6 32.4 - - + -
525N SMA 4.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 133 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N PHE* 3.1 46.7 - - - -
130N LEU* 3.3 9.8 + - - +
131N GLY 3.1 0.8 - - - -
132N TYR* 1.3 80.2 - - - +
134N CYS* 1.3 55.6 + - - +
136N TYR* 2.9 26.0 + - - +
140N SER* 3.6 10.2 - - - +
143N GLY* 4.9 0.4 - - - -
144N ALA* 3.8 27.1 - - + -
176N ILE* 4.3 14.3 - - + +
179N PHE* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N TYR* 2.6 42.4 + - + +
61N ALA* 4.1 5.4 - - - +
65N VAL* 4.3 0.8 - - - +
130N LEU 3.6 15.7 - - - -
131N GLY* 3.1 17.0 + - - +
133N CYS* 1.3 75.7 - - - +
135N VAL* 1.3 59.7 + - - +
136N TYR* 3.1 0.9 - - - -
176N ILE* 4.7 6.5 - - - -
179N PHE* 4.5 1.8 - - - -
180N PHE* 3.7 44.9 - - - -
183N HIS* 4.5 4.5 - - - -
521N HEC 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il