Contacts of the helix formed by residues 110 - 131 (chain B) in PDB entry 7KAC
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 SER 110 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER 4.1 0.6 + - - -
109B LEU* 1.3 73.0 - - - +
111B GLU* 1.3 64.7 + - - +
112B LEU* 3.7 7.6 + - - +
113B GLN* 3.0 39.6 + - - +
114B ILE* 3.0 25.7 + - - +
243B TRP* 4.9 1.6 - - - -
283B LEU* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 1.3 73.8 - - - +
112B LEU* 1.3 55.9 + - + +
114B ILE* 3.5 7.0 + - - +
115B SER* 2.7 36.1 + - - +
242B LYS 4.6 0.9 - - - +
243B TRP* 3.5 29.3 - - + -
244B SER* 2.6 49.0 + - - -
247B PHE* 3.7 24.7 - - + -
273B LEU* 3.5 16.4 - - + +
276B GLN* 5.2 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 3.2 6.3 + - - +
111B GLU* 1.3 76.8 - - + +
113B GLN* 1.3 66.1 + - - +
115B SER* 3.3 2.4 + - - -
116B TYR 3.1 17.8 + - - -
276B GLN* 3.7 32.8 - - - +
277B PRO 5.5 2.7 - - - +
278B GLY 5.7 2.2 - - - +
279B LEU* 3.6 9.8 - - + +
283B LEU* 3.4 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER 5.0 0.2 - - - +
109B LEU* 3.7 10.4 - - + -
110B SER* 3.0 38.5 + - - +
112B LEU* 1.3 76.3 - - - +
114B ILE* 1.4 60.7 + - - +
116B TYR* 3.5 3.3 + - - +
117B VAL* 3.2 27.5 + - - +
283B LEU* 3.0 44.5 + - + +
284B ILE* 4.0 10.4 - - + +
286B ASP* 4.4 5.9 - - - +
287B LEU* 3.6 40.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.7 27.1 - - + +
110B SER 3.0 22.6 + - - +
111B GLU* 3.8 4.9 - - - +
113B GLN* 1.4 74.6 - - - +
115B SER* 1.3 59.5 + - - +
117B VAL* 3.4 5.6 + - - +
118B CYS* 2.9 43.1 + - - -
205B ALA* 4.1 13.9 - - + +
208B LEU* 3.8 13.5 - - + -
209B ALA* 3.7 37.0 - - + +
243B TRP* 4.6 1.1 - - + -
247B PHE* 4.0 28.0 - - + -
273B LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 2.7 23.4 + - - +
112B LEU 3.3 6.5 + - - -
114B ILE* 1.3 73.9 - - - +
116B TYR* 1.3 60.3 + - - +
118B CYS* 4.0 6.5 - - - +
119B ARG* 3.1 27.5 + - - +
273B LEU* 3.3 50.1 - - - +
274B VAL* 4.5 2.9 - - - +
276B GLN* 3.5 12.1 + - - -
279B LEU* 3.8 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU 3.1 16.0 + - - +
113B GLN* 3.8 4.0 - - - +
114B ILE 3.3 0.2 - - - -
115B SER* 1.3 74.4 - - - +
117B VAL* 1.3 65.5 + - - +
119B ARG* 3.2 15.2 + - - +
120B GLU* 3.0 54.9 + - + +
149B GLY 3.2 26.3 + - - -
150B GLU* 4.0 9.5 - - - +
151B VAL* 3.6 15.0 - - + -
279B LEU* 3.9 11.8 - - + +
280B ASN* 3.5 33.0 - - - -
281B ARG* 3.4 19.5 + - - +
283B LEU* 3.9 13.0 - - + -
284B ILE* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.5 37.2 - - + -
109B LEU* 4.6 4.3 - - + -
113B GLN 3.2 17.3 + - - +
114B ILE 3.4 4.2 + - - +
116B TYR* 1.3 77.9 - - - +
118B CYS* 1.3 57.6 + - - +
120B GLU* 3.2 2.3 + - - +
121B VAL* 2.9 42.9 + - + +
143B ILE* 4.4 7.9 - - + -
151B VAL* 4.4 15.7 - - + -
201B LEU* 5.9 1.1 - - + -
204B THR* 5.8 0.7 - - + -
208B LEU* 4.0 14.1 - - + -
284B ILE* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 2.9 40.9 + - - +
115B SER* 4.0 6.5 - - - +
117B VAL* 1.3 77.7 - - - +
119B ARG* 1.4 57.8 + - - +
121B VAL* 4.0 0.7 - - - +
122B LEU* 2.9 37.3 + - - +
201B LEU* 4.2 18.1 - - + +
205B ALA* 4.0 10.8 - - - -
208B LEU* 5.7 1.3 - - - -
250B PHE* 3.8 37.9 - - + -
273B LEU* 5.3 2.0 - - + -
274B VAL* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER 3.1 19.2 + - - +
116B TYR* 3.2 16.3 + - - +
118B CYS* 1.4 74.4 - - - +
120B GLU* 1.3 80.5 + - - +
122B LEU* 3.3 3.3 + - - +
123B GLN* 3.0 46.7 + - - +
269B LEU* 3.9 5.7 - - + +
274B VAL* 3.5 42.3 + - + +
276B GLN 5.3 2.2 + - - -
279B LEU* 3.1 40.6 + - + +
280B ASN* 4.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 3.0 37.1 + - - +
116B TYR* 3.0 50.9 + - + +
117B VAL 3.2 1.1 + - - +
119B ARG* 1.3 106.2 + - - +
121B VAL* 1.3 61.4 + - - +
123B GLN* 3.1 20.9 + - - +
124B GLY 3.2 16.6 + - - -
150B GLU* 5.9 0.3 - - - -
151B VAL* 3.5 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 2.9 26.8 + - + +
118B CYS 4.0 0.4 - - - +
120B GLU* 1.3 74.7 - - - +
122B LEU* 1.3 57.2 + - - +
124B GLY* 3.1 3.1 + - - -
125B LEU* 2.8 43.0 + - + +
138B ILE* 4.4 9.0 - - + -
143B ILE* 3.7 28.3 - - + -
151B VAL* 4.4 8.1 - - + -
153B LEU* 3.8 27.8 - - + +
201B LEU* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B CYS 2.9 22.3 + - - +
119B ARG 3.6 4.3 - - - +
121B VAL* 1.3 75.1 - - - +
123B GLN* 1.3 56.5 + - - +
125B LEU* 3.3 6.1 + - + +
126B ALA* 2.9 30.8 + - - +
198B ILE* 4.2 11.0 - - + -
201B LEU* 3.5 20.4 - - + -
250B PHE* 4.2 9.0 - - + -
265B ALA* 3.9 18.6 - - + +
268B MET* 3.6 40.4 - - + +
269B LEU* 3.7 13.6 - - + +
274B VAL* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 3.7 18.8 + - + +
73B ASN* 2.9 24.0 + - - +
119B ARG* 3.0 43.3 + - - +
120B GLU* 3.1 23.2 + - - +
121B VAL 3.2 0.2 - - - -
122B LEU* 1.3 75.5 - - - +
124B GLY* 1.3 62.9 + - - +
126B ALA* 3.5 3.5 + - - +
127B TYR 3.3 16.6 + - - -
269B LEU* 4.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 4.3 1.6 - - - -
73B ASN* 3.8 12.4 - - - +
74B ILE* 3.5 24.8 - - - +
120B GLU 3.2 5.6 + - - -
121B VAL 3.1 6.7 + - - -
123B GLN* 1.3 80.0 - - - +
125B LEU* 1.3 55.8 + - - +
127B TYR* 3.5 0.9 + - - +
128B LEU* 3.1 31.7 + - - +
153B LEU* 4.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 2.8 40.3 + - + +
122B LEU* 3.8 10.8 - - + +
124B GLY* 1.3 69.4 - - - +
126B ALA* 1.3 61.3 + - - +
128B LEU* 4.3 8.3 - - + -
129B HIS* 2.9 42.2 + - + +
135B HIS* 4.4 0.4 - - + -
138B ILE* 3.9 20.6 - - + -
153B LEU* 3.9 7.4 - - + -
197B ASP* 3.7 52.0 - - + +
198B ILE* 4.3 11.4 - - + -
201B LEU* 4.7 4.0 - - + -
265B ALA* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU 2.9 17.6 + - - +
123B GLN* 3.9 5.4 - - - +
125B LEU* 1.3 76.0 - - - +
127B TYR* 1.3 61.9 + - - +
129B HIS* 3.7 3.3 + - - +
130B SER* 3.1 24.4 + - - -
265B ALA* 3.6 12.7 - - + +
266B THR* 3.7 31.1 - - + +
269B LEU* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR 3.2 13.9 + - - -
69B CYS* 3.8 23.3 - - + -
70B ARG* 2.9 39.2 + - - +
71B HIS* 3.5 43.7 - + + +
74B ILE* 3.9 9.0 - - + -
123B GLN 3.3 6.1 + - - +
124B GLY 3.7 5.8 - - - +
125B LEU 3.2 0.2 - - - -
126B ALA* 1.3 75.1 - - - +
128B LEU* 1.3 68.8 + - - +
130B SER* 2.6 23.5 + - - -
131B GLN* 3.1 44.0 + - + +
133B LYS* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B CYS* 3.5 32.3 - - - -
74B ILE* 4.4 5.6 - - + -
124B GLY 3.1 21.1 + - - +
125B LEU* 3.4 9.2 + - + +
127B TYR* 1.3 76.5 - - - +
129B HIS* 1.3 63.3 + - + +
131B GLN* 3.2 10.0 + - - +
132B LYS 3.4 0.2 + - - -
133B LYS* 2.9 49.9 + - + +
134B ILE 6.0 0.2 - - - -
135B HIS* 4.2 16.6 - - + +
153B LEU* 3.9 21.3 - - + -
156B PHE* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 2.9 35.4 + - + +
126B ALA* 4.2 4.5 - - - +
128B LEU* 1.3 76.4 - - + +
130B SER* 1.3 60.1 + - - +
132B LYS* 3.0 32.1 + - - -
133B LYS 3.3 20.2 - - - +
194B GLU* 3.2 49.4 + - + +
195B LEU* 5.9 1.0 - - + +
197B ASP* 2.9 32.0 + - + +
198B ILE* 4.6 10.5 - - + +
264B SER* 6.2 0.2 - - - -
265B ALA* 4.2 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 3.1 15.5 + - - -
127B TYR* 2.6 25.3 + - - -
129B HIS* 1.3 75.0 - - - +
131B GLN* 1.3 70.5 + - - +
132B LYS* 3.2 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.8 4.3 - - - +
127B TYR* 3.1 45.0 + - + +
128B LEU* 3.2 6.9 + - - +
130B SER* 1.3 89.5 + - - +
132B LYS* 1.3 69.5 + - - +
133B LYS* 3.3 35.0 + - - +
----------------------------------------------------------
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