Contacts of the helix formed by residues 117 - 143 (chain D) in PDB entry 4CKG
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 LEU 117 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 4.2 12.6 - - + +
31D LEU* 4.9 13.2 - - + -
32D GLU* 3.7 31.4 - - + +
35D LEU* 5.4 3.1 - - + -
112D LEU* 4.1 24.0 - - + +
113D VAL* 5.1 7.2 + - - +
115D GLU 3.6 0.2 - - - -
116D GLY* 1.3 82.1 - - - +
118D ARG* 1.3 56.2 + - - +
119D GLY 3.4 1.8 - - - -
120D PHE* 3.4 13.1 + - + +
121D ARG* 2.9 66.3 + - + +
180D ILE* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LYS* 4.9 15.6 + - - +
115D GLU* 3.7 38.0 + - - +
116D GLY 3.5 1.2 - - - -
117D LEU* 1.3 76.3 - - - +
119D GLY* 1.3 57.7 + - - +
121D ARG* 3.4 7.2 + - - +
122D GLU* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLU 5.4 0.2 + - - -
116D GLY 5.4 0.6 + - - -
117D LEU 3.4 0.2 - - - -
118D ARG* 1.3 75.7 - - - +
120D PHE* 1.3 58.8 + - - +
122D GLU* 3.6 8.9 - - - +
123D ALA* 2.9 30.5 + - - +
176D GLN* 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.1 29.8 - - + -
25D GLU* 4.3 4.9 - - + -
28D VAL* 3.6 34.5 - - + -
116D GLY 5.7 0.9 + - - +
117D LEU 3.4 9.5 + - - +
119D GLY* 1.3 76.2 - - - +
121D ARG* 1.4 68.5 + - + +
123D ALA* 3.5 1.5 + - - +
124D ARG* 3.0 49.8 + - - +
173D TYR* 3.4 37.6 - + - -
176D GLN* 3.5 24.2 + - + +
177D ILE* 4.3 6.1 - - + -
180D ILE* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 3.7 24.2 + - - +
29D SER* 4.9 4.6 + - - +
32D GLU* 2.8 45.0 + - - +
113D VAL 5.8 0.4 + - - -
117D LEU* 2.9 37.3 + - + +
118D ARG* 3.4 7.1 + - - +
119D GLY 3.3 0.2 - - - -
120D PHE* 1.4 85.8 - - + +
122D GLU* 1.4 57.3 + - - +
124D ARG* 3.7 11.7 + - - +
125D ARG* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ARG* 3.0 23.6 + - - +
119D GLY* 3.6 10.5 - - - +
121D ARG* 1.4 71.8 - - - +
123D ALA* 1.4 61.4 + - - +
125D ARG* 2.8 35.8 + - - +
126D ASP* 3.2 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D GLY 2.9 21.9 + - - +
120D PHE 4.0 2.5 - - - +
122D GLU* 1.4 70.8 - - - +
124D ARG* 1.4 52.7 + - - +
126D ASP* 3.5 4.9 + - - +
127D PHE* 2.8 38.7 + - - +
169D ARG 5.1 0.7 - - - +
172D ASP* 4.0 28.9 - - + +
173D TYR* 4.1 13.4 - - + +
176D GLN* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 2.7 43.1 + - - +
120D PHE* 3.0 36.3 + - - +
121D ARG* 3.7 11.7 + - - +
123D ALA* 1.4 76.2 - - - +
125D ARG* 1.4 61.1 + - - +
127D PHE* 3.4 2.8 + - - +
128D TRP* 3.0 50.5 + - + +
173D TYR* 3.4 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ARG 3.0 20.6 + - - +
122D GLU* 2.8 36.0 + - - +
124D ARG* 1.4 77.1 - - - +
126D ASP* 1.4 59.3 + - - +
128D TRP* 4.5 5.1 - - - +
129D ARG* 3.0 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLU* 3.2 20.4 + - + +
123D ALA* 3.8 5.4 - - - +
125D ARG* 1.4 77.0 - - - +
127D PHE* 1.3 57.0 + - - +
129D ARG* 3.2 5.8 - - - +
130D GLY 2.9 23.9 + - - -
169D ARG* 2.8 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PHE* 3.7 21.5 - + - -
21D ILE* 3.8 20.4 - - + -
123D ALA 2.8 22.8 + - - +
124D ARG 3.6 5.6 - - - +
126D ASP* 1.3 71.4 - - - +
128D TRP* 1.3 88.3 + + - +
130D GLY* 3.2 4.2 + - - -
131D ALA* 3.1 23.6 + - - +
166D TYR* 3.5 37.8 - + - -
169D ARG* 3.9 14.5 - - + +
170D ALA* 3.8 25.6 - - + -
173D TYR* 3.4 36.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ARG* 4.3 24.2 - - - -
21D ILE* 3.4 39.7 - - + -
22D GLU* 6.2 0.2 - - - -
25D GLU* 3.6 22.0 + - - -
124D ARG* 3.0 50.1 + - + +
125D ARG* 4.5 3.8 - - - +
127D PHE* 1.3 85.6 - + - +
129D ARG* 1.4 60.5 + - - +
131D ALA* 3.3 18.3 + - + +
132D GLU* 2.9 29.0 + - - +
166D TYR* 5.3 2.5 - - - -
173D TYR* 4.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ARG* 3.0 31.8 + - - +
126D ASP* 3.2 11.4 - - - +
128D TRP* 1.4 74.4 - - - +
130D GLY* 1.4 60.7 + - - +
132D GLU* 2.8 49.5 + - - +
133D SER* 3.1 29.3 + - - +
169D ARG* 3.7 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP 2.9 15.5 + - - -
127D PHE 3.2 5.7 + - - -
129D ARG* 1.4 70.6 - - - +
131D ALA* 1.3 56.7 + - - +
133D SER* 4.0 5.1 + - - -
134D LEU* 3.1 25.1 + - - +
162D ALA 4.3 3.1 - - - +
166D TYR* 3.9 17.5 + - - +
169D ARG* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D PHE 3.1 8.2 + - - +
128D TRP* 3.5 29.4 - - + +
129D ARG 3.3 0.2 - - - -
130D GLY* 1.3 74.6 - - - +
132D GLU* 1.4 55.6 + - - +
133D SER 3.5 0.2 - - - -
134D LEU* 3.7 5.2 - - - +
135D GLU* 2.7 37.5 + - - +
166D TYR* 3.7 27.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D TRP 2.9 14.0 + - - +
129D ARG* 2.8 50.3 + - - +
131D ALA* 1.4 73.1 - - - +
133D SER* 1.3 67.6 + - - +
135D GLU* 3.4 9.5 + - - +
136D ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ARG* 3.1 19.3 + - - +
130D GLY* 4.0 6.2 - - - -
132D GLU* 1.3 83.6 - - - +
134D LEU* 1.4 54.8 + - - -
136D ALA* 3.4 9.1 - - - +
137D ALA* 3.0 29.0 + - - +
162D ALA* 4.5 7.9 - - - -
169D ARG* 5.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP* 6.0 0.2 - - - +
130D GLY 3.1 20.5 + - - +
131D ALA* 3.8 6.1 - - - +
132D GLU 3.4 0.4 - - - -
133D SER* 1.4 70.9 - - - +
135D GLU* 1.4 55.6 + - - +
138D LEU* 2.8 58.9 + - + +
159D LEU* 4.5 7.0 - - + +
162D ALA* 4.0 15.0 - - + +
163D ARG* 3.7 50.7 - - + +
166D TYR* 3.3 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 5.7 8.7 - - - -
131D ALA 2.7 22.9 + - - +
132D GLU* 3.6 8.9 - - - +
134D LEU* 1.4 70.1 - - - +
136D ALA* 1.4 61.7 + - - +
138D LEU* 3.5 13.1 - - + +
139D THR* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLU* 3.1 14.1 + - + +
133D SER* 3.4 13.7 - - - +
135D GLU* 1.4 74.9 - - - +
137D ALA* 1.3 56.5 + - - +
139D THR* 3.2 11.2 - - - -
140D HIS* 2.8 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D SER 3.0 17.1 + - - +
134D LEU* 3.8 2.9 - - + +
136D ALA* 1.3 71.7 - - - +
138D LEU* 1.4 59.7 + - - +
140D HIS* 3.7 11.3 - - + +
141D ASN* 2.9 29.6 + - - +
158D ALA* 4.1 14.1 - - + +
159D LEU* 4.1 11.4 + - - +
162D ALA* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C GLU* 3.6 17.7 - - - +
273C PHE* 3.6 7.7 - - + -
285C ARG* 3.7 39.3 - - - +
343C ASP* 3.9 13.2 - - + +
134D LEU* 2.8 44.0 + - + +
135D GLU* 3.5 11.7 - - + +
137D ALA* 1.4 70.1 - - - +
139D THR* 1.4 61.5 + - - +
141D ASN* 3.6 6.0 + - - +
142D ALA* 3.4 22.7 + - - +
159D LEU* 3.6 21.8 - - + -
163D ARG* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 3.8 22.4 - - + -
285C ARG* 5.9 0.5 - - - -
325C ARG* 5.4 1.3 + - - +
135D GLU* 3.2 13.1 + - - +
136D ALA* 3.2 14.3 + - - -
138D LEU* 1.4 76.5 - - - +
140D HIS* 1.4 64.2 + - - +
142D ALA* 3.0 12.7 + - + +
143D GLU* 3.1 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA 2.8 19.5 + - - +
137D ALA* 3.7 10.3 - - - +
138D LEU 3.4 0.2 - - - -
139D THR* 1.4 74.4 - - - +
141D ASN* 1.4 57.1 + - - +
142D ALA 3.3 0.9 + - - -
143D GLU* 3.5 29.9 + - - +
151D GLU* 5.7 5.8 - - + -
154D GLU* 4.5 8.8 + - - +
155D ALA* 4.0 30.1 - - + +
158D ALA* 3.8 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ARG* 2.8 49.9 + - - +
327C PHE* 6.1 0.2 - - - -
343C ASP* 2.9 39.0 + - - +
137D ALA 2.9 19.1 + - - +
138D LEU 3.7 6.9 + - - +
139D THR 3.4 0.2 - - - -
140D HIS* 1.4 59.5 - - - +
142D ALA* 1.3 60.6 - - - +
143D GLU 3.6 0.2 - - - -
144D VAL* 3.9 5.0 - - - +
155D ALA* 4.3 8.5 - - - +
156D GLY* 3.8 9.2 - - - -
159D LEU* 3.4 38.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 3.4 40.6 - - + -
325C ARG* 3.5 18.4 - - - +
326C ARG* 5.9 0.2 - - - +
341C GLN* 3.4 32.6 + - + +
342C ALA 6.5 0.2 - - - -
343C ASP* 5.3 1.8 - - - +
138D LEU 3.4 5.9 + - - +
139D THR 3.0 6.1 + - - +
141D ASN* 1.3 78.8 - - - +
143D GLU* 1.4 53.9 + - - +
144D VAL* 2.9 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ARG* 3.4 27.7 + - - +
139D THR* 3.1 25.3 + - + +
140D HIS* 3.5 28.6 + - - +
142D ALA* 1.4 71.2 - - - +
144D VAL* 1.3 64.6 + - - +
145D PRO* 3.6 10.1 - - - +
151D GLU* 4.5 8.3 - - - +
----------------------------------------------------------
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