Contacts of the helix formed by residues 144 - 157 (chain B) in PDB entry 1G8I
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 THR 144 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.7 10.8 + - - -
142B GLU 3.3 1.3 - - - +
143B ASN* 1.3 94.4 + - - +
145B PRO* 1.3 74.6 - - + +
146B GLU* 3.6 13.1 + - - +
147B LYS* 3.0 39.4 + - + +
148B ARG 3.2 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.8 13.2 - - + -
125B VAL* 3.7 24.2 - - + -
126B ASP* 3.8 36.8 - - + +
129B TYR* 3.8 21.9 - - + -
144B THR* 1.3 84.0 - - + +
146B GLU* 1.3 75.5 + - - +
148B ARG* 3.3 2.1 + - + +
149B VAL* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 4.0 18.1 + - - +
122B LEU* 3.8 28.3 - - + +
144B THR* 3.1 11.5 - - - +
145B PRO* 1.3 92.6 - - - +
147B LYS* 1.3 57.3 + - + +
149B VAL* 3.9 2.6 - - - +
150B ASP* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 2.8 38.3 + - - +
141B GLU* 3.6 22.9 - - - +
142B GLU* 4.4 1.1 - - - -
143B ASN* 2.8 22.2 + - - +
144B THR* 3.0 30.4 + - - +
146B GLU* 1.3 75.8 - - + +
148B ARG* 1.3 65.3 + - - +
150B ASP* 3.5 7.5 + - - +
151B ARG* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.9 24.0 - - + -
129B TYR* 3.8 22.7 - - + +
142B GLU* 5.1 17.5 + - + +
144B THR 3.2 3.4 + - - +
145B PRO 3.6 7.0 - - - +
147B LYS* 1.3 78.9 - - - +
149B VAL* 1.3 62.5 + - - +
151B ARG* 3.3 15.4 + - - +
152B ILE* 3.1 54.4 + - + +
155B MET* 6.1 0.4 - - - -
176B ASP* 5.4 4.6 + - - -
178B SER* 5.7 2.2 + - - -
179B ILE* 4.6 15.0 - - - +
953B 1PE 3.0 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.6 41.1 - - + +
121B MET* 4.0 5.8 - - + -
122B LEU* 3.6 34.1 - - + +
125B VAL* 3.9 17.5 - - + -
145B PRO 3.0 19.5 + - - +
146B GLU* 3.9 4.3 - - - +
148B ARG* 1.3 74.0 - - - +
150B ASP* 1.3 64.2 + - - +
152B ILE* 3.8 5.8 - - - +
153B PHE* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.3 31.7 + - - -
146B GLU* 3.0 25.8 + - - +
147B LYS* 3.9 7.9 - - - +
148B ARG 3.3 0.4 - - - -
149B VAL* 1.3 78.7 - - - +
151B ARG* 1.3 56.3 + - - +
153B PHE* 3.8 4.1 - - - +
154B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU 6.1 0.2 - - - +
147B LYS 3.2 17.7 + - - +
148B ARG* 3.6 18.2 - - - +
149B VAL 3.3 0.2 - - - -
150B ASP* 1.3 74.3 - - - +
152B ILE* 1.3 66.4 + - - +
154B ALA* 3.2 9.6 + - - +
155B MET* 3.0 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B MET* 3.7 34.5 - - + -
148B ARG* 3.1 60.4 + - + +
149B VAL 3.8 4.3 - - - +
151B ARG* 1.3 75.4 - - - +
153B PHE* 1.3 60.5 + - + +
155B MET* 3.2 11.1 + - - -
156B MET* 2.8 58.9 + - + +
164B LEU* 4.7 1.3 - - + -
176B ASP* 5.6 0.4 - - - +
179B ILE* 4.5 5.8 - - + -
953B 1PE 4.2 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.5 19.7 - - + -
117B THR 3.7 1.8 - - - -
118B ARG* 3.6 30.3 - - + -
121B MET* 3.7 28.3 - - + -
149B VAL* 3.0 28.3 + - + +
150B ASP* 4.1 3.8 - - - +
152B ILE* 1.3 74.6 - - + +
154B ALA* 1.3 67.6 + - - +
155B MET 3.0 1.8 - - - -
156B MET* 4.3 1.6 - - - +
157B ASP* 3.0 42.8 + - + +
162B GLY* 3.7 28.0 - - - -
163B LYS 3.8 1.1 - - - -
164B LEU* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP 2.9 19.8 + - - +
151B ARG* 3.2 12.5 + - - +
153B PHE* 1.3 78.5 - - - +
155B MET* 1.3 62.1 + - + +
157B ASP 4.9 4.3 + - - +
158B LYS* 5.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 6.1 0.7 - - - -
151B ARG* 3.0 69.8 + - - +
152B ILE* 3.7 9.9 - - + +
154B ALA* 1.3 80.7 - - - +
156B MET* 1.3 66.8 + - + +
158B LYS* 3.6 23.9 + - - -
172B GLY* 4.9 10.1 - - - +
175B ALA* 5.8 2.5 - - + -
176B ASP* 3.2 40.4 - - + +
179B ILE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 2.8 45.1 + - + +
155B MET* 1.3 83.2 - - + +
157B ASP* 1.3 60.3 + - - +
158B LYS* 3.0 17.4 + - - +
164B LEU* 3.9 22.7 - - + -
168B GLU* 3.5 26.9 - - - +
169B PHE* 4.0 13.5 - - - +
172B GLY* 3.6 41.1 - - - +
173B SER* 3.7 16.6 - - - +
179B ILE* 3.9 18.4 - - + -
953B 1PE 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 3.0 28.6 + - + +
154B ALA 4.9 3.3 - - - +
155B MET 3.9 0.4 - - - -
156B MET* 1.3 74.3 - - - +
158B LYS* 1.3 61.9 + - - +
159B ASN* 3.2 4.2 - - - +
160B ALA* 3.3 19.3 + - - +
161B ASP* 3.0 6.3 + - - +
162B GLY* 2.7 31.2 + - - -
163B LYS 3.7 5.8 - - - -
164B LEU* 3.6 15.3 - - + +
168B GLU* 3.9 0.7 - - - -
1602B CA 2.3 29.9 - - - -
----------------------------------------------------------
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