Contacts of the helix formed by residues 161 - 178 (chain B) in PDB entry 4BPK
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 VAL 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 5.7 6.3 - - + -
159B MET* 4.7 4.3 - - + +
160B GLN* 1.3 86.1 + - - +
162B LEU* 1.3 76.3 + - + +
163B VAL 3.4 0.4 + - - -
164B SER* 3.8 10.6 + - - +
165B ARG* 3.5 42.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 4.0 12.1 - - + -
116B PRO* 4.1 21.1 - - + +
119B ALA* 3.7 28.9 - - + -
154B SER* 3.9 22.4 - - - +
159B MET* 3.4 31.9 - - + +
160B GLN 3.0 1.0 - - - -
161B VAL* 1.3 92.1 - - + +
163B VAL* 1.3 60.5 + - - +
165B ARG* 3.0 25.1 + - - +
166B ILE* 2.8 37.9 + - + +
169B TRP* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.4 0.2 - - + -
17A LEU* 3.9 15.7 - - + -
24A TRP* 3.8 26.4 - - + +
151B CYS* 3.8 34.5 - - + +
154B SER* 4.9 3.1 - - - -
155B VAL* 3.9 28.9 - - + -
160B GLN* 3.1 21.9 + - + +
162B LEU* 1.3 77.2 - - - +
164B SER* 1.3 57.8 + - - +
166B ILE* 3.4 3.5 + - - +
167B ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 4.7 4.5 + - - -
24A TRP* 4.1 20.2 - - - -
160B GLN 4.6 1.2 + - - -
161B VAL* 3.8 10.8 + - - +
163B VAL* 1.3 76.9 - - - +
165B ARG* 1.3 69.0 + - - +
167B ALA* 3.5 2.6 + - - +
168B ALA* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 4.8 9.5 + - - +
161B VAL* 3.5 48.1 + - - +
162B LEU* 3.0 23.1 + - - +
164B SER* 1.3 77.8 + - - +
166B ILE* 1.3 61.4 + - - +
168B ALA* 3.0 8.1 + - - +
169B TRP* 2.9 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 5.8 1.8 - - + -
123B PHE* 4.8 2.0 - - + -
147B GLY* 4.1 6.7 - - - +
150B LEU* 3.7 49.4 - - + +
151B CYS* 3.8 20.6 - - - -
154B SER* 3.9 10.3 - - - +
162B LEU* 2.8 26.6 + - + +
163B VAL 3.7 4.7 - - - +
165B ARG* 1.3 75.9 - - - +
167B ALA* 1.3 57.0 + - - +
169B TRP* 3.1 30.7 + - + +
170B MET* 2.9 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 4.2 9.5 + - - +
9A VAL* 3.7 12.2 - - + +
10A VAL* 4.9 2.9 - - + -
13A LEU* 3.6 26.8 - - + +
24A TRP* 3.6 30.7 - - + -
163B VAL 3.1 8.4 + - - +
164B SER 3.7 3.4 - - - +
166B ILE* 1.3 74.6 - - - +
168B ALA* 1.3 58.1 + - - +
170B MET* 3.4 2.6 + - - +
171B ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 4.2 13.0 - - - +
164B SER 3.2 11.0 + - - +
165B ARG* 3.0 11.3 + - - +
167B ALA* 1.3 78.0 - - - +
169B TRP* 1.3 68.9 + - + +
171B ALA* 3.3 4.8 + - - +
172B THR* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO 6.0 0.2 - - - -
119B ALA* 3.9 15.7 - - + -
120B TYR* 3.5 60.7 - + + -
123B PHE* 3.6 37.5 - + + -
150B LEU* 5.2 0.4 - - + -
162B LEU* 5.3 3.1 - - + -
165B ARG* 2.9 47.0 + - + +
166B ILE* 3.1 31.6 + - + +
168B ALA* 1.3 78.7 - - + +
170B MET* 1.3 59.3 + - - +
172B THR* 3.9 5.0 - - - -
173B TYR* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.0 12.1 - - + -
13A LEU* 4.0 25.1 - - + -
123B PHE* 3.7 21.8 - - + -
143B PHE* 3.6 25.5 - - + +
144B PHE* 3.9 43.7 - - + +
147B GLY* 3.7 25.1 - - - -
166B ILE* 2.9 24.2 + - + +
167B ALA 3.6 4.7 - - - +
169B TRP* 1.3 76.5 - - - +
171B ALA* 1.3 60.7 + - - +
173B TYR 3.2 0.3 + - - -
174B LEU* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 5.7 0.4 - - - +
5A ASN* 5.5 0.2 - - + -
6A ARG* 4.2 35.0 - - + +
9A VAL* 4.1 10.5 - - + +
167B ALA 2.9 18.9 + - - +
168B ALA* 3.3 6.9 + - - +
170B MET* 1.3 76.9 - - - +
172B THR* 1.3 57.4 + - - +
174B LEU* 3.5 5.2 + - - +
175B ASN* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 3.0 18.6 + - - +
169B TRP* 3.9 5.6 - - - -
171B ALA* 1.3 75.1 - - - +
173B TYR* 1.3 60.5 + - - +
175B ASN* 3.4 5.0 + - - +
176B ASP* 2.8 48.7 + - + +
1197B CD 4.0 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 4.8 7.0 - + + -
124B GLU* 6.5 1.3 - - + -
127B VAL* 3.5 24.4 + - + +
128B ASN* 3.9 16.9 + - - -
131B PHE* 3.4 42.3 - + - +
143B PHE* 3.8 21.3 - + + -
169B TRP 3.0 18.9 + - - +
170B MET* 3.8 3.4 - - - +
172B THR* 1.3 73.2 - - - +
174B LEU* 1.3 62.3 + - - +
177B HIS* 2.9 61.0 + + + +
178B LEU* 3.3 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.5 48.0 - - + +
8A LEU* 4.8 5.8 - - + -
9A VAL* 4.0 13.5 - - + -
140B ILE* 5.4 0.4 - - + -
143B PHE* 4.5 3.1 - - + -
144B PHE* 4.0 18.8 - - + -
170B MET 2.8 16.8 + - - +
171B ALA 3.6 4.0 - - - +
173B TYR* 1.3 76.5 - - - +
175B ASN* 1.3 58.5 + - - +
178B LEU* 3.2 32.9 + - + -
179B GLU* 2.7 32.6 + - - +
182B ILE* 4.0 17.9 - - + -
188B TRP* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 25.3 - - - +
2A SER* 3.4 31.7 + - - +
5A ASN* 2.7 38.7 + - - +
171B ALA* 2.9 18.4 + - - +
172B THR* 3.7 5.4 - - - +
174B LEU* 1.3 78.7 - - - +
176B ASP* 1.3 69.5 + - - +
179B GLU* 3.6 15.4 - - - +
180B PRO* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 2.8 33.6 + - + +
175B ASN* 1.3 82.7 + - - +
177B HIS* 1.3 80.8 + - + +
180B PRO* 4.1 11.9 - - - +
1197B CD 2.5 30.5 - - - -
1198B CD 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.6 8.5 - - - +
172B THR* 6.4 0.2 - - + -
173B TYR* 2.9 54.5 + + + +
176B ASP* 1.3 94.0 + - + +
178B LEU* 1.3 66.0 + - - +
179B GLU 3.9 0.4 - - - -
180B PRO* 4.1 6.4 - - - +
181B TRP* 5.1 2.6 + - - +
1198B CD 2.4 30.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.6 42.0 - - + -
135B VAL* 4.0 16.2 - - + -
140B ILE* 4.4 10.8 - - + -
143B PHE* 4.0 17.5 - - + -
173B TYR* 3.3 31.4 + - + +
174B LEU* 3.2 32.7 + - + +
177B HIS* 1.3 82.9 - - - +
179B GLU* 1.3 68.0 + - - +
180B PRO* 3.3 2.2 - - - -
181B TRP* 3.2 8.9 + - - +
182B ILE* 3.0 31.1 + - + +
----------------------------------------------------------
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