Contacts of the helix formed by residues 23 - 34 (chain B) in PDB entry 4JVS
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 GLY 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.2 3.4 + - - -
22B VAL* 1.3 80.1 - - - +
24B LYS* 1.3 58.9 + - - +
26B CYS* 3.2 2.8 + - - +
27B LEU* 2.9 36.5 + - - +
124B ASN* 3.4 11.4 + - - -
400B GDP 3.0 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 20.5 - - + +
17B ILE* 3.4 33.4 - - - +
18B GLY* 3.3 13.0 - - - +
19B ASP 2.8 21.6 + - - -
22B VAL* 3.9 10.7 - - + -
23B GLY* 1.3 72.1 - - - +
25B SER* 1.3 60.1 + - - +
27B LEU* 3.5 4.4 + - - +
28B LEU* 3.2 23.4 + - - +
66B ASP* 3.7 11.7 - - - +
67B THR* 3.1 27.1 - - - +
69B GLY 4.1 1.1 - - - +
90B VAL* 4.1 14.8 - - + -
400B GDP 2.6 46.2 + - - +
401B AF3 3.4 5.7 - - - -
402B MG 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 1.3 73.8 - - - +
26B CYS* 1.3 57.7 + - - +
28B LEU* 3.5 3.8 + - - +
29B LEU* 3.1 26.5 + - - +
41B ILE 5.8 1.6 - - - -
43B THR* 2.5 19.4 + - - -
49B LYS* 5.5 1.2 + - - -
66B ASP* 2.9 20.0 + - - -
400B GDP 2.2 42.1 + - - -
402B MG 2.7 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.6 7.2 - - - +
25B SER* 1.3 76.6 - - - +
27B LEU* 1.3 59.2 + - - +
29B LEU* 3.1 10.2 + - - +
30B ARG* 2.9 29.1 + - - +
35B THR 4.8 1.2 - - - +
36B TYR* 3.9 19.1 - - + -
37B THR* 4.0 15.9 - - - -
155B ALA* 3.8 19.6 - - + +
400B GDP 3.1 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.4 8.5 - - + -
23B GLY 2.9 21.3 + - - +
24B LYS* 3.7 5.4 - - - +
26B CYS* 1.3 76.5 - - - +
28B LEU* 1.3 62.1 + - - +
30B ARG 3.3 1.2 + - - -
31B PHE* 3.1 20.6 + - - +
88B ILE* 6.1 0.4 - - + -
90B VAL* 3.7 37.7 - - + -
122B VAL* 4.3 6.1 - - + -
124B ASN* 3.7 15.9 - - - +
153B THR* 3.2 28.7 - - + +
155B ALA* 3.8 6.2 - - + +
161B VAL* 3.5 37.7 - - + +
164B SER* 6.2 1.1 - - - -
165B PHE* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.2 8.3 - - + -
24B LYS 3.2 14.8 + - - +
25B SER* 3.9 5.8 - - - +
27B LEU* 1.3 79.9 - - - +
29B LEU* 1.3 56.8 + - - +
31B PHE* 3.6 3.3 + - + -
32B ALA* 3.1 26.9 + - + +
47B ASP* 5.3 1.1 - - + +
48B PHE 4.7 1.3 - - - -
49B LYS* 3.9 34.3 + - + +
64B ILE* 3.7 46.9 - - + +
66B ASP* 3.5 36.1 - - + +
165B PHE* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 3.1 18.1 + - - +
26B CYS* 3.1 10.3 + - - +
28B LEU* 1.3 76.6 - - - +
30B ARG* 1.3 58.8 + - - +
32B ALA* 5.0 0.2 - - - -
33B ASP* 3.0 47.9 + - - +
34B ASP 3.3 4.3 + - - -
35B THR* 3.6 27.7 + - - +
36B TYR* 5.1 0.4 - - - -
37B THR* 4.2 27.1 - - + +
49B LYS* 3.6 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS 2.9 16.3 + - - +
27B LEU* 3.6 6.1 - - - +
29B LEU* 1.3 74.4 - - - +
31B PHE* 1.3 63.4 + - - +
34B ASP* 2.9 63.4 + - - +
35B THR* 3.6 9.4 + - - +
36B TYR* 3.4 18.9 - - + +
155B ALA* 2.9 20.9 + - - +
156B LYS 2.8 29.9 + - - -
157B ASN 4.5 0.4 - - - -
158B ALA* 3.6 25.1 - - + +
161B VAL* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU 3.1 8.1 + - - +
28B LEU* 3.8 5.6 - - + +
29B LEU 3.3 0.2 - - - -
30B ARG* 1.3 80.2 - - - +
32B ALA* 1.3 64.8 + - - +
33B ASP 3.7 0.2 + - - -
34B ASP* 4.5 0.9 + - - +
51B ARG* 3.4 47.1 + - + -
62B LEU* 4.0 11.4 - - + -
64B ILE* 3.6 33.2 - - + -
161B VAL* 4.0 4.4 - - + +
162B GLU* 3.6 34.8 - - - +
165B PHE* 3.5 56.1 - + + -
166B MET* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.1 18.0 + - + +
29B LEU 4.5 0.2 - - - +
31B PHE* 1.3 80.8 - - + +
33B ASP* 1.3 73.2 + - - +
49B LYS* 3.8 33.4 - - + -
50B ILE 5.8 1.1 - - - +
51B ARG* 4.5 25.1 + - + +
64B ILE* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.0 28.5 + - - +
32B ALA* 1.3 98.4 - - - +
34B ASP* 1.3 69.1 + - - +
35B THR* 3.1 24.5 + - + +
49B LYS* 4.2 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 3.3 1.0 + - - -
30B ARG* 2.9 59.6 + - - +
31B PHE 4.5 1.0 + - - +
32B ALA 3.8 0.4 - - - -
33B ASP* 1.3 77.9 - - - +
35B THR* 1.3 60.1 + - - +
158B ALA* 4.8 4.0 - - - +
----------------------------------------------------------
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