Contacts of the helix formed by residues 25 - 33 (chain B) in PDB entry 2CVP
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 LYS 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.5 17.7 + - - +
23B ASN* 3.3 9.6 + - - +
24B LEU* 1.3 78.8 - - - +
26B LEU* 1.3 65.9 + - - +
27B ARG* 3.2 3.8 - - + +
28B GLU* 3.0 41.5 + - + +
29B LEU* 2.9 26.1 + - - +
471B ASN* 3.4 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 1.3 70.8 - - - +
27B ARG* 1.3 64.2 + - - +
29B LEU* 3.2 10.3 + - + +
30B PHE* 3.1 34.3 + - + -
56B SER 4.2 3.8 - - - +
57B LYS* 3.6 27.8 - - - +
58B ASN 3.2 33.9 - - - +
59B LEU* 3.9 10.0 - - + +
437B MET* 3.6 28.9 - - + +
471B ASN* 2.7 33.9 + - - +
472B ARG 3.8 21.8 - - - +
473B PRO* 4.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.9 3.4 - - + -
26B LEU* 1.3 77.9 - - - +
28B GLU* 1.3 61.8 + - + +
30B PHE* 3.5 4.8 + - - +
31B GLU* 3.1 34.3 + - + +
437B MET* 4.6 7.4 + - + +
438B LYS* 2.9 75.7 + - + +
439B GLY 3.8 8.1 + - - -
441B LEU* 3.9 34.2 - - - +
444B GLU* 3.9 15.0 + - - -
471B ASN* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN 4.1 11.6 - - - +
25B LYS* 3.0 40.2 + - + +
27B ARG* 1.3 80.1 - - + +
29B LEU* 1.3 61.8 + - + +
31B GLU* 3.3 6.0 + - - +
32B ALA* 3.0 33.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
24B LEU* 4.2 26.9 - - + -
25B LYS 2.9 24.0 + - - +
26B LEU* 3.2 16.8 + - + +
28B GLU* 1.3 80.1 - - + +
30B PHE* 1.3 60.9 + - - +
32B ALA* 3.7 3.8 + - - +
33B ASP* 3.5 23.2 + - - +
36B ARG* 3.8 43.9 + - - +
58B ASN 4.1 7.6 - - - +
59B LEU* 4.7 2.9 - - - -
60B VAL 3.9 9.6 - - - +
61B SER* 4.9 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ASP* 4.1 15.7 - - + -
540A SER* 3.5 35.1 - - - +
541A SER* 3.6 23.8 - - - -
26B LEU* 3.1 28.9 + - + +
27B ARG* 4.0 3.8 - - - +
29B LEU* 1.3 74.8 - - - +
31B GLU* 1.3 66.7 + - + +
33B ASP 3.4 17.4 + - - +
34B PRO* 4.2 3.5 - - - +
36B ARG* 3.6 19.3 - - + +
56B SER* 3.3 44.9 - - - -
57B LYS* 4.0 4.0 - - + -
437B MET* 3.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.1 23.0 + - + +
28B GLU* 3.3 7.2 + - - +
30B PHE* 1.3 79.0 - - + +
32B ALA* 1.3 60.7 + - - +
33B ASP 3.5 0.5 + - - -
34B PRO* 5.0 3.5 - - - +
----------------------------------------------------------
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 GLU 3.0 17.3 + - - +
29B LEU* 4.2 5.2 - - - +
31B GLU* 1.3 77.8 - - - +
33B ASP* 1.3 58.6 + - + +
34B PRO* 4.0 5.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
540A SER* 4.6 1.0 + - - -
29B LEU 3.5 12.5 + - - +
30B PHE 3.4 10.6 + - - +
31B GLU 3.3 2.4 - - - -
32B ALA* 1.3 82.5 - - + +
34B PRO* 1.3 60.7 - - - +
35B GLU* 3.1 18.8 + - - +
36B ARG* 3.0 46.7 + - + +
39B ASN* 4.0 10.0 + - - -
40B PHE* 4.5 8.7 - - - -
----------------------------------------------------------
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