Contacts of the strand formed by residues 26 - 32 (chain A) in PDB entry 2COD
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 GLN 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.5 2.9 - - - -
16A LYS 2.6 43.3 + - - +
18A SER* 4.9 9.6 - - - +
19A PRO* 5.7 1.7 - - + +
24A MET* 5.3 9.2 - - - +
25A PHE* 1.3 78.0 + - - +
27A LYS* 1.3 62.4 + - - +
28A ARG* 3.2 36.1 - - - +
41A ASN* 5.4 2.0 - - - +
42A ASN* 5.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.7 45.6 - - + +
14A LEU 3.5 10.8 - - - +
15A ASP* 3.1 24.7 + - - +
25A PHE 4.2 0.6 + - - -
26A GLN* 1.3 75.1 - - - +
28A ARG* 1.3 69.2 + - - +
42A ASN* 2.8 30.1 - - + +
80A ARG* 5.2 7.7 - - - +
82A GLU* 5.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.9 5.8 - - - -
14A LEU 2.8 31.8 + - - +
16A LYS* 3.5 20.3 - - + +
18A SER* 4.0 21.8 - - - +
26A GLN* 3.2 35.8 - - - +
27A LYS* 1.3 93.8 - - - +
29A TRP* 1.3 65.4 + - - +
30A VAL* 3.5 5.5 + - + +
39A TYR* 3.5 40.1 + - + -
40A TYR 3.4 8.3 - - - +
41A ASN* 3.8 25.6 + - - +
42A ASN 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 4.1 24.7 - - - -
12A GLY* 4.6 12.8 - - - -
13A TRP* 3.7 41.1 - + + -
28A ARG* 1.3 70.9 - - - +
30A VAL* 1.3 73.8 + - - +
31A LYS* 3.9 15.0 - - + +
39A TYR* 2.9 5.9 - - - +
40A TYR* 2.8 65.2 + + + +
41A ASN 5.3 3.1 - - - +
42A ASN* 4.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.2 22.4 - - - -
12A GLY 3.3 10.8 + - - +
14A LEU* 3.6 31.9 - - + +
28A ARG* 3.5 11.3 + - + +
29A TRP* 1.3 81.9 + - - +
31A LYS* 1.3 68.4 + - - +
37A ILE* 3.6 26.2 - - + -
38A SER 3.7 1.1 - - - -
39A TYR* 3.3 26.5 - - + -
79A PHE* 4.5 9.2 - - + -
90A TRP* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 6.4 0.2 - - - -
10A LYS 3.4 7.0 - - - -
11A SER* 3.9 15.0 - - - +
29A TRP* 3.9 14.8 - - + +
30A VAL* 1.3 84.6 - - - +
32A PHE* 1.3 74.2 + - - +
33A ASP* 4.3 11.6 + - - +
36A SER 4.3 0.2 - - - +
37A ILE* 3.8 2.5 - - - -
38A SER* 3.0 43.0 + - - +
40A TYR* 5.7 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS 3.1 28.5 - - - -
9A VAL* 3.0 26.1 - - - +
10A LYS 2.8 19.9 + - - +
31A LYS* 1.3 85.0 - - - +
33A ASP* 1.3 60.8 + - - +
34A GLY* 3.4 33.0 - - - -
35A LEU 4.1 1.8 - - - -
36A SER* 3.3 25.4 - - - -
37A ILE* 3.9 17.9 - - + -
54A LEU* 4.9 6.7 - - + -
57A ILE* 6.2 0.4 - - + -
90A TRP* 4.0 14.6 - + + -
93A ILE* 3.2 31.4 - - + -
94A LEU* 4.9 11.9 - - + -
97A ALA* 3.8 18.2 - - + -
----------------------------------------------------------
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