Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 2KQ7
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 ARG 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.5 4.2 + - - +
23A ILE* 4.0 11.5 + - - +
24A ALA* 3.6 34.2 - - - +
27A PHE* 3.8 11.3 + - + +
28A LYS 3.4 12.9 + - - +
29A ASN* 1.3 74.8 - - - +
31A ILE* 1.3 68.8 + - - +
32A PRO* 4.4 2.3 - - - +
52A LEU* 3.3 51.5 - - + +
53A VAL 3.3 7.9 - - - +
54A PRO* 4.5 0.2 - - + -
55A ALA* 3.9 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 1.3 81.8 - - - +
32A PRO* 1.3 65.6 - - + +
33A VAL* 2.8 39.6 + - + +
51A TYR 4.3 1.0 - - - +
52A LEU* 5.3 0.9 - - - +
53A VAL* 2.8 32.2 + - + +
54A PRO 4.3 5.2 - - - +
55A ALA* 4.7 13.2 - - + -
93A MET* 3.8 32.3 - - + +
94A SER* 4.5 4.9 - - - +
97A TYR* 3.5 46.4 - - + -
107A LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG 4.4 1.8 - - - +
31A ILE* 1.3 83.4 - - + +
33A VAL* 1.3 60.1 + - - +
34A ILE* 4.8 0.9 - - + -
97A TYR* 4.0 25.4 - - + +
105A GLY 4.7 2.5 - - - +
106A PHE* 3.6 41.3 - - + -
107A LEU* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 2.8 45.3 + - + +
32A PRO* 1.3 71.6 - - - +
34A ILE* 1.3 67.9 + - - +
35A CYS 5.1 0.2 - - - +
51A TYR* 3.6 25.6 + - - +
53A VAL* 3.4 27.6 - - + -
62A PHE* 4.8 7.0 - - + -
93A MET* 3.6 13.7 - - + -
107A LEU* 3.2 28.3 - - + -
109A VAL* 3.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 5.2 0.9 - - + -
33A VAL* 1.3 82.7 - - - +
35A CYS* 1.3 67.2 + - - +
36A GLU* 3.6 15.1 + - + +
49A ARG* 4.5 9.4 - - + +
50A LYS* 4.2 34.5 - - + -
51A TYR* 4.4 0.4 - - - -
106A PHE* 3.6 31.0 - - + -
107A LEU 3.3 13.2 + - - +
108A TYR* 4.1 11.9 - - + -
109A VAL* 3.3 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 1.3 73.9 - - - +
36A GLU* 1.3 62.5 + - - +
46A ILE* 5.7 0.7 - - + -
49A ARG 5.1 0.5 - - - +
51A TYR* 3.4 42.3 + - + +
62A PHE* 3.8 16.2 - - + -
66A ILE* 4.9 3.6 - - + -
80A ILE* 3.6 22.7 - - - -
109A VAL* 3.3 24.3 - - + +
111A TYR* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 4.3 17.3 - - + +
35A CYS* 1.3 76.5 - - - +
37A LYS* 1.3 62.7 + - - +
108A TYR* 3.3 31.4 - - - +
109A VAL 2.8 12.6 + - - +
110A THR* 3.3 13.2 - - + +
111A TYR* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 1.3 76.2 - - - +
38A ALA* 1.3 73.8 + - - +
39A GLU* 3.9 5.6 + - - +
41A SER* 3.2 22.2 + - - -
43A ILE* 2.8 38.3 + - + +
44A PRO* 4.7 0.4 - - - -
45A GLU* 3.5 43.1 - - + +
110A THR* 4.5 1.3 - - - -
111A TYR* 3.5 22.4 - - + +
----------------------------------------------------------
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