Contacts of the strand formed by residues 58 - 67 (chain B) in PDB entry 2GZD
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 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 3.5 27.4 - - + +
10B TYR* 4.0 21.1 - - + +
54B GLN* 3.3 6.3 - - - +
55B VAL 2.9 38.4 + - - +
56B ASP* 4.8 0.7 - - + +
57B GLY* 1.3 91.4 - - - +
59B THR* 1.3 61.8 + - - +
60B ILE* 3.8 13.1 + - + +
173B TYR* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU 3.2 25.6 + - - +
8B TYR* 3.7 6.4 - - - +
9B ASP* 2.7 48.0 + - - +
10B TYR 3.3 5.9 + - - -
52B SER* 4.3 11.4 - - - -
53B ILE 3.6 2.7 - - - -
54B GLN* 3.2 29.8 - - - +
57B GLY 4.9 1.8 - - - +
58B LYS* 1.3 73.4 - - - +
60B ILE* 1.3 59.8 + - - +
61B LYS 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.5 21.8 - - + +
12B PHE* 3.7 28.0 - - + -
51B ARG 3.7 0.2 - - - +
52B SER* 3.3 3.9 - - - -
53B ILE* 2.8 43.9 + - + +
55B VAL* 3.6 29.8 - - + -
58B LYS* 4.2 11.7 - - + +
59B THR* 1.3 78.2 + - - +
61B LYS* 1.3 69.8 + - - +
62B ALA 3.6 1.4 + - - +
169B LEU* 4.5 15.7 - - + -
173B TYR* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 5.4 7.8 + - - +
8B TYR* 3.7 46.1 - - + +
10B TYR 2.8 9.1 + - - +
11B LEU* 3.4 21.7 - - + +
12B PHE* 2.7 34.0 + - - +
50B THR* 3.5 34.6 + - + -
51B ARG* 3.8 5.5 - - - +
52B SER* 2.6 42.2 + - - +
59B THR 4.1 1.0 + - - -
60B ILE* 1.3 71.4 - - - +
62B ALA* 1.3 60.8 + - - +
63B GLN 3.7 0.3 + - - -
497D ARG* 4.3 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE 3.6 5.4 - - - +
31B PHE* 4.3 8.3 - - + -
49B ALA 3.9 0.2 - - - +
50B THR* 3.0 27.0 - - - -
51B ARG 2.9 16.4 + - - +
60B ILE 3.6 1.8 + - - -
61B LYS* 1.3 71.6 - - - +
63B GLN* 1.3 60.0 - - - +
64B ILE* 3.6 22.6 + - + +
169B LEU* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.6 38.7 - - + +
12B PHE 2.8 13.2 + - - +
13B LYS* 3.4 14.4 - - - +
14B VAL 2.8 28.2 + - - +
48B PHE* 3.4 38.4 - - + -
49B ALA 4.0 1.6 - - - -
50B THR* 4.1 7.1 - - + +
61B LYS 3.7 0.6 + - - -
62B ALA* 1.3 73.4 - - - +
64B ILE* 1.3 58.5 + - - +
65B TRP* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 3.3 24.2 - - + +
16B LEU* 3.7 28.9 - - + -
28B LEU* 3.4 27.9 - - + +
31B PHE* 4.4 1.8 - - + -
32B THR* 4.3 11.0 - - + -
48B PHE* 3.1 6.2 - - - +
49B ALA 2.9 38.3 + - - +
62B ALA* 3.6 30.5 - - + +
63B GLN* 1.3 72.4 - - - +
65B TRP* 1.3 61.1 + - - +
165B PHE* 3.8 32.3 - - + -
169B LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 3.5 34.8 - - + +
14B VAL 2.9 11.0 + - - +
15B VAL* 4.1 6.5 - - + -
16B LEU* 3.0 31.2 + - - +
46B VAL* 3.6 28.7 - - + -
47B GLU 3.5 10.5 - - - -
48B PHE* 3.6 33.2 - + + -
63B GLN* 2.7 48.2 + - - +
64B ILE* 1.3 74.4 - - - +
66B ASP* 1.3 63.6 + - - +
80B TYR* 3.2 15.6 + + + -
489D MSE 4.0 24.2 - - + -
493D PRO* 4.2 18.4 - - + -
496D LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.1 10.0 - - + +
24B LYS* 3.6 18.7 - - - +
25B SER* 2.4 40.4 + - - -
28B LEU* 3.4 23.3 - - + +
43B THR* 3.8 6.5 + - - +
46B VAL* 3.4 6.2 - - - +
47B GLU* 3.0 41.4 + - + +
64B ILE 4.1 0.2 + - - -
65B TRP* 1.3 77.1 - - - +
67B THR* 1.3 77.0 + - - +
80B TYR* 3.6 4.9 - - - -
950B MG 3.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 4.8 1.9 - - - +
24B LYS* 3.4 13.3 - - - -
43B THR* 4.1 7.2 - - - -
45B GLY 2.5 28.0 + - - -
46B VAL* 3.6 7.6 - - - +
66B ASP* 1.3 87.4 + - - +
68B ALA* 1.3 76.3 + - - +
71B GLU* 4.3 13.9 - - - +
74B ARG* 3.3 21.2 + - - +
76B ILE* 5.1 2.2 - - + -
80B TYR* 3.6 34.6 + - + +
900B GTP 4.1 0.2 + - - -
950B MG 4.2 0.2 - - - -
----------------------------------------------------------
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