Contacts of the strand formed by residues 76 - 82 (chain A) in PDB entry 2GBA
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.6 36.3 + - + +
11A PHE* 3.2 12.3 + - - +
12A ALA* 5.2 1.1 - - - +
46A ILE* 3.5 3.1 - - - -
47A ASN* 2.9 27.9 + - - +
71A MET 4.1 1.2 - - - +
72A MET* 3.7 8.3 - - + +
73A LYS* 2.9 52.7 + - + +
74A LYS 4.0 5.8 - - - +
75A GLU* 1.3 83.8 - - - +
77A ALA* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.2 9.2 - - - +
11A PHE* 2.7 43.9 + - + +
12A ALA 4.6 1.1 - - - +
13A ALA* 4.6 1.6 - - - -
16A VAL* 3.6 31.4 - - + -
44A THR* 3.9 5.6 - - + -
45A TRP 3.1 12.3 - - - +
46A ILE* 4.0 5.6 - - + -
72A MET* 3.8 3.1 - - - -
76A GLN* 1.3 75.3 - - - +
78A TYR* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.6 21.2 - - + +
7A SER 3.3 26.2 - - - -
8A GLU* 4.1 3.3 + - - -
9A SER 4.5 5.2 - - - -
10A PRO* 5.0 0.2 - - + -
11A PHE* 4.0 4.5 - - - -
44A THR* 3.4 1.4 - - - -
45A TRP* 2.9 37.3 + + + -
55A VAL* 4.0 20.9 - - + -
67A LEU* 3.6 20.8 - - + +
69A GLY* 4.0 9.3 - - - -
70A PRO* 3.3 41.8 - - + +
72A MET* 3.8 22.6 - - + -
77A ALA* 1.3 76.6 - - - +
79A SER* 1.3 67.3 + - - +
80A LEU* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.2 2.9 - - - +
6A PRO* 3.4 26.1 - - - +
7A SER 4.9 1.7 + - - +
11A PHE* 3.5 24.4 - - - -
42A THR* 3.7 15.4 - - - +
43A VAL 3.1 9.6 - - - -
44A THR* 2.7 21.6 + - - -
78A TYR* 1.3 83.0 - - - +
80A LEU* 1.3 72.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 4.6 4.9 - - + -
4A THR 3.6 5.2 - - - +
5A ILE* 3.7 20.6 - - + -
6A PRO* 4.2 0.2 - - - -
42A THR* 4.2 1.6 - - - -
43A VAL 2.8 30.8 + - - +
45A TRP* 3.9 16.5 - - + -
55A VAL* 4.5 1.1 - - + -
57A PHE* 3.6 34.1 - - + -
62A LEU* 4.3 11.4 - - + -
67A LEU* 3.9 12.1 - - + -
78A TYR* 3.7 30.3 - - + +
79A SER* 1.3 81.9 - - - +
81A THR* 1.3 61.3 + - - +
82A PHE* 3.8 19.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.0 5.6 - - - -
4A THR* 2.8 53.9 + - - +
6A PRO* 3.8 12.8 - - - +
40A GLY* 3.8 21.5 - - - +
41A ASP 3.5 4.0 - - - +
42A THR* 2.7 27.8 + - - +
80A LEU* 1.3 72.3 - - - +
82A PHE* 1.3 66.0 + - - +
83A THR* 3.8 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS 3.6 3.8 - - - +
3A ALA* 4.5 2.2 - - + -
37A VAL* 4.8 3.4 - - + -
38A LYS 5.2 0.2 - - - +
39A VAL* 3.8 1.0 - - - -
40A GLY* 2.7 35.0 + - - -
41A ASP 3.0 12.1 + - - +
43A VAL* 3.7 30.3 - - + -
45A TRP* 4.2 9.6 - + - -
57A PHE* 4.2 7.2 - + - -
62A LEU* 3.7 30.5 - - + -
80A LEU* 3.8 27.1 - - + -
81A THR* 1.3 72.5 - - - +
83A THR* 1.3 55.8 + - - +
84A GLU 3.7 0.9 - - - +
88A TYR* 3.9 19.3 - + + -
102A VAL* 3.9 26.5 - - + -
104A VAL* 3.6 34.3 - - + -
----------------------------------------------------------
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