Contacts of the strand formed by residues 76 - 82 (chain B) in PDB entry 3GB9
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 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.0 23.1 + - - +
27B VAL* 4.1 20.2 - - + -
72B PHE* 3.1 6.2 - - - -
73B LEU 2.9 34.7 + - - +
74B ASN 3.3 2.2 - - - +
75B GLY* 1.3 78.4 - - - +
77B ALA* 1.3 65.6 + - - +
78B CYS* 3.1 4.1 + - - -
279B MET* 2.7 51.3 + - + +
280B ALA* 4.1 9.1 + - - +
282B ILE* 2.7 32.0 + - + +
283B PRO 2.7 23.2 + - - -
284B LEU* 3.6 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 6.0 3.1 - - - +
24B ARG 3.4 25.6 - - - +
25B PRO* 3.9 2.0 - - + -
26B GLN* 2.8 35.3 + - + +
27B VAL* 3.1 10.2 + - - +
71B GLY 3.8 4.5 - - - -
72B PHE* 3.7 20.4 - - + -
75B GLY 3.9 0.6 + - - -
76B ARG* 1.3 71.2 - - - +
78B CYS* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 5.4 0.9 + - - +
25B PRO* 3.7 7.8 - - - +
27B VAL* 3.2 14.8 - - - -
29B ILE* 3.8 26.9 - - - -
42B LEU* 4.2 13.5 - - + -
70B PHE* 3.4 5.9 - - - +
71B GLY 2.8 36.1 + - - +
73B LEU* 3.9 15.7 - - - -
76B ARG 3.1 10.9 + - - +
77B ALA* 1.3 74.1 - - - +
79B VAL* 1.3 62.3 + - - +
80B MET* 4.4 5.2 - - + -
279B MET* 4.0 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 3.9 13.7 - - + -
27B VAL 2.8 18.0 + - - +
28B ALA* 3.1 17.6 - - + +
29B ILE* 2.8 26.2 + - - +
68B LEU* 4.0 21.8 - - + -
69B VAL 3.5 8.3 - - - +
70B PHE* 3.8 33.4 - - + -
78B CYS* 1.3 75.7 - - - +
80B MET* 1.3 62.7 + - - +
81B MET 4.2 0.2 + - - -
103B PHE* 4.1 18.5 - - + -
106B LEU* 5.0 0.9 - - + -
108B VAL* 4.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.4 32.5 - - + +
31B CYS* 3.7 22.0 - - - -
38B LEU* 3.6 21.5 - - + +
39B THR* 3.6 40.6 - - + -
42B LEU* 3.2 33.7 - - + -
67B ARG 3.8 0.3 - - - +
68B LEU* 3.4 8.3 - - - +
69B VAL* 2.8 39.5 + - + +
73B LEU* 4.2 5.6 - - + -
78B CYS* 4.4 5.2 - - + -
79B VAL* 1.3 73.5 - - - +
81B MET* 1.3 61.9 + - - +
82B GLN 3.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE 2.9 13.9 + - - +
30B ILE* 4.2 25.1 - - + +
31B CYS* 3.1 28.8 + - - +
50B TYR* 3.0 26.2 - - + +
56B PHE* 5.3 0.2 - - - -
67B ARG 3.9 1.8 - - - -
68B LEU* 3.8 14.6 - - + -
79B VAL 4.2 0.2 - - - -
80B MET* 1.3 72.1 - - - +
82B GLN* 1.3 58.4 + - - +
83B GLY 3.8 2.8 + - - +
84B ARG* 3.8 28.4 + - + -
85B PHE* 4.1 14.6 - - + -
96B VAL 5.3 2.0 - - - +
99B PRO* 3.6 41.3 - - + -
103B PHE* 4.1 10.5 - - + -
224B GLU* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS* 4.7 3.8 - - + -
36B GLY* 3.6 30.9 + - - +
39B THR* 3.3 20.0 + - + +
50B TYR* 3.5 2.7 + - - -
66B GLY* 3.5 4.5 - - - -
67B ARG* 2.7 85.5 + - + +
80B MET 3.8 1.2 + - - +
81B MET* 1.3 70.3 - - - +
83B GLY* 1.3 60.2 + - - +
294B SO4 3.4 20.8 + - - +
----------------------------------------------------------
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