Contacts of the strand formed by residues 83 - 90 (chain B) in PDB entry 3GNI
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 MET 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ATP 3.0 41.3 - - - +
77B LYS* 3.4 12.6 - - - +
78B GLY* 3.0 38.9 + - - +
79B PHE* 3.9 1.8 + - + -
82B LEU* 1.3 78.8 - - - +
84B THR* 1.3 73.6 + - - +
85B VAL* 3.9 12.6 - - + -
100B ARG* 3.6 37.5 - - - +
101B ARG 3.2 13.0 - - - +
102B ILE* 3.4 25.4 - - + -
215B ARG* 3.4 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.1 22.7 - - + -
76B GLY 4.1 2.7 - - - -
77B LYS* 3.2 21.2 + - + +
82B LEU 4.1 1.4 + - - -
83B MET* 1.3 72.8 - - - +
85B VAL* 1.3 64.5 + - - +
86B ASN* 3.5 17.2 - - - +
99B VAL 3.6 2.3 - - - +
100B ARG* 3.6 1.2 - - - -
101B ARG* 2.8 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ATP 3.8 40.6 - - + +
74B VAL* 3.5 3.6 - - - +
75B ILE* 2.8 43.2 + - + -
76B GLY* 3.0 25.2 + - - +
77B LYS 4.3 0.9 - - - +
83B MET* 3.9 24.9 - - + -
84B THR* 1.3 74.3 - - - +
86B ASN* 1.3 55.2 + - - +
98B THR* 3.5 30.7 - - + -
99B VAL 3.7 3.1 - - - +
100B ARG* 4.3 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.2 18.6 - - + +
72B LEU 3.5 12.9 + - - -
73B THR 3.4 16.7 + - - -
74B VAL* 3.7 16.4 - - - +
75B ILE* 4.1 4.0 - - - -
84B THR* 3.5 6.5 - - - +
85B VAL* 1.3 75.1 - - - +
87B LEU* 1.3 65.4 + - - +
98B THR* 3.4 7.3 - - - +
99B VAL* 2.8 44.7 + - + +
101B ARG* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.8 0.3 - - - -
72B LEU* 2.8 49.4 + - + -
73B THR* 2.8 22.0 + - - +
75B ILE* 3.7 27.1 - - + +
86B ASN* 1.3 75.3 - - - +
88B ALA* 1.3 57.1 + - - +
96B TYR* 3.7 38.1 - - + +
97B VAL 3.7 4.5 - - - +
149B PHE* 3.8 40.8 - - + -
400B ILE* 5.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 4.4 8.1 - - + -
70B GLU 3.4 15.0 - - - +
71B LEU* 4.5 3.6 - - + -
72B LEU* 3.7 7.0 - - - -
87B LEU* 1.3 76.4 - - - +
89B ARG* 1.3 60.6 + - - +
90B TYR 4.0 0.4 - - - -
96B TYR* 3.3 9.4 - - - -
97B VAL* 2.8 39.9 + - + +
99B VAL* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 3.5 3.8 - - - -
70B GLU* 3.0 61.4 + - + +
72B LEU* 3.6 10.4 - - + +
88B ALA* 1.3 72.3 - - - +
90B TYR* 1.3 60.9 + - - +
91B LYS* 3.2 69.9 + - - +
94B GLY* 3.4 34.1 - - - +
95B GLU 3.6 2.9 - - - -
96B TYR* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER 4.6 1.8 + - - -
62B PHE* 3.6 32.0 - + + -
63B LEU* 2.8 38.5 + - - +
68B CYS* 3.6 15.9 - - + -
69B TYR* 3.5 35.4 - + - -
88B ALA 4.0 1.4 + - - -
89B ARG* 1.3 68.1 - - - +
91B LYS* 1.3 55.2 - - - +
92B PRO* 3.7 26.7 - - + +
93B THR* 3.1 30.4 + - + +
94B GLY* 2.7 33.0 + - - -
95B GLU* 2.8 18.5 + - + +
97B VAL* 4.3 16.1 - - + +
----------------------------------------------------------
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