Contacts of the helix formed by residues 78 - 91 (chain B) in PDB entry 2FV7
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 ASP 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY* 2.8 8.1 + - - -
77B LYS* 1.3 76.5 + - - +
79B SER* 1.3 66.0 + - - +
80B PHE* 3.3 8.2 + - - +
81B GLY 2.8 19.8 + - - -
82B ASN* 3.0 28.8 + - - -
104B ALA 4.4 0.3 - - - +
105B ALA* 3.3 14.9 - - - +
106B THR* 2.5 45.4 + - - -
505B UNX 3.6 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP* 1.3 74.6 - - - +
80B PHE* 1.3 71.7 + - - +
82B ASN* 3.7 9.1 - - - +
83B ASP* 2.8 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.5 30.6 + - + +
28B LEU* 3.7 31.4 - - + -
49B ILE* 4.4 15.7 - - + -
51B PHE* 5.2 1.4 - - - -
78B ASP* 3.2 12.9 + - - +
79B SER* 1.3 93.3 + - - +
81B GLY* 1.3 56.8 + - - +
83B ASP* 3.5 9.4 + - - +
84B TYR* 2.9 26.9 + - - +
105B ALA* 6.2 1.8 - - + -
106B THR* 3.7 12.1 - - - -
108B THR* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.7 13.4 - - - +
76B GLY 3.6 12.6 - - - -
78B ASP* 2.8 10.9 + - - -
80B PHE* 1.3 72.8 - - - +
82B ASN* 1.3 59.9 + - - +
84B TYR* 3.2 2.1 + - - +
85B ILE* 2.9 34.1 + - - +
100B GLN* 3.9 7.0 - - - -
106B THR* 3.1 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 5.2 1.8 - - - +
78B ASP 3.0 23.7 + - - +
79B SER* 3.7 8.0 - - - +
81B GLY* 1.3 77.7 - - - +
83B ASP* 1.3 65.0 + - - +
85B ILE* 3.5 6.8 + - - +
86B GLU* 3.2 27.4 + - - +
100B GLN* 2.6 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 5.8 4.0 - - - +
51B PHE* 3.8 21.7 - - + -
79B SER* 2.8 33.3 + - - +
80B PHE* 3.8 10.1 - - - +
82B ASN* 1.3 78.8 - - - +
84B TYR* 1.4 57.3 + - - +
86B GLU* 3.1 8.8 + - - +
87B ASN* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B CYS* 3.7 23.3 - - + -
25B MET 3.6 23.1 - - - -
26B THR* 4.6 7.0 - - - -
51B PHE* 3.6 30.2 - + + -
52B GLY 2.6 29.1 + - - -
56B ALA* 2.8 29.0 - - + +
75B VAL* 4.3 13.7 - - + -
80B PHE 2.9 16.1 + - - +
81B GLY 3.2 4.2 + - - +
83B ASP* 1.4 73.9 - - - +
85B ILE* 1.3 64.7 + - - +
87B ASN* 3.2 8.8 + - - +
88B LEU* 3.0 36.3 + - + +
106B THR* 5.2 1.8 - - + -
308B GLN* 2.9 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.2 3.6 - - + -
81B GLY 2.9 18.5 + - - +
82B ASN* 3.8 7.2 - - - +
84B TYR* 1.3 75.5 - - - +
86B GLU* 1.3 60.1 + - + +
88B LEU* 3.2 11.3 + - - +
89B LYS* 3.0 53.3 + - - +
95B THR* 4.4 12.1 - - + +
98B THR* 3.8 25.4 - - + +
100B GLN* 3.3 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASN 3.2 13.4 + - - +
83B ASP* 3.1 11.3 + - - +
85B ILE* 1.3 76.6 - - + +
87B ASN* 1.3 59.6 + - - +
89B LYS* 3.3 36.0 + - - +
90B GLN* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.2 45.8 - - + +
60B VAL* 4.9 2.4 - - - +
83B ASP 2.8 13.8 + - - +
84B TYR* 3.2 21.8 + - - +
86B GLU* 1.3 76.4 - - - +
88B LEU* 1.3 61.9 + - - +
90B GLN* 3.4 13.0 + - - +
91B ASN* 2.9 46.2 + - - +
308B GLN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B CYS* 4.5 2.7 - - - -
56B ALA* 4.4 13.0 - - + -
60B VAL* 5.0 1.6 - - + -
71B MET* 4.3 20.4 - - + -
75B VAL* 6.2 0.4 - - + -
84B TYR* 3.0 45.2 + - + +
85B ILE* 3.2 6.7 + - - +
87B ASN* 1.3 78.2 - - - +
89B LYS* 1.3 62.7 + - - +
91B ASN* 3.0 12.5 + - - -
93B ILE* 3.0 50.2 + - + +
95B THR* 3.7 15.7 - - + -
98B THR* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.0 34.4 + - - +
86B GLU* 3.3 36.8 + - - +
88B LEU* 1.3 77.6 - - - +
90B GLN* 1.3 54.4 + - + +
92B ASP* 2.8 29.5 + - - +
93B ILE 4.2 7.2 - - - +
95B THR* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 5.4 5.2 - - - -
86B GLU* 2.9 37.2 + - - +
87B ASN* 3.6 17.0 + - - +
89B LYS* 1.3 72.3 - - - +
91B ASN* 1.3 60.2 + - - +
92B ASP* 3.2 9.4 + - - +
313B TYR* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 3.8 16.8 - - + +
63B ALA* 3.5 20.9 - - + +
64B ARG* 2.9 46.0 + - + +
87B ASN* 2.9 41.0 + - - +
88B LEU 3.0 9.4 + - - +
90B GLN* 1.3 77.6 - - - +
92B ASP* 1.3 70.3 + - - +
93B ILE* 3.3 16.5 + - + -
308B GLN* 4.6 0.8 + - - -
313B TYR* 4.1 5.9 + - - -
----------------------------------------------------------
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