Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 3VF1
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 TYR 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 3.4 10.8 - - - +
10A GLY* 2.9 43.9 + - - -
11A ASP* 4.1 6.4 + - - -
12A LEU* 3.7 44.8 + - + +
42A PHE* 5.9 0.6 - - - -
79A ASP 3.6 4.0 + - - -
80A TRP* 1.3 72.4 - - - +
82A ILE* 1.3 59.3 + - - +
105A TYR* 3.8 49.2 + + - +
106A ARG* 3.6 13.0 - - - -
107A TRP* 3.6 43.5 - + + -
173A ASP* 5.4 0.2 - - - -
403A TYR* 5.6 0.2 + - - -
407A LYS* 4.7 9.9 + - - -
628A ASP* 4.4 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 16.6 - - + -
8A GLU 3.6 11.9 - - - +
9A THR* 4.5 0.2 - - - +
10A GLY* 4.1 1.1 - - - +
21A VAL* 5.2 1.3 - - + -
38A LEU* 6.4 0.4 - - + -
69A LEU* 4.0 21.1 - - + -
80A TRP* 3.8 37.0 - - + +
81A TYR* 1.3 76.1 - - - +
83A ALA* 1.3 55.8 + - - +
84A LYS* 3.7 21.8 - - - +
85A VAL* 4.0 8.1 - - + -
104A CYS* 3.5 11.7 - - + +
105A TYR* 2.8 34.6 + - - -
106A ARG 3.1 9.2 + - - +
108A VAL* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 2.8 26.3 + - + +
9A THR 4.1 3.1 - - - +
10A GLY* 3.4 21.4 - - - +
82A ILE* 1.3 69.4 - - - +
84A LYS* 1.3 65.3 + - + +
104A CYS 2.9 8.5 + - - -
105A TYR* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 4.1 0.3 - - - +
8A GLU* 3.0 62.1 + - + +
82A ILE* 3.6 3.8 - - - +
83A ALA* 1.3 86.3 - - + +
85A VAL* 1.3 67.4 + - - +
86A ILE* 4.6 11.4 - - + +
101A ILE* 4.1 20.5 - - + +
102A PHE 3.3 16.6 - - - +
103A PRO* 4.0 9.6 - - + -
104A CYS* 4.1 1.1 - - - +
105A TYR* 4.5 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 24.0 - - + -
6A THR 3.4 9.2 - - - +
7A VAL* 4.5 11.7 - - + -
23A ILE* 4.3 4.7 - - + -
67A ILE* 3.9 29.8 - - + -
69A LEU* 4.8 9.9 - - + -
82A ILE* 4.0 16.6 - - + -
84A LYS* 1.3 81.1 - - - +
86A ILE* 1.3 64.3 + - - +
87A ILE* 4.0 12.8 - - + -
101A ILE* 3.6 1.7 - - - +
102A PHE* 2.8 41.7 + - + +
104A CYS* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 3.3 3.8 - - - +
6A THR* 2.7 54.9 + - + +
8A GLU* 3.8 26.0 - - + +
84A LYS* 4.6 12.1 - - + -
85A VAL* 1.3 77.2 - - - +
87A ILE* 1.3 63.2 + - - +
88A GLU* 4.9 2.2 - - + +
99A LYS* 4.4 24.5 - - + -
100A TYR 3.7 2.7 - - - +
101A ILE* 3.6 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 4.5 8.1 - - + -
4A LYS 3.5 3.4 - - - +
5A ILE* 4.1 17.9 - - + -
23A ILE* 4.1 7.6 - - + -
25A LEU* 3.4 39.9 - - + -
64A ILE* 3.5 24.6 - - + +
67A ILE* 3.7 20.0 - - + -
85A VAL* 4.0 12.3 - - + -
86A ILE* 1.3 75.8 - - - +
88A GLU* 1.3 65.1 + - - +
89A LYS* 5.2 0.2 - - + -
98A ASN 3.6 3.6 - - - +
99A LYS* 4.5 0.9 - - - -
100A TYR* 3.0 36.5 + - - +
102A PHE* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 4.2 12.7 + - - +
3A TYR* 3.8 1.4 - - - -
4A LYS* 2.9 63.5 + - + +
86A ILE* 4.0 3.2 + - + +
87A ILE* 1.3 71.6 - - - +
89A LYS* 1.3 70.5 + - - +
97A SER* 3.6 21.6 + - - -
98A ASN 3.5 10.8 - - - +
99A LYS* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.1 9.2 - - - -
2A LYS* 3.8 13.2 - - - +
3A TYR* 3.6 41.1 - - + -
60A ASP* 4.4 1.8 + - - -
61A VAL* 4.9 0.4 - - - -
62A GLY* 2.8 38.5 + - - +
64A ILE* 4.0 19.7 - - + -
87A ILE* 5.2 0.4 - - + -
88A GLU* 1.3 75.5 - - - +
90A ILE* 1.3 93.6 + - - +
91A ASP* 3.8 9.3 - - - +
97A SER* 3.3 2.8 - - - -
98A ASN* 2.9 27.9 + - + +
100A TYR* 3.9 20.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 24.3 - - + +
2A LYS* 3.7 30.5 - - + +
89A LYS* 1.3 98.4 + - - +
91A ASP* 1.3 63.3 + - - +
92A GLU* 3.3 4.2 + - - +
95A GLY* 4.6 8.1 - - - -
96A PHE* 3.1 24.9 - - - +
97A SER* 3.7 8.1 - - - -
98A ASN* 5.8 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