Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 2VJV
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 HIS 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.2 13.0 - - + -
23A TRP 3.4 8.5 - - - +
24A CYS* 3.7 16.6 - - - +
32A LEU* 3.7 10.4 - - - +
59A GLN* 4.9 3.8 + - - +
60A THR* 3.5 2.4 - - - -
61A ASP* 3.0 56.1 + - + +
63A ASP* 1.3 92.1 + - - +
65A ILE* 1.3 74.4 - - - +
66A HIS* 4.2 7.6 - - + +
128B ILE 4.5 6.3 + - - -
129B GLU* 5.5 0.4 - - - -
130B ASN* 4.0 8.7 - - - -
-1E C 3.3 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE 3.8 0.3 - - - +
22A VAL* 3.2 7.1 - - - +
23A TRP* 3.1 63.1 + - + +
32A LEU* 4.4 8.3 - - + -
40A LEU* 3.7 30.5 - - + -
41A LYS* 5.6 0.2 - - + -
44A ILE* 4.2 5.2 - - + -
58A MET* 4.1 22.7 - - + -
59A GLN 3.4 11.2 - - - +
60A THR* 3.7 13.7 - - + -
64A HIS* 1.3 77.5 - - - +
66A HIS* 1.3 68.5 + - - +
67A ILE* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 2.8 35.6 + + - -
21A ILE 3.3 10.1 - - - -
22A VAL* 3.8 18.2 - - + -
57A GLU* 3.7 22.0 - - + -
58A MET* 3.2 4.7 - - - +
59A GLN* 2.8 65.6 + - + +
64A HIS* 4.2 7.6 - - + +
65A ILE* 1.3 74.1 - - - +
67A ILE* 1.3 80.3 + - - +
68A LEU* 4.8 0.7 - - + -
128B ILE* 4.0 27.5 + - + +
129B GLU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR 3.4 0.7 - - - +
20A HIS* 3.3 3.5 - - - -
21A ILE* 2.8 42.3 + - + +
23A TRP* 3.7 35.2 - - + -
44A ILE* 3.9 21.8 - - + -
55A ILE* 3.9 15.5 - - + -
57A GLU 3.3 6.1 - - - +
58A MET* 4.1 17.3 - - + -
65A ILE* 4.2 10.8 - - + -
66A HIS* 1.3 83.2 - - - +
68A LEU* 1.3 72.3 + - - +
69A ALA* 3.8 15.3 - - + -
80A PHE* 4.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 4.4 6.1 - - + -
19A TYR 3.2 19.3 - - - +
20A HIS* 3.9 17.7 - - + +
55A ILE* 3.8 1.2 - - - -
56A ILE* 2.8 54.2 + - + -
57A GLU* 2.9 37.6 + - + +
66A HIS* 4.4 0.4 + - - +
67A ILE* 1.3 73.5 - - - +
69A ALA* 1.3 60.7 + - - +
116A VAL* 3.7 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS 3.7 0.9 - - - +
18A LYS* 3.2 3.6 - - - -
19A TYR* 2.9 35.5 + - - +
21A ILE* 4.8 3.8 - - + -
53A VAL* 3.9 18.6 - - + -
54A GLU 3.2 11.7 - - - +
55A ILE* 4.1 3.1 - - + -
56A ILE* 4.4 4.3 - - - +
67A ILE* 3.8 16.8 - - + -
68A LEU* 1.3 75.0 - - - +
70A ASP* 1.3 61.4 + - - +
71A ILE* 3.9 12.2 + - + -
80A PHE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU 4.7 1.6 - - - +
8A LYS* 2.9 31.3 + - - +
15A TYR* 3.9 11.3 - - - -
16A SER* 4.2 9.9 + - - -
17A CYS 3.0 32.5 + - - +
18A LYS* 4.2 17.3 - - + +
52A ARG 4.6 1.7 - - - +
53A VAL* 3.8 2.9 - - - -
54A GLU* 2.9 44.2 + - + +
56A ILE* 4.4 7.7 - - + +
69A ALA* 1.3 70.4 - - - +
71A ILE* 1.3 62.9 + - - +
----------------------------------------------------------
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