Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 2VPF
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 LYS 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 4.1 3.6 - - - +
57A CYS* 4.0 0.5 - - - -
70A PRO* 3.4 6.2 - - - +
71A THR* 2.8 37.5 + - - +
72A GLU* 3.2 36.2 + - + +
99A HIS 3.7 0.2 - - - -
100A ASN* 1.3 82.6 + - + +
102A CYS* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS* 3.6 24.9 - - - +
27A HIS* 3.7 6.7 - - - -
28A PRO* 3.6 27.0 - - - +
57A CYS* 2.0 53.2 - - - -
68A CYS* 4.0 0.2 - - - -
69A VAL 3.2 6.5 - - - +
71A THR* 4.2 3.7 + - - -
99A HIS* 4.7 0.7 - - - -
101A LYS* 1.3 77.6 - - - +
103A GLU* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 6.3 0.9 - - - -
26A CYS* 3.9 6.7 - - - -
67A GLU 3.5 0.9 - - - +
68A CYS* 3.7 0.3 - - - -
69A VAL* 2.9 34.5 + - - +
71A THR* 3.9 15.6 - - + +
102A CYS* 1.3 74.6 - - - +
104A CYS* 1.3 74.4 + - - +
105A ARG* 3.3 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.5 25.2 + - - +
26A CYS* 3.5 20.8 - - - -
61A CYS* 2.1 54.3 - - + -
62A ASN 4.8 0.2 - - - -
66A LEU* 4.3 17.0 - - + +
67A GLU 3.5 4.0 - - - -
103A GLU* 1.3 81.5 - - - +
105A ARG* 1.3 61.4 + - - +
106A PRO* 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.6 5.8 - - - -
67A GLU* 2.9 32.8 + - + +
69A VAL* 4.0 26.4 - - + +
70A PRO 5.3 1.8 + - - -
71A THR* 3.6 24.9 - - - +
103A GLU* 3.3 29.4 + - + +
104A CYS* 1.3 79.2 - - - +
106A PRO* 1.3 79.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 3.4 10.8 - - - +
66A LEU* 3.5 13.4 - - + -
67A GLU* 4.6 3.5 - - - +
104A CYS 4.8 0.2 - - - +
105A ARG* 1.3 91.9 - - + +
107A LYS* 1.3 66.9 + - - +
108A LYS* 3.8 3.8 + - - +
----------------------------------------------------------
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