Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 1VPW
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 SER 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.0 23.7 + - - +
60A LYS* 1.3 78.2 - - - +
62A ILE* 1.3 62.1 + - - +
90A TYR* 3.7 1.8 - - - -
91A THR* 3.0 35.4 - - - +
93A ILE* 4.6 7.0 - - - +
114A LYS* 5.0 1.6 + - - +
116A VAL* 3.6 14.9 - - - +
117A ASP* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 1.3 73.3 - - - +
63A GLY* 1.3 76.9 + - - +
81A VAL* 5.4 0.4 - - + -
85A CYS* 4.0 21.1 - - - -
90A TYR* 3.1 39.9 - - + -
91A THR 2.8 11.6 + - - +
92A LEU* 2.9 27.9 - - + +
93A ILE* 3.0 11.5 + - - +
116A VAL* 4.4 3.4 - - - -
117A ASP* 5.1 0.2 - - + -
118A GLY 3.7 14.1 - - - +
120A LEU* 3.3 37.5 - - + +
302A PHE* 4.4 9.4 - - + -
305A LEU* 4.2 10.8 - - + -
306A LEU* 5.8 0.7 - - + -
309A ILE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 1.3 75.3 - - - +
64A LEU* 1.3 56.8 + - - -
93A ILE* 3.6 9.2 - - - -
111A MET* 4.0 10.3 - - - -
116A VAL* 4.1 7.9 - - - +
118A GLY 3.2 10.9 + - - -
119A LEU* 2.9 21.0 - - - +
120A LEU 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 5.2 0.2 - - + -
63A GLY* 1.3 72.0 - - - -
65A LEU* 1.3 63.2 + - - +
66A ALA* 3.3 6.4 + - + +
78A ILE* 3.8 29.8 - - + -
81A VAL* 4.5 24.5 - - + -
92A LEU* 3.7 23.7 - - + +
93A ILE 2.8 10.9 + - - +
94A LEU* 4.3 13.5 - - + -
95A GLY* 2.7 34.1 + - - +
111A MET* 3.9 2.5 - - - +
120A LEU* 3.3 29.6 - - + +
122A MET* 4.5 17.9 - - + +
145A MET* 4.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 3.7 1.2 + - - -
64A LEU* 1.3 69.2 - - - +
66A ALA* 1.3 60.0 + - - +
95A GLY 4.0 7.9 - - - +
97A ALA* 4.6 10.1 - - + -
104A GLN* 4.8 9.0 - - + +
107A TYR* 3.5 34.1 - - + -
108A LEU* 3.5 36.3 - - + +
111A MET* 4.6 13.0 - - - -
119A LEU* 5.0 2.7 - - + -
120A LEU 2.8 15.8 + - - +
121A VAL* 4.7 12.8 - - + -
122A MET 2.9 25.8 + - - -
123A CYS* 3.9 22.1 - - - -
130A LEU* 6.0 1.1 - - + -
134A LEU* 5.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.3 17.0 + - + -
65A LEU* 1.3 75.8 - - - +
67A THR* 1.3 60.1 + - - +
68A SER 4.3 7.2 - - - +
78A ILE* 4.8 3.4 - - + -
94A LEU* 4.3 5.2 - - + -
95A GLY 2.7 10.5 + - - +
96A ASN* 3.5 19.3 - - - +
97A ALA* 2.8 29.5 + - - +
122A MET* 3.4 23.3 - - + +
123A CYS* 5.1 2.1 - - - -
----------------------------------------------------------
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