Contacts of the strand formed by residues 21 - 27 (chain B) 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 VAL 21 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 3.7 9.4 - - - +
20B SER* 1.3 79.8 - - - +
22B SER* 1.3 57.0 + - - +
37B SER* 3.6 2.1 - - - -
38B LEU* 2.6 56.5 + - + +
69B LEU* 4.2 15.3 - - + -
70B LYS 3.2 18.4 - - - +
71B GLU* 4.2 3.8 - - - -
72B ASN* 3.3 9.9 - - - +
80B TRP* 3.9 25.1 - - + -
82B ILE* 5.2 2.7 - - + -
108B VAL* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 1.3 75.1 - - - +
23B ILE* 1.3 60.7 + - - +
24B LYS 4.2 0.2 - - - -
35B ALA* 4.0 19.1 - - - +
36B PHE 2.9 19.7 - - - -
37B SER* 4.9 0.7 - - - -
68B THR 3.4 1.3 - - - +
69B LEU* 3.3 9.6 - - - +
70B LYS* 2.9 48.1 + - - +
72B ASN* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.8 32.8 - - + -
22B SER* 1.3 74.1 - - - +
24B LYS* 1.3 60.6 - - - +
25B LEU* 3.5 24.9 + - + -
35B ALA* 4.4 0.9 - - - -
36B PHE* 3.2 44.7 + - + -
38B LEU* 3.6 26.9 - - + -
67B ILE* 4.1 21.5 - - + -
68B THR 3.2 7.2 - - - +
69B LEU* 3.9 13.2 - - + -
85B VAL* 4.3 4.0 - - + -
87B ILE* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 4.2 0.6 - - - -
23B ILE* 1.3 71.7 - - - +
25B LEU* 1.3 72.3 + - - +
26B THR* 4.2 3.1 + - - -
32B GLU* 3.4 31.0 + - - +
33B THR* 3.5 28.3 - - - +
34B SER 4.5 1.3 - - - -
35B ALA* 4.4 15.9 - - + +
67B ILE* 3.6 1.7 - - - -
68B THR* 3.0 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.5 41.1 - - + -
5B ILE* 4.6 4.0 - - + -
23B ILE* 3.5 25.6 - - + +
24B LYS* 1.3 73.5 - - - +
26B THR* 1.3 65.6 + - - +
32B GLU* 3.3 2.8 - - - +
33B THR* 3.1 44.2 + - + +
36B PHE* 4.4 5.8 - - + -
61B VAL* 4.8 4.0 - - + -
64B ILE* 3.9 26.7 - - + -
66B MET 4.0 3.6 - - - -
67B ILE* 4.0 4.0 - - + -
87B ILE* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 4.2 6.8 + - - +
25B LEU* 1.3 78.3 + - - +
27B GLY* 1.3 72.0 + - - +
30B GLY* 4.3 16.2 - - - +
31B ALA 3.8 3.1 - - - -
32B GLU* 3.7 16.5 + - + +
61B VAL* 4.5 1.6 - - - -
64B ILE* 3.5 5.2 - - - +
65B ALA* 2.9 24.2 + - + -
66B MET* 3.1 32.2 + - + +
68B THR* 4.9 4.9 + - - -
130B THR* 3.9 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 1.3 84.4 - - - +
28B LYS* 1.3 66.1 + - - -
29B ASP 3.1 3.4 - - - -
30B GLY* 3.1 11.2 + - - -
31B ALA 2.8 21.2 + - - -
61B VAL* 3.5 20.7 - - - +
63B GLU 3.0 10.8 - - - -
65B ALA* 4.2 1.9 - - - +
130B THR* 4.0 4.9 - - - +
----------------------------------------------------------
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