Contacts of the strand formed by residues 50 - 56 (chain B) in PDB entry 1V1A
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 50 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.9 6.6 - - - +
4B VAL* 3.4 13.7 - - + +
6B THR* 3.8 20.0 - - + -
40B ALA* 3.2 26.9 - - - +
43B LEU* 3.7 31.2 - - + -
44B ALA* 3.9 13.7 - - + +
48B VAL 2.9 7.0 + - - +
49B LYS* 1.3 76.0 - - - +
51B GLY* 1.3 68.9 + - - +
73B GLY 4.6 3.0 + - - +
74B VAL* 3.8 19.7 - - + -
75B ASP* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.0 4.2 - - - +
4B VAL 3.2 7.0 + - - -
5B VAL* 3.4 7.2 - - - +
6B THR* 3.1 26.5 + - - +
50B VAL* 1.3 79.9 - - - +
52B PHE* 1.3 61.0 + - - -
74B VAL* 3.9 2.2 - - - -
75B ASP* 3.4 9.2 - - - -
122B TYR* 3.4 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.5 12.6 - - - -
8B GLY 2.9 30.3 - - - -
10B PRO* 3.3 29.2 - - + -
36B GLU* 3.8 30.5 - - + -
37B VAL* 3.9 10.8 - - + -
40B ALA* 4.1 9.9 - - + -
51B GLY* 1.3 73.3 - - - -
53B VAL* 1.3 71.1 + - - +
54B GLY 3.9 6.1 - - - -
69B LEU* 3.6 23.1 - - + -
74B VAL* 3.5 17.1 - - + +
75B ASP 2.9 15.7 + - - +
76B LEU* 4.3 3.8 - - + -
78B HIS 4.3 1.9 + - - -
79B PHE* 3.4 42.1 + + - +
122B TYR* 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.0 16.6 - - + -
6B THR 3.1 5.7 + - - -
7B ALA* 3.3 16.0 - - + +
8B GLY 3.1 26.7 + - - +
52B PHE* 1.3 80.6 - - - +
54B GLY* 1.3 61.1 + - - +
78B HIS* 4.2 13.7 - - + +
113B LEU* 4.0 5.3 - - + +
117B ALA 3.9 20.6 - - - +
118B PHE* 4.1 20.0 - - + -
122B TYR* 3.7 30.1 - - + -
145B PHE* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 3.7 12.6 - - - -
52B PHE* 3.9 6.8 - - - -
53B VAL* 1.3 78.6 - - - +
55B ARG* 1.3 79.3 + - - -
78B HIS 4.0 3.8 + - - -
79B PHE* 2.8 24.7 - - - -
80B ARG 3.5 0.2 + - - -
113B LEU* 4.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 4.7 0.2 + - - -
10B PRO* 3.5 13.2 - - - +
53B VAL* 5.1 0.8 - - - +
54B GLY* 1.3 79.3 + - - -
56B VAL* 1.3 65.6 + - - +
78B HIS* 2.7 33.8 + - - +
79B PHE* 3.3 0.6 - - - +
80B ARG* 3.0 73.6 - - - +
82B ALA* 4.4 14.6 - - + -
109B ALA 3.1 25.6 - - - +
110B GLY* 2.8 27.9 - - - -
112B ALA* 5.7 1.6 - - + -
113B LEU* 4.5 20.5 - - + +
117B ALA* 3.3 24.9 + - - +
118B PHE* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 4.1 9.0 - - + +
55B ARG* 1.3 76.0 - - - +
57B GLY* 1.3 59.5 + - - +
62B GLY* 3.5 16.6 - - - +
65B VAL* 3.7 27.4 - - + -
79B PHE* 3.3 35.2 - - + -
80B ARG 3.7 1.4 + - - -
81B ARG* 3.3 34.5 - - + -
82B ALA 3.1 23.2 + - - +
86B THR* 3.6 8.3 - - + +
109B ALA* 3.2 11.4 - - - +
110B GLY 4.7 0.9 - - - +
----------------------------------------------------------
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