Contacts of the strand formed by residues 51 - 62 (chain B) in PDB entry 2V5Q
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 ARG 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 3.7 1.0 - - - +
45B VAL* 3.4 4.7 - - - -
46B ASP* 3.0 38.7 + - + +
49B SER* 3.4 33.9 + - - +
50B ARG* 1.3 76.0 - - - +
52B ARG* 1.3 60.8 + - - +
53B TYR* 3.3 34.0 + - + +
72B ASP* 3.7 24.2 + - - +
75B THR* 5.6 4.9 - - - +
79B PHE* 5.9 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.8 20.4 - - + -
44B LEU 3.3 4.0 - - - +
45B VAL* 5.0 6.3 - - + -
51B ARG* 1.3 76.9 - - - +
53B TYR* 1.3 60.9 + - - +
54B VAL* 5.7 0.7 - - + -
72B ASP* 3.4 5.8 + - - +
73B ALA* 2.8 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.3 4.7 - - - -
44B LEU* 2.7 49.5 + - + +
46B ASP* 5.6 0.3 + - - -
51B ARG* 3.3 45.3 + - + -
52B ARG* 1.3 74.9 - - - +
54B VAL* 1.3 61.8 + - - +
55B ARG 3.7 0.7 + - - -
70B ILE* 3.7 30.3 - - + -
71B SER 3.2 6.1 - - - +
72B ASP* 4.1 25.4 - - - -
79B PHE* 4.1 25.6 - + - -
117B HIS 5.6 1.7 + - - -
120B PHE* 3.6 38.4 - + - -
129B VAL* 4.2 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.7 9.4 - - - +
43B VAL* 4.6 14.8 - - + +
52B ARG* 5.4 0.9 - - + +
53B TYR* 1.3 71.5 - - - +
55B ARG* 1.3 70.2 + - - +
56B GLY* 3.3 2.1 + - - -
70B ILE* 3.2 5.6 - - - -
71B SER* 2.7 50.0 + - - +
72B ASP 5.5 0.7 - - - +
73B ALA* 5.2 11.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
39B GLU 5.5 1.2 - - - +
40B ILE* 2.7 49.7 + - - +
41B PRO 3.3 12.5 + - - -
42B GLU* 2.9 39.6 + - - +
44B LEU* 4.1 14.6 - - + -
53B TYR 3.7 1.4 + - - -
54B VAL* 1.3 75.7 - - - +
56B GLY* 1.3 60.8 + - - +
68B PHE* 3.6 50.2 - - + -
70B ILE* 4.0 9.4 - - + -
83B ILE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.3 5.9 + - - -
55B ARG* 1.3 76.6 - - - +
57B ARG* 1.3 70.1 + - - +
58B PHE 3.4 1.0 + - - -
68B PHE* 3.5 13.7 - - - -
69B GLU* 2.8 17.8 + - - +
71B SER* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY* 1.3 70.7 - - - +
58B PHE* 1.3 74.5 + - - +
59B LEU* 4.0 4.0 - - + +
68B PHE* 3.3 1.2 - - - -
69B GLU* 2.7 69.1 + - - +
134B ARG* 4.3 6.5 - - - +
110C ASP 4.4 5.3 + - - -
111C MET* 2.8 71.5 + - - +
113C GLY* 4.6 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 3.4 1.8 + - - -
57B ARG* 1.3 85.8 - - - +
59B LEU* 1.3 65.4 + - - +
60B GLY* 3.3 38.4 - - - -
61B LYS* 3.9 21.8 - - + -
66B LYS* 3.6 25.8 - - + -
67B CYS 3.5 6.7 - - - -
68B PHE* 3.5 29.1 - + + -
136B ARG* 5.4 2.1 + - - -
111C MET* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 4.3 7.2 - - + -
58B PHE* 1.3 80.8 - - - +
60B GLY* 1.3 56.0 + - - +
67B CYS* 2.7 26.2 + - + +
68B PHE* 3.9 9.6 - - - +
69B GLU* 3.8 47.3 - - + +
80B ALA* 4.5 7.6 - - + -
132B LEU* 4.0 21.3 - - + -
133B CYS 5.8 3.6 - - - +
134B ARG* 6.1 2.9 - - - -
136B ARG* 2.7 38.4 + - - +
111C MET* 5.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.3 25.8 - - - -
59B LEU* 1.3 80.5 - - - +
61B LYS* 1.3 61.8 + - - -
67B CYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 4.3 17.3 - - + -
60B GLY* 1.3 74.8 - - - -
62B GLY* 1.3 58.2 + - - +
63B GLY 3.9 6.5 + - - +
65B ALA 3.4 9.2 - - - +
66B LYS* 4.5 28.7 - - + +
67B CYS* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY 4.0 1.2 + - - -
61B LYS* 1.3 73.9 - - - +
63B GLY* 1.3 61.7 + - - +
64B PHE 3.5 3.3 + - - -
65B ALA* 2.9 24.5 + - - +
67B CYS* 5.0 7.1 - - - -
82B LYS* 4.7 10.0 + - - -
----------------------------------------------------------
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