Contacts of the strand formed by residues 76 - 82 (chain B) in PDB entry 2YVC
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 LEU 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.0 18.6 - - + -
6B ASN 2.8 12.7 + - - +
7B VAL* 3.6 21.2 - - + +
8B ARG* 2.6 34.7 + - - +
65B VAL* 4.8 10.1 - - + +
66B THR* 6.3 0.7 - - + -
70B VAL* 3.8 36.3 - - + +
71B LYS 4.4 8.5 - - - +
72B LYS* 5.0 15.9 - - - +
73B GLU* 3.5 22.9 - - - +
74B ASN 2.7 11.7 + - - +
75B PRO* 1.3 70.1 - - - +
77B GLN* 1.3 55.9 + - - +
78B PHE* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.0 7.8 - - - +
54A GLY* 3.7 25.9 + - - -
71A LYS* 3.5 24.6 + - - +
8B ARG* 3.5 34.4 + - + +
10B THR* 5.7 1.3 - - - +
48B GLN 4.2 0.5 - - - +
49B TYR* 4.1 15.2 - - - +
50B VAL* 5.0 4.1 + - + +
70B VAL* 4.9 2.2 - - - +
73B GLU* 3.1 35.1 + - - +
75B PRO 3.0 18.0 + - - -
76B LEU* 1.3 73.2 - - - +
78B PHE* 1.3 67.9 + - - +
79B LYS* 5.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.1 14.8 - - + -
8B ARG 3.0 8.7 + - - +
9B VAL* 4.2 19.3 - - + -
10B THR* 3.1 27.9 + - - -
29B LEU* 4.5 18.2 - - + -
47B LEU* 4.4 15.3 - - + -
48B GLN 3.2 15.3 - - - +
49B TYR* 4.0 14.1 - + + -
59B LEU* 3.6 36.1 - - + -
65B VAL* 4.7 7.2 - - + -
70B VAL* 4.2 11.2 - - + -
76B LEU* 3.7 43.7 - - + -
77B GLN* 1.3 79.5 - - - +
79B LYS* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 5.5 8.2 - - - +
73A GLU* 5.1 10.3 - - - -
10B THR* 3.7 9.1 + - - +
47B LEU* 3.3 8.7 - - - +
48B GLN* 2.7 54.3 + - + +
77B GLN* 5.4 7.5 + - - +
78B PHE* 1.3 81.4 + - - +
80B PHE* 1.3 58.9 - - - +
81B ARG* 3.2 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.8 14.8 - - + +
10B THR 2.8 19.5 + - - +
11B THR* 3.9 27.8 - - + -
12B MET* 4.6 2.9 + - - +
30B PHE* 3.5 25.8 - + - -
33B VAL* 3.7 20.9 - - + -
34B VAL* 3.9 10.3 - - + -
37B VAL* 5.0 4.9 - - + -
39B LEU* 3.5 22.4 - - + -
45B PHE* 3.4 39.5 - + + -
46B GLY 3.9 4.9 - - - -
47B LEU* 3.7 12.3 - - + -
78B PHE 4.2 0.2 + - - -
79B LYS* 1.3 73.3 - - - +
81B ARG* 1.3 68.8 + - - +
101B LEU* 4.5 11.5 - - + +
105B GLN* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 4.2 3.4 + - - -
11B THR 3.7 20.6 + - - -
12B MET* 3.1 29.2 - - - +
45B PHE* 3.5 8.4 - - - +
46B GLY 3.1 29.6 + - - +
48B GLN* 3.9 18.2 - - - +
58B TRP* 4.0 13.7 - - + -
79B LYS* 3.2 43.4 + - + +
80B PHE* 1.3 81.4 + - - +
82B ALA* 1.3 66.3 + - - +
83B LYS 3.4 0.3 + - - -
105B GLN* 3.3 24.1 - - - +
108B GLU* 3.9 17.0 + - - -
22F ARG* 5.2 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE 3.7 5.6 - - - +
45B PHE* 3.8 15.1 - - + -
58B TRP* 4.0 6.5 - - - -
81B ARG* 1.3 72.7 - - - +
83B LYS* 1.3 60.3 + - - +
84B PHE 4.6 0.9 - - - +
85B PHE* 4.3 8.0 - - + -
102B PHE* 3.6 43.5 - - + -
105B GLN* 2.7 38.4 + - - +
----------------------------------------------------------
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