Contacts of the strand formed by residues 75 - 82 (chain A) in PDB entry 2CGY
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 GLY 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE 3.3 13.9 - - - -
37A PHE* 3.2 21.4 - - - -
71A VAL* 3.8 0.3 - - - -
72A SER* 2.9 33.7 + - - +
74A THR* 1.3 81.7 - - - +
76A PHE* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.4 3.6 - - + -
34A ASN* 4.9 3.6 + - - -
35A ILE* 3.0 62.0 + - + +
37A PHE* 3.6 28.3 - + - -
47A VAL* 4.3 9.4 - - + -
49A LEU* 4.4 10.5 - - + -
68A LEU* 4.0 9.2 - - + -
70A SER 3.1 19.7 - - - +
71A VAL* 4.0 11.9 - - + -
75A GLY* 1.3 73.4 - - - +
77A LYS* 1.3 55.7 + - - +
78A ALA* 3.8 27.6 + - + -
95A TRP* 3.4 42.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.7 7.7 + - - -
32A ALA* 3.7 21.4 - - + +
33A LYS 3.7 11.2 - - - +
34A ASN* 4.3 12.5 + - - +
68A LEU* 4.1 1.6 - - - +
69A TYR* 3.1 68.7 + - + +
70A SER* 3.3 23.3 + - - +
76A PHE* 1.3 71.7 - - - +
78A ALA* 1.3 64.5 + - - +
1101A NAG 3.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.7 11.7 - - + +
32A ALA* 3.6 1.4 - - - +
33A LYS* 3.0 30.6 + - - +
35A ILE* 5.8 0.2 - - - +
49A LEU* 3.9 17.5 - - + -
67A ARG 3.1 16.2 - - - +
68A LEU* 4.1 2.7 - - + +
69A TYR* 4.5 2.0 - - - +
76A PHE* 3.8 24.9 + - + -
77A LYS* 1.3 76.5 - - - +
79A SER* 1.3 64.2 + - - +
93A ILE* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 6.3 1.8 - - - -
30A GLU* 3.3 20.6 + - - -
31A LEU 3.2 15.5 - - - -
32A ALA* 3.5 17.7 - - - -
65A ILE 3.5 1.7 - - - +
67A ARG* 2.9 48.5 + - - +
69A TYR* 3.7 4.8 - - - -
78A ALA* 1.3 76.2 - - - +
80A CYS* 1.3 65.0 + - - +
81A TYR* 4.1 2.3 - - - +
93A ILE* 3.5 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A CYS* 2.0 47.0 - - + -
15A TRP* 3.4 24.7 - - + -
30A GLU* 3.2 4.9 - - - +
31A LEU 2.9 31.6 + - - +
65A ILE 3.6 5.2 - - - -
79A SER* 1.3 73.7 - - - +
81A TYR* 1.3 59.7 + - - +
91A MET* 3.6 24.0 - - - -
93A ILE* 3.4 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.9 2.8 - - - -
18A VAL* 4.3 13.3 - - + +
19A PRO 5.4 0.2 + - - -
20A SER* 4.5 4.5 + - - -
21A ASP* 3.9 10.5 + - - -
22A ASP* 5.5 0.3 + - - +
25A ARG* 4.4 9.9 + - - -
28A THR* 3.0 33.6 + - + +
29A ARG 3.7 13.7 - - - -
30A GLU* 3.5 24.2 - - - -
64A VAL* 3.3 6.9 - - - +
65A ILE* 2.9 62.1 + - + +
67A ARG* 3.4 34.4 + - + -
69A TYR* 4.5 1.6 - - - -
79A SER* 4.1 7.4 - - - +
80A CYS* 1.3 75.3 - - - +
82A THR* 1.3 65.2 + - - +
83A TRP* 4.1 17.5 - + - -
91A MET* 4.7 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 4.3 4.5 - - - +
15A TRP* 3.7 25.1 - - + -
28A THR* 3.4 2.4 - - - -
29A ARG* 2.8 62.7 + - + +
63A ARG 2.5 24.7 + - - -
81A TYR* 1.3 76.3 - - - +
83A TRP* 1.3 71.0 + - - +
86A THR* 3.1 19.1 - - - +
88A VAL* 4.0 7.4 - - + -
----------------------------------------------------------
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