Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 2CR9
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 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 2.5 59.2 + - + +
70A GLU* 5.2 15.3 + - + -
71A ASN* 1.3 78.8 - - - +
73A TYR* 1.3 76.6 + - - +
74A TRP* 4.3 13.1 - - + -
93A GLN* 3.1 47.1 + - + +
94A MET 4.4 4.5 - - - +
95A PRO 5.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.9 11.4 - - + -
64A LEU* 4.6 2.7 - - + -
65A LEU 3.5 7.6 - - - +
66A GLU* 3.1 44.6 + - + -
67A ASP 5.2 2.5 - - - -
71A ASN* 4.6 6.4 - - + -
72A ARG* 1.3 102.0 - - - +
74A TRP* 1.3 64.5 + - - +
93A GLN* 3.3 7.8 - - - +
94A MET* 2.6 37.9 + - + -
95A PRO 5.8 0.7 - - - -
96A SER* 4.5 2.0 - - - -
97A LYS* 2.9 66.8 - - + +
100A ALA* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 44.1 - - + +
32A SER* 6.2 1.3 - - - -
33A ALA* 4.3 11.0 - - + -
64A LEU* 3.1 25.6 - - - +
65A LEU* 3.1 16.4 + - + +
67A ASP* 3.2 50.5 - - + -
72A ARG* 4.3 20.9 - - + -
73A TYR* 1.3 77.9 - - - +
75A ILE* 1.3 64.5 + - - +
76A PHE 4.0 0.9 - - - -
91A LEU* 3.9 20.5 - - + +
92A GLU* 3.0 8.3 - - - +
93A GLN* 3.4 39.2 - - + +
94A MET* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.5 1.1 - - + -
63A GLN 4.5 0.4 - - - +
64A LEU* 4.1 7.0 - - + -
74A TRP* 1.3 80.3 - - - +
76A PHE* 1.3 61.4 + - - +
77A ARG* 3.3 35.6 + - + +
90A LYS 3.0 12.7 - - - +
91A LEU* 4.5 2.0 - - - -
92A GLU 2.8 24.6 + - - +
94A MET* 3.6 30.7 - - + -
100A ALA 3.2 26.7 - - - +
103A HIS* 3.7 16.4 - - + -
104A PHE* 3.9 22.4 - - + +
107A LEU* 3.9 4.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
24A ASP* 2.9 33.0 - - + -
26A ASP* 3.4 24.9 - - - -
27A SER* 3.8 24.5 - - - -
61A LYS* 4.9 5.4 - - + -
62A LEU* 3.9 7.4 - - - +
63A GLN* 3.3 58.2 + - + +
65A LEU* 4.1 15.2 - - + +
74A TRP 4.0 1.0 - - - -
75A ILE* 1.3 71.7 - - - +
77A ARG* 1.3 70.2 + - - +
78A SER* 3.8 22.7 - - - -
89A ASN* 3.8 18.4 - - + -
90A LYS 3.2 10.8 - - - -
91A LEU* 4.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 4.3 13.2 - - + +
61A LYS 3.7 5.4 - - - -
62A LEU* 4.5 0.9 - - + -
75A ILE* 3.3 21.9 + - + +
76A PHE* 1.3 83.7 - - - +
78A SER* 1.3 59.8 + - - +
79A TRP* 3.3 20.6 - - + -
89A ASN* 3.2 4.9 - - - -
90A LYS* 2.8 66.6 + - + +
92A GLU* 3.8 32.5 + - - +
94A MET* 5.6 1.4 - - - +
103A HIS* 3.0 34.2 + - - -
107A LEU* 3.4 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 5.4 0.9 - - - -
59A TYR* 3.5 19.0 - - - -
60A TYR* 3.5 8.3 - - - -
61A LYS* 3.0 46.7 + - - +
76A PHE* 3.8 25.2 - - - -
77A ARG* 1.3 74.3 - - - +
79A TRP* 1.3 64.6 + - - +
88A SER 3.7 7.2 - - - -
89A ASN* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.6 22.1 + - - +
60A TYR* 4.6 17.7 - + + -
77A ARG* 3.3 39.9 - - + -
78A SER* 1.3 77.7 + - - +
80A GLY* 1.3 64.3 + - - +
86A ILE* 5.4 3.8 - - + -
88A SER* 3.2 51.8 + - - +
89A ASN 4.4 2.5 - - - -
90A LYS* 3.7 44.9 - - + -
111A LYS* 5.4 4.5 - - - +
----------------------------------------------------------
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