Contacts of the strand formed by residues 92 - 99 (chain A) in PDB entry 2A3W
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 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 4.1 0.2 - - - +
38A ARG* 3.3 6.7 - - - +
39A ALA* 2.9 47.4 + - + +
65A LYS* 6.1 0.4 - - - +
71A TYR* 3.7 16.8 - - - +
86A GLU* 4.4 4.9 - - + +
90A ALA* 4.3 5.4 - - + +
91A PRO* 1.3 77.5 - - - +
93A HIS* 1.3 68.6 + - - +
94A ILE* 3.8 22.8 - - + +
109A ILE* 3.6 30.7 - - + -
110A ASN* 3.6 9.9 - - - +
203A TRP* 4.8 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 4.2 12.1 - - + +
37A PHE* 3.6 9.9 + - - -
38A ARG* 3.6 38.8 - - + +
92A VAL* 1.3 74.9 - - - +
94A ILE* 1.3 61.8 + - - +
95A CYS* 3.4 32.0 - - - -
108A TRP 3.4 4.5 + - - +
109A ILE* 3.4 3.3 - - - -
110A ASN* 2.8 37.5 + - - +
111A GLY 4.9 4.0 + - - -
156A ASP* 5.2 3.9 + - + +
169A ILE* 4.5 0.8 - - + +
172A ALA* 3.9 8.4 + - - +
173A TYR* 3.5 55.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 3.8 0.7 - - - +
36A CYS* 3.1 2.3 - - - -
37A PHE* 2.8 78.3 + - + +
39A ALA* 4.9 1.3 - - + -
49A LEU* 3.8 13.9 - - + -
63A VAL* 4.9 2.7 - - + -
71A TYR* 3.5 23.8 - - + -
92A VAL* 3.8 21.8 - - + -
93A HIS* 1.3 78.7 - - - +
95A CYS* 1.3 73.0 + - - +
96A VAL* 4.7 1.3 - - + +
107A PHE* 4.2 23.3 - - + -
108A TRP 3.5 2.5 - - - -
109A ILE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.8 0.7 - - + -
35A LEU 3.1 4.7 - - - -
36A CYS* 2.0 47.1 - - - -
93A HIS* 3.4 20.2 - - - -
94A ILE* 1.3 73.4 - - - +
96A VAL* 1.3 61.6 + - - +
106A GLU 3.7 1.0 - - - +
107A PHE* 3.4 5.0 - - - -
108A TRP* 2.8 38.6 + - + +
169A ILE* 3.7 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.9 10.1 - - + -
34A THR* 3.3 3.4 - - - -
35A LEU* 2.8 48.5 + - + +
63A VAL* 3.9 27.6 - - + -
73A LEU* 3.8 29.2 - - + -
94A ILE* 5.4 2.5 - - + -
95A CYS* 1.3 76.9 - - - +
97A SER* 1.3 65.3 + - - +
105A ALA* 5.1 0.2 - - + -
106A GLU 3.1 12.3 - - - +
107A PHE* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.2 14.8 - - - -
34A THR* 3.5 16.4 - - - -
96A VAL* 1.3 78.7 - - - +
98A TRP* 1.3 63.1 + - - +
104A ILE 4.3 0.6 + - - -
105A ALA* 3.2 6.2 - - - +
106A GLU* 2.9 57.2 + - - +
108A TRP* 5.5 1.0 - - - -
163A VAL* 3.7 20.6 - - - +
164A LEU 4.8 2.9 - - - -
169A ILE* 5.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 3.9 6.1 - - - -
31A GLN 3.7 17.3 - - - -
32A ASN* 3.5 4.9 - - - -
33A PHE* 3.1 62.9 + + + +
73A LEU* 4.1 5.8 - - + -
75A ILE* 3.8 27.6 - - + -
97A SER* 1.3 75.6 - - - +
99A GLU* 1.3 65.8 + - - +
100A SER* 3.7 10.3 - - - -
103A GLY 3.3 18.4 + - - -
104A ILE 3.3 7.4 - - - -
105A ALA* 4.3 2.5 - - + -
119A LEU* 3.0 35.8 + - + +
120A ARG 3.2 23.1 - - - -
123A TYR* 3.3 26.0 - - + -
125A VAL* 3.5 22.4 - - + -
163A VAL* 3.6 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.4 17.1 - - - +
98A TRP* 1.3 78.1 - - - +
100A SER* 1.3 55.2 + - - +
101A SER* 3.4 21.1 + - - +
102A SER* 2.6 20.7 + - - +
103A GLY* 2.6 37.2 + - - -
104A ILE* 3.2 10.8 + - + +
163A VAL* 3.7 20.5 - - + +
199E LYS* 2.6 33.1 + - - +
----------------------------------------------------------
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