Contacts of the strand formed by residues 94 - 102 (chain A) in PDB entry 2QBX
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 ILE 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.7 26.0 - - + -
91A ALA* 3.8 13.5 - - + -
93A ARG* 1.3 74.1 - - - +
95A HIS* 1.3 66.7 + - - +
96A VAL* 4.4 0.4 - - + -
173A SER* 3.1 5.4 - - - -
174A PHE* 2.8 72.4 + - + +
177A VAL* 3.6 31.2 - - + -
182A PHE* 3.8 15.3 - - + -
200A VAL* 3.5 28.9 - - + -
201A PHE 3.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 4.0 26.8 - - + +
94A ILE* 1.3 75.4 - - - +
96A VAL* 1.3 62.4 + - - +
97A GLU 4.1 0.4 - - - -
171A VAL* 4.6 8.5 - - + +
172A ARG 3.7 2.4 + - - +
173A SER* 3.0 31.7 - - - -
200A VAL* 3.3 5.4 - - - +
201A PHE* 2.7 81.6 + + + +
202A TYR* 4.4 6.3 - - - -
203A ARG 4.5 10.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
94A ILE* 4.4 4.3 - - + -
95A HIS* 1.3 75.7 - - - +
97A GLU* 1.3 58.8 + - - +
98A MET* 3.5 21.0 - - + +
121A LEU* 4.5 15.7 - - + -
171A VAL* 3.4 6.6 - - - -
172A ARG 2.8 37.3 + - - +
174A PHE* 3.6 31.2 - - + -
184A LEU* 3.6 31.6 - - + -
198A VAL* 4.0 16.6 - - + -
199A ARG 3.5 3.6 - - - +
200A VAL* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS 4.1 1.0 - - - -
96A VAL* 1.3 71.4 - - - +
98A MET* 1.3 61.7 + - - +
99A LYS* 4.1 20.7 + - + +
169A THR* 4.0 19.1 - - + +
170A GLU 3.6 3.1 - - - -
171A VAL* 3.9 21.8 - - + +
197A ALA* 3.6 1.4 - - - +
198A VAL* 3.4 4.5 - - - -
199A ARG* 2.7 81.3 + - + +
201A PHE* 4.2 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.5 29.2 - - + +
97A GLU* 1.3 75.6 - - - +
99A LYS* 1.3 60.9 + - - +
100A PHE* 3.7 17.0 - - + -
119A PHE* 4.1 23.3 - - - -
121A LEU* 3.9 26.5 - - + -
149A ILE* 3.9 23.8 - - + -
169A THR* 3.4 5.1 - - - +
170A GLU* 2.9 43.1 + - + +
172A ARG* 4.1 9.6 - - + -
186A PHE* 4.3 15.9 - - + -
195A LEU* 4.3 9.2 - - + -
197A ALA 3.3 6.5 - - - +
198A VAL* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.0 28.6 + - - +
97A GLU* 4.1 19.9 + - + +
98A MET* 1.3 70.4 - - - +
100A PHE* 1.3 63.4 + - - +
167A ILE* 4.1 11.9 - - + -
168A ASN 3.4 3.4 - - - +
169A THR* 2.7 44.2 + - + +
195A LEU* 3.8 1.9 - - - +
196A ILE* 2.8 30.2 + - + -
197A ALA* 2.8 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 3.7 18.2 - - + -
99A LYS* 1.3 78.5 - - - +
101A SER* 1.3 64.6 + - - +
102A VAL* 4.0 23.6 - - + -
119A PHE* 3.8 22.9 - + + -
149A ILE* 3.9 12.3 - - + -
150A ALA* 3.7 21.1 - - - -
151A ALA* 4.2 10.8 - - + -
167A ILE* 3.6 3.1 - - - +
168A ASN* 2.9 59.1 + - + +
170A GLU* 3.8 21.5 - - + -
193A MET* 6.0 1.6 - - + -
194A SER 3.2 14.4 - - - +
195A LEU* 4.1 12.1 - - + -
196A ILE* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 1.3 71.3 - - - +
102A VAL* 1.3 62.4 + - - +
165A MET* 4.5 0.3 - - - +
166A LYS 2.8 28.0 + - - -
167A ILE* 3.8 2.3 - - - +
168A ASN* 5.4 0.2 - - - -
193A MET* 3.2 4.9 - - - +
194A SER 2.8 37.9 + - - -
196A ILE* 3.1 20.7 - - - +
2P ASN* 3.5 16.0 + - - -
4P TRP* 3.9 18.2 - - - -
5P ILE* 3.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 4.0 25.7 + - + -
101A SER* 1.3 76.3 - - - +
103A ARG* 1.3 62.6 + - - +
104A ASP* 3.6 17.1 + - - +
116A LYS 5.2 0.7 - - - +
117A GLU* 3.8 42.8 - - + +
118A THR* 5.6 0.2 - - - -
119A PHE* 5.4 2.2 - - + -
150A ALA* 6.0 0.2 - - - -
151A ALA* 4.7 13.9 - - + +
166A LYS* 4.5 3.0 + - - +
168A ASN* 5.2 3.6 + - - -
192A CYS 3.8 7.6 - - - +
193A MET* 4.2 15.3 - - + -
1P SER* 4.3 3.1 + - - +
2P ASN* 2.6 26.0 + - - +
----------------------------------------------------------
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