Contacts of the strand formed by residues 186 - 194 (chain A) in PDB entry 3QWR
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE* 4.0 13.0 - - + -
136A SER* 3.4 23.1 - - - +
137A SER 3.5 3.4 - - - +
138A ARG* 3.6 50.5 - - + +
146A VAL* 4.2 12.1 - - + -
173A GLU* 4.4 7.4 - - + +
185A PRO* 1.3 73.3 - - - +
187A GLU* 1.3 63.5 + - - +
188A VAL* 4.2 0.2 - - + -
203A SER 4.0 0.2 - - - +
204A SER* 3.3 5.7 + - - -
205A PHE* 2.8 66.8 + - + +
207A ILE* 4.4 11.9 - - + -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 2.9 28.2 + - - -
137A SER* 2.9 19.8 + - - +
139A GLY* 4.4 14.5 - - - +
140A SER* 4.7 9.0 + - - -
185A PRO* 3.8 15.9 - - - +
186A ILE* 1.3 72.1 - - - +
188A VAL* 1.3 62.3 + - - +
189A MET* 4.4 16.4 - - + -
202A THR* 4.8 7.8 + - - +
203A SER 3.5 5.2 - - - +
204A SER* 2.6 30.5 + - - -
81D TYR* 4.1 3.1 + - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.6 7.4 - - + -
118A PHE* 4.0 13.2 - - + -
120A CYS* 4.1 16.4 - - + -
134A VAL* 4.0 22.9 - - + -
135A LYS 3.6 3.1 - - - +
136A SER* 3.8 11.4 - - - +
171A CYS* 5.8 0.9 - - - -
186A ILE* 4.2 0.4 - - + -
187A GLU* 1.3 78.8 - - - +
189A MET* 1.3 68.7 + - - +
190A VAL* 4.4 8.3 - - + -
202A THR* 3.1 8.1 + - - -
203A SER* 2.8 41.6 + - - +
205A PHE* 3.8 30.3 - - + -
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Residues in contact with MET 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A SER 3.6 1.6 - - - +
134A VAL* 3.5 4.9 - - - +
135A LYS* 2.8 61.1 + - + +
136A SER* 4.7 3.4 - - - +
137A SER* 5.1 8.1 - - - +
187A GLU* 4.3 24.2 - - + +
188A VAL* 1.3 79.2 - - - +
190A VAL* 1.3 63.9 + - - +
191A ASP* 4.2 1.0 - - - +
200A ASN* 6.1 2.7 - - - +
201A TYR 3.4 6.7 - - - +
202A THR* 4.8 6.7 - - - -
1C NAG 4.3 27.8 - - + -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 5.3 1.6 - - + -
107A LEU* 4.2 16.4 - - + -
122A TRP* 4.0 27.1 - - + -
132A PHE* 3.8 23.1 - - + -
133A SER 3.4 5.2 - - - +
134A VAL* 3.9 22.2 - - + -
188A VAL* 4.4 4.5 - - + -
189A MET* 1.3 78.6 - - - +
191A ASP* 1.3 73.0 + - - +
192A ALA* 3.7 3.0 + - + +
200A ASN* 3.4 6.9 - - - +
201A TYR* 2.7 48.8 + - + +
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.9 20.9 - - + +
131A THR 3.8 0.3 - - - +
132A PHE* 3.1 7.6 - - - -
133A SER* 2.8 52.6 + - - +
189A MET 5.5 0.8 - - - +
190A VAL* 1.3 73.3 - - - +
192A ALA* 1.3 60.7 + - - +
193A VAL* 5.2 2.5 - - + -
198A TYR* 2.6 33.9 + - + -
199A GLU 3.9 3.8 - - - -
200A ASN* 4.1 1.9 - - - +
1C NAG 3.4 25.1 - - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 4.0 15.5 - - + +
131A THR 3.6 3.8 - - - -
132A PHE* 3.5 25.1 - - + -
190A VAL* 3.7 1.0 + - + -
191A ASP* 1.3 73.3 - - - +
193A VAL* 1.3 68.5 + - - +
197A LYS 3.7 0.5 - - - +
198A TYR* 3.5 1.1 - - - -
199A GLU 2.8 40.3 + - - +
201A TYR* 4.0 22.4 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.6 8.5 - - + -
81A LEU* 3.5 29.2 - - + -
94A ILE* 4.3 1.5 - - - +
129A ASP 3.4 4.9 - - - +
130A LEU* 3.4 2.9 - - - +
131A THR* 2.9 48.4 + - - +
191A ASP* 5.2 2.5 - - + -
192A ALA* 1.3 80.3 - - - +
194A HIS* 1.3 61.2 + - - +
195A LYS 3.4 23.6 - - - +
197A LYS 3.4 6.1 - - - +
198A TYR* 4.0 18.8 - - + -
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 3.7 23.6 - - + +
126A ILE* 3.4 29.9 - - + +
128A THR* 3.1 24.6 + - - -
129A ASP* 3.3 6.1 + - - -
130A LEU* 3.2 20.0 - - + +
193A VAL* 1.3 70.2 - - - +
195A LYS* 1.3 101.3 + - + +
196A LEU 3.0 0.5 + - - -
197A LYS* 2.9 50.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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