Contacts of the strand formed by residues 113 - 121 (chain B) in PDB entry 1WQS
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 LEU 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B GLU* 5.4 2.6 - - - +
106B SER* 4.3 19.1 - - - -
107B MET 3.4 5.2 - - - +
108B LYS* 4.7 18.4 - - + -
112B ARG* 1.3 82.8 + - - +
114B VAL* 1.4 70.4 + - - +
115B HIS* 4.2 7.2 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU* 4.7 12.3 - - + +
105B ALA 3.4 3.1 - - - +
106B SER* 3.1 4.0 - - - -
107B MET* 2.8 38.8 + - - +
109B ILE* 3.4 29.2 - - + -
110B GLN* 6.0 0.2 - - + -
112B ARG* 4.2 17.3 - - + +
113B LEU* 1.4 75.2 - - - +
115B HIS* 1.3 67.3 + - - +
116B GLY 3.7 0.3 + - - -
158B ALA* 4.6 13.7 - - + -
159B ALA* 3.9 20.4 - - + -
168B VAL* 3.8 24.4 - - + +
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS* 5.8 4.6 - - - +
54B GLU* 4.4 16.5 + - - +
104B ILE* 4.0 24.4 - - + -
105B ALA* 3.6 13.2 + - - -
106B SER* 3.8 21.7 + - - +
113B LEU* 4.2 9.2 + - + +
114B VAL* 1.3 82.3 - - - +
116B GLY* 1.3 64.7 + - - +
170B ALA* 4.5 5.0 - - - -
171B VAL* 5.0 1.9 + - + +
173B ALA* 5.2 11.1 + - - -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE* 3.4 8.4 - - - +
105B ALA 3.2 27.9 + - - +
107B MET* 5.0 0.5 - - - +
115B HIS* 1.3 82.5 + - - +
117B GLN* 1.3 59.0 + - - -
118B SER 3.9 0.9 + - - -
168B VAL* 3.3 13.3 - - - +
169B CYS 3.3 14.1 - - - -
170B ALA* 4.4 2.2 - - - -
171B VAL* 4.5 7.0 - - - -
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLY* 3.7 4.2 - - - -
77B CYS* 2.5 44.6 + - - +
79B GLU* 4.7 0.4 - - - +
101B MET* 3.3 31.3 - - + +
102B GLY 2.2 41.8 + - - +
103B ALA 3.5 7.4 + - - +
104B ILE* 3.6 25.4 - - + +
116B GLY* 1.3 68.5 - - - -
118B SER* 1.3 64.0 + - - +
154B CYS* 4.8 2.9 - - - -
168B VAL* 3.7 1.2 - - - -
169B CYS* 2.8 38.6 + - - +
171B VAL* 4.1 13.8 - - + +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 5.8 3.4 - - - -
166A THR* 5.9 0.5 - - - +
101B MET* 3.1 9.7 - - - +
102B GLY* 2.4 33.9 + - - -
103B ALA* 2.9 34.9 + - - +
107B MET* 3.7 28.3 - - - +
116B GLY 3.9 2.6 + - - -
117B GLN* 1.3 71.7 - - - +
119B GLY* 1.3 56.6 + - - +
166B THR* 5.1 5.8 - - - -
167B VAL 3.3 9.6 - - - -
168B VAL* 4.4 3.2 - - - +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A MET* 5.3 0.7 - - - -
99B VAL* 4.1 3.4 - - - -
100B ARG 3.6 10.8 - - - -
101B MET* 4.1 9.0 - - - -
102B GLY* 3.8 2.7 - - - -
118B SER* 1.3 81.5 + - - +
120B MET* 1.3 63.3 + - - -
166B THR* 3.1 6.6 - - - +
167B VAL* 2.4 46.7 + - - +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.6 44.0 - - + +
101A MET 4.7 0.2 - - - +
102A GLY* 4.5 12.6 - - - -
119A GLY* 5.8 0.7 - - - -
120A MET* 3.4 45.3 - - + +
99B VAL* 3.4 0.6 - - - -
100B ARG* 2.6 38.1 + - - +
119B GLY* 1.3 72.7 - - - -
121B LEU* 1.3 67.0 + - - +
122B LEU* 4.0 0.3 - - - +
165B ASN* 3.1 39.0 - - - +
166B THR* 3.8 11.0 - - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.1 20.4 + - - -
85B ILE* 5.4 2.0 - - + -
97B LEU* 4.0 14.6 - - + -
98B ALA 3.7 4.3 - - - +
99B VAL* 3.9 18.8 - - + -
120B MET* 1.3 73.9 - - - +
122B LEU* 1.3 60.6 + - - +
123B THR* 4.0 11.0 - - - +
124B GLY 3.4 12.2 - - - +
125B ALA 5.8 1.8 - - - +
132B LEU 4.0 5.2 - - - +
133B GLY* 3.8 26.7 - - - -
134B THR* 4.3 4.7 - - - +
164B GLY 2.9 22.7 - - - +
165B ASN 2.8 12.9 + - - +
167B VAL* 3.8 31.9 - - + -
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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