Contacts of the strand formed by residues 120 - 126 (chain B) in PDB entry 1WSQ
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 TRP 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B PHE* 3.3 10.4 - - - -
78B VAL* 2.8 55.2 + - + +
79B ASN 4.8 0.2 - - - -
80B ASN* 4.2 24.9 - - - -
81B GLU* 4.3 15.7 - - + -
84B LEU* 3.9 25.6 - - + +
111B ILE* 4.1 21.3 - - + -
112B ASN 3.3 5.6 - - - +
113B ASN* 2.9 46.7 - - + +
114B VAL* 5.5 0.2 - - - -
117B GLY 4.3 5.2 - - - -
118B ASP* 3.6 28.3 - - - -
119B VAL* 1.3 74.2 - - - +
121B GLU* 1.3 61.1 + - - +
122B VAL 3.8 1.1 + - - -
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Residues in contact with GLU 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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39B PHE* 3.9 7.1 - - - -
40B GLY 4.6 4.4 + - - -
75B ARG* 2.9 35.3 + - + +
77B PHE* 3.6 25.3 - - + -
110B SER 3.7 1.4 - - - +
111B ILE* 3.3 4.9 - - - -
112B ASN* 2.7 59.9 + - - +
114B VAL* 4.7 11.1 - - + +
120B TRP* 1.3 71.8 - - - +
122B VAL* 1.3 62.2 + - - +
123B LEU* 3.8 25.9 + - + +
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Residues in contact with VAL 122 (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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74B LYS* 3.4 2.0 - - - +
75B ARG* 3.3 6.6 - - - +
76B MET* 2.8 47.6 + - + +
78B VAL* 4.3 18.4 - - + -
84B LEU* 4.8 1.1 - - + -
87B CYS* 4.0 38.1 - - + -
90B GLU* 5.6 0.2 - - - +
91B ILE* 4.4 10.3 - - + -
110B SER 3.8 2.9 - - - -
111B ILE* 4.3 18.2 - - + -
120B TRP 4.5 0.2 - - - +
121B GLU* 1.3 74.8 - - - +
123B LEU* 1.3 62.1 + - - +
124B ILE* 4.1 23.8 - - + -
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Residues in contact with LEU 123 (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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39B PHE* 4.1 14.8 - - + -
40B GLY* 3.5 37.0 - - - +
44B GLN 5.6 1.1 - - - +
46B VAL* 6.2 0.4 - - + -
73B LEU* 4.0 16.6 - - + -
74B LYS 3.5 1.8 - - - -
75B ARG* 3.7 33.4 - - + -
109B SER* 3.2 6.9 - - - -
110B SER* 2.9 52.4 + - - +
112B ASN* 4.0 4.0 - - - +
121B GLU* 3.8 25.6 - - + +
122B VAL* 1.3 74.2 - - - +
124B ILE* 1.3 62.5 + - - +
125B LEU 4.2 0.4 - - - -
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Residues in contact with ILE 124 (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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73B LEU* 3.5 4.6 - - - +
74B LYS* 2.9 46.9 + - + +
90B GLU* 3.8 21.1 - - - +
91B ILE* 3.8 25.4 - - + -
94B MET* 3.6 37.0 - - + -
106B TYR* 4.3 11.0 - - + -
108B ASP 3.8 7.9 - - - +
109B SER* 4.2 0.7 - - - -
122B VAL* 4.1 15.3 - - + -
123B LEU* 1.3 78.7 - - - +
125B LEU* 1.3 62.9 + - - +
126B MET* 3.4 25.5 - - + +
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Residues in contact with LEU 125 (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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44B GLN 5.9 0.7 - - - +
46B VAL* 4.2 13.0 - - + -
63B VAL* 3.7 22.0 - - + -
65B THR* 4.0 21.1 - - + -
71B CYS* 3.6 30.1 - - + -
72B ALA 3.5 4.5 - - - +
73B LEU* 4.2 12.8 - - + -
106B TYR* 3.8 1.2 - - - -
107B ILE* 2.7 39.2 + - + -
108B ASP* 2.8 41.7 + - + +
109B SER* 5.5 0.2 - - - -
123B LEU 4.2 0.8 - - - -
124B ILE* 1.3 73.3 - - - +
126B MET* 1.3 57.5 + - - +
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Residues in contact with MET 126 (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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60B VAL* 5.6 0.7 - - + -
71B CYS* 3.4 1.6 - - - +
72B ALA* 2.8 28.2 + - + +
73B LEU 4.6 0.4 - - - -
74B LYS* 3.5 28.9 - - + +
94B MET* 4.2 23.3 - - + +
104B VAL* 4.1 11.0 - - + -
105B GLY 3.3 13.7 - - - +
106B TYR* 4.7 1.1 - - - -
107B ILE* 3.3 15.5 - - - +
124B ILE* 3.4 32.3 - - + +
125B LEU* 1.3 78.9 - - - +
127B ASP* 1.3 71.3 + - - +
128B PHE 3.4 0.3 + - - -
193B CYS* 5.8 0.4 - - - -
404B KSA 3.8 41.7 - - + -
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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