Contacts of the strand formed by residues 115 - 120 (chain B) in PDB entry 2WZJ
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.4 5.8 - - + +
104B MET* 4.0 38.3 + - + +
105B LYS* 3.8 26.2 - - + -
113B VAL 3.9 2.0 + - - -
114B LYS* 1.3 90.0 + - + +
116B PHE* 1.3 60.4 + - - +
117B GLU 3.9 11.9 - - - +
118B VAL* 3.8 22.4 - - + -
127B LEU* 4.3 18.6 - - + -
128B VAL 3.4 19.5 - - - +
129B MET* 4.4 9.9 - - + +
351B TYR* 3.2 25.4 - - + -
359B LEU* 4.3 1.6 - - - +
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Residues in contact with PHE 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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78B GLU 5.3 1.6 - - - -
79B VAL* 3.7 16.8 - - + -
114B LYS* 4.2 10.1 - - + -
115B LEU* 1.3 80.0 - - - +
117B GLU* 1.3 61.2 + - + +
128B VAL* 2.7 22.5 + - + +
129B MET* 3.8 13.0 - - - -
130B GLU* 3.7 29.4 - - + -
131B TYR 5.2 0.2 - - - -
351B TYR* 3.7 15.3 - - - -
355B MET* 4.5 1.6 - - - +
356B ALA* 3.7 24.8 + - + +
359B LEU* 4.1 27.1 - - + +
360B LEU* 3.5 33.4 - - + -
363B TYR* 3.7 39.7 - + - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 5.8 0.2 - - - +
53B TYR* 2.3 48.5 + - - +
72B HIS* 5.5 0.2 + - - -
115B LEU* 3.9 3.4 - - - +
116B PHE* 1.3 82.6 - - - +
118B VAL* 1.3 72.3 + - - +
119B ILE* 3.5 28.9 - - + +
126B TYR 3.9 0.9 - - - +
128B VAL* 3.0 33.0 + - + +
351B TYR* 3.5 16.7 - - - +
352B ASN* 3.5 13.0 - - - +
353B GLU* 3.7 22.3 + - - +
356B ALA* 3.4 9.1 - - + +
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Residues in contact with VAL 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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98B PHE* 6.0 2.0 - - + -
101B VAL* 4.4 8.1 - - + -
105B LYS* 4.2 18.6 - - - +
115B LEU* 3.8 25.6 - - + -
117B GLU* 1.3 81.5 - - - +
119B ILE* 1.3 65.6 + - - +
120B GLU* 4.2 5.2 + - + +
125B LEU* 3.9 24.2 - - + -
126B TYR 3.7 2.7 - - - -
127B LEU* 3.9 15.9 - - + -
350B ARG 5.8 0.4 - - - +
351B TYR* 3.0 21.6 + - + +
352B ASN* 4.9 2.6 - - - -
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Residues in contact with ILE 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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50B ILE* 4.7 16.8 - - + -
51B GLY* 4.7 13.2 - - - -
53B TYR* 4.3 18.6 - - + -
117B GLU* 3.5 32.8 - - + +
118B VAL* 1.3 73.1 - - - +
120B GLU* 1.3 64.8 + - - +
121B THR* 5.0 6.3 - - + -
125B LEU* 3.6 2.7 - - - +
126B TYR* 2.9 67.1 + - + +
128B VAL* 4.8 5.2 - - + -
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Residues in contact with GLU 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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170A PHE* 4.1 7.3 - - - -
86B LYS* 2.8 34.0 + - + +
98B PHE* 3.4 33.7 - - - -
118B VAL* 4.2 5.4 + - + +
119B ILE* 1.3 76.3 - - - +
121B THR* 1.3 62.9 + - - +
124B THR 3.7 3.8 - - - +
125B LEU* 3.9 14.6 - - + +
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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