Contacts of the helix formed by residues 116 - 123 (chain A) in PDB entry 2WNW
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 PHE 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A TYR* 3.4 55.0 - + + -
114A LEU* 4.2 25.1 - - + -
115A SER* 1.3 75.1 - - - +
117A SER* 1.3 65.9 + - - +
118A ARG* 3.1 3.8 - - - -
119A ASP* 3.0 11.5 + - + +
120A GLU* 2.9 25.9 + - + +
173A ILE 4.8 0.9 - - - -
176A ASN* 3.8 23.6 - - + -
177A TYR* 3.8 20.0 - + + -
180A GLU* 3.4 46.0 - - + +
181A TYR* 5.0 1.1 - + - -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.2 16.2 + - - -
116A PHE* 1.3 76.9 - - - +
118A ARG* 1.3 65.7 + - - +
120A GLU* 3.2 18.8 + - - +
121A ALA* 3.1 23.9 + - - +
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Residues in contact with ARG 118 (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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54A GLU* 2.9 40.1 + - - +
97A LEU* 3.6 10.5 - - - +
98A GLY* 3.5 26.1 + - - +
99A ASN 4.0 7.5 + - - -
100A TYR* 3.4 39.2 - - + +
115A SER* 5.0 0.9 + - - +
116A PHE 3.1 1.0 - - - -
117A SER* 1.3 83.5 + - - +
119A ASP* 1.3 65.2 + - - +
121A ALA* 3.3 4.1 + - - +
122A HIS* 3.0 37.7 + - + +
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Residues in contact with ASP 119 (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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89A PRO 4.7 0.3 - - - +
100A TYR* 3.2 31.2 + - - -
102A TYR* 2.6 36.4 + - + -
116A PHE* 3.0 12.0 + - + +
118A ARG* 1.3 77.4 - - - +
120A GLU* 1.3 57.7 + - - +
122A HIS* 5.2 0.2 - - - -
123A LEU* 2.9 40.1 + - + +
124A ILE* 2.9 14.6 + - + -
177A TYR* 4.3 0.2 - - - -
181A TYR* 2.8 34.5 + - + +
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Residues in contact with GLU 120 (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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116A PHE* 2.9 28.5 + - - +
117A SER* 3.2 19.3 + - - +
119A ASP* 1.3 77.9 - - + +
121A ALA* 1.3 56.9 + - - +
124A ILE* 3.8 18.5 - - + +
125A PRO* 3.3 20.6 - - - +
180A GLU* 2.8 30.5 - - - +
183A ARG* 4.7 4.0 + - - -
184A HIS* 3.0 20.8 + - + +
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Residues in contact with ALA 121 (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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61A ASN* 2.9 20.3 + - - -
117A SER 3.1 13.6 + - - +
118A ARG* 4.0 2.9 - - - +
120A GLU* 1.3 80.3 - - - +
122A HIS* 1.3 72.5 + - + +
125A PRO* 3.6 11.7 - - - +
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Residues in contact with HIS 122 (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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54A GLU* 2.7 41.6 + - + +
57A GLY* 3.1 31.9 - - - +
58A VAL* 3.9 16.4 - - + +
61A ASN* 3.9 10.3 + - - +
97A LEU* 3.8 22.8 - - + +
118A ARG* 3.0 25.3 + - + +
121A ALA* 1.3 96.1 - - + +
123A LEU* 1.3 61.7 + - + +
125A PRO* 4.2 2.3 - - - +
126A LEU* 4.9 1.4 - - - +
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Residues in contact with LEU 123 (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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52A PHE* 3.9 15.9 - - + +
53A THR* 3.3 42.6 - - - +
54A GLU* 4.2 6.7 - - + +
57A GLY* 5.3 0.7 - - - +
88A MET* 5.5 2.2 - - + -
89A PRO* 4.6 14.1 - - + +
100A TYR* 3.8 16.8 - - - +
119A ASP* 2.9 34.6 + - - +
122A HIS* 1.3 75.3 - - + +
124A ILE* 1.3 65.7 + - - +
125A PRO* 3.3 2.9 - - - -
126A LEU* 3.2 9.1 + - + +
127A ILE* 3.1 30.1 + - + +
181A TYR* 3.7 22.2 - - - +
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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