Contacts of the helix formed by residues 122 - 128 (chain G) in PDB entry 2WQT
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 THR 122 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G ASP 3.8 9.0 - - - +
121G ILE* 1.3 80.4 - - - +
123G PHE* 1.3 64.8 + - - +
124G ASP* 2.8 24.2 + - - +
125G GLU* 3.0 41.4 + - - +
126G LEU* 3.0 12.1 + - - +
209G VAL* 4.3 3.6 - - - -
213G ARG* 4.2 6.5 - - - +
57J VAL* 4.9 2.9 - - + -
84J ALA* 3.8 35.4 - - + +
87J CYS* 4.0 11.9 - - + -
164J TYR* 5.3 1.1 - - - +
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Residues in contact with PHE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G THR* 1.3 72.6 - - - +
124G ASP* 1.3 61.6 + - - +
126G LEU* 3.4 4.7 + - - +
127G TYR* 3.3 41.6 + + - -
203G HIS* 3.8 31.9 - + - -
205G LEU* 3.5 30.6 - - + +
206G ASN* 3.3 27.8 - - - -
209G VAL* 3.8 15.7 - - + +
213G ARG* 5.2 0.8 - - - +
87J CYS* 4.4 12.3 + - - -
88J TYR 4.8 0.2 - - - +
89J GLY* 3.5 17.7 - - - +
90J ASP* 3.9 12.6 - - + -
166J ILE* 3.6 30.7 - - + -
167J GLY 3.8 6.5 - - - -
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Residues in contact with ASP 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G THR* 2.8 22.0 + - - +
123G PHE* 1.3 77.6 - - - +
125G GLU* 1.3 76.7 + - - +
127G TYR* 3.3 25.8 - - - +
128G ASN* 3.6 6.2 + - - +
57J VAL* 6.2 0.3 - - - +
87J CYS* 3.8 12.3 - - - -
111J VAL* 4.8 16.0 - - + +
132J TRP* 5.6 2.8 - - - -
134J LEU* 5.0 5.6 - - + +
164J TYR* 4.4 4.3 + - - -
166J ILE* 3.9 20.8 - - + +
225J GLY 5.2 4.5 - - - +
227J ILE* 4.1 24.6 - - + +
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ARG* 5.8 0.3 + - - -
116G LEU* 5.6 0.3 - - - +
118G ALA* 5.4 1.7 - - - +
121G ILE* 3.4 18.0 - - + +
122G THR* 3.0 36.9 + - - +
124G ASP* 1.3 83.1 - - - +
126G LEU* 1.3 65.8 + - - +
128G ASN* 3.3 16.9 + - - +
129G ALA* 3.6 9.5 + - - +
55J ARG* 2.9 39.3 + - - -
57J VAL* 4.0 9.2 - - - +
225J GLY 5.9 3.4 - - - +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G LEU* 4.7 2.0 - - + -
112G LEU* 5.2 6.7 - - + -
116G LEU* 4.2 24.0 - - + -
121G ILE* 4.1 13.6 - - + +
122G THR 3.0 11.6 + - - +
123G PHE 3.6 8.3 - - - +
124G ASP 3.3 0.2 - - - -
125G GLU* 1.3 74.5 - - - +
127G TYR* 1.3 64.3 + - - +
129G ALA* 2.8 18.6 + - + +
130G ILE* 3.4 12.1 + - + +
205G LEU* 3.8 35.2 - - + +
208G ALA* 3.4 46.7 - - + +
209G VAL* 4.0 8.3 - - + +
212G ALA* 4.4 3.1 - - + -
228G ILE* 5.6 1.3 - - + -
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Residues in contact with TYR 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G PHE* 3.3 38.9 + + - -
124G ASP* 3.3 12.6 - - - +
125G GLU 3.3 0.4 - - - -
126G LEU* 1.3 79.3 - - - +
128G ASN* 1.3 61.0 + - - +
129G ALA 3.1 1.4 + - - -
130G ILE* 3.3 27.4 + - + +
173G PRO* 4.6 20.2 - - + +
176G LEU 4.8 2.4 + - - -
178G LEU* 4.2 19.1 + - + +
203G HIS* 4.5 7.8 + - - -
205G LEU* 3.6 23.6 - - + +
132J TRP* 4.7 14.2 - + + +
134J LEU* 4.0 15.9 - - + -
167J GLY 3.7 10.4 + - - -
168J GLY* 3.9 11.3 - - - -
169J PRO* 4.1 3.3 - - - +
170J ALA* 3.8 37.8 + - + -
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Residues in contact with ASN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G ASN* 2.6 25.5 + - - -
114G ARG* 3.1 31.8 + - - +
124G ASP 3.6 5.5 + - - +
125G GLU* 3.3 13.3 + - - +
126G LEU 3.2 0.8 - - - -
127G TYR* 1.3 78.7 - - - +
129G ALA* 1.3 49.4 + - - +
130G ILE 3.5 1.6 - - - +
111J VAL* 6.4 1.3 - - + -
131J GLU* 3.0 30.9 + - - +
132J TRP* 3.0 35.3 - - + +
172J ARG* 5.1 1.0 - - - +
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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