Contacts of the helix formed by residues 122 - 128 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P VAL* 4.8 3.6 - - + -
84P ALA* 3.8 34.1 - - + +
87P CYS* 3.9 13.0 - - + -
164P TYR* 5.0 1.6 - - - +
120S ASP 3.8 9.0 - - - +
121S ILE* 1.3 79.6 - - - +
123S PHE* 1.3 64.5 + - - +
124S ASP* 2.8 26.4 + - - +
125S GLU* 3.0 39.0 + - - +
126S LEU* 3.0 12.1 + - - +
209S VAL* 4.3 2.9 - - - -
213S ARG* 4.3 5.2 - - - +
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Residues in contact with PHE 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P CYS* 4.3 10.7 + - - -
88P TYR 4.7 0.2 - - - +
89P GLY* 3.4 18.6 - - - +
90P ASP* 3.8 13.2 - - + -
166P ILE* 3.5 31.9 - - + -
167P GLY 3.6 5.8 - - - -
122S THR* 1.3 74.0 - - - +
124S ASP* 1.3 61.6 + - - +
126S LEU* 3.3 5.4 + - - +
127S TYR* 3.3 41.9 + + - -
203S HIS* 3.9 30.7 - + - -
205S LEU* 3.5 29.6 - - + +
206S ASN* 3.4 27.4 - - - -
209S VAL* 3.8 15.9 - - + +
213S ARG* 5.2 0.6 - - - +
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Residues in contact with ASP 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P CYS* 3.8 3.1 - - - -
111P VAL* 4.5 16.9 - - + +
132P TRP* 5.4 3.5 - - - -
134P LEU* 4.8 5.1 - - + +
164P TYR* 4.3 3.8 + - - -
166P ILE* 3.6 30.7 - - + +
225P GLY 5.1 4.0 - - - +
227P ILE* 3.8 28.5 - - + +
122S THR* 2.8 21.7 + - - -
123S PHE* 1.3 82.2 - - - +
125S GLU* 1.3 77.1 + - - +
127S TYR* 3.3 23.8 - - - +
128S ASN* 3.6 6.8 + - - +
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Residues in contact with GLU 125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P ARG* 3.1 37.6 + - - -
57P VAL* 3.9 11.1 - - - +
225P GLY 5.5 6.7 - - - +
114S ARG* 5.7 0.5 + - - -
116S LEU* 5.5 0.2 - - - +
118S ALA* 5.4 1.7 - - - +
121S ILE* 3.5 17.9 - - + +
122S THR* 3.0 35.8 + - - +
124S ASP* 1.3 82.0 - - - +
126S LEU* 1.3 65.0 + - - +
128S ASN* 3.3 16.1 + - - +
129S ALA* 3.6 10.2 + - - +
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Residues in contact with LEU 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S LEU* 4.7 2.2 - - + -
112S LEU* 5.2 6.7 - - + -
116S LEU* 4.2 23.3 - - + -
121S ILE* 4.1 10.4 - - + +
122S THR 3.0 11.0 + - - +
123S PHE 3.6 7.6 - - - +
125S GLU* 1.3 75.0 - - - +
127S TYR* 1.3 59.4 + - - +
129S ALA* 2.8 25.7 + - + +
130S ILE* 3.4 12.3 + - + +
205S LEU* 3.7 36.3 - - + +
208S ALA* 3.5 46.4 - - + +
209S VAL* 4.1 8.5 - - + +
212S ALA* 4.4 5.8 - - + -
228S ILE* 5.6 1.3 - - + -
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Residues in contact with TYR 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P TRP* 4.4 14.6 - + + +
134P LEU* 3.8 16.8 - - + -
167P GLY 3.6 19.9 + - - -
168P GLY* 3.7 17.0 - - - -
169P PRO* 3.9 4.2 - - - +
170P ALA* 3.6 35.0 + - + -
123S PHE* 3.3 29.0 + + - -
124S ASP* 3.3 11.9 - - - +
125S GLU 3.3 0.4 - - - -
126S LEU* 1.3 78.8 - - - +
128S ASN* 1.3 61.2 + - - +
129S ALA 3.1 1.6 + - - -
130S ILE* 3.3 27.5 + - + +
173S PRO* 4.7 18.1 - - + +
176S LEU 4.8 1.4 + - - -
178S LEU* 4.2 19.0 + - + +
203S HIS* 4.5 7.4 + - - -
205S LEU* 3.6 24.3 - - + +
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Residues in contact with ASN 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P VAL* 6.0 2.0 - - + -
131P GLU* 2.8 34.1 + - - +
132P TRP* 2.7 39.6 - - + +
172P ARG* 4.7 2.2 - - - +
113S ASN* 2.6 25.1 + - - -
114S ARG* 3.1 32.9 + - - +
124S ASP 3.6 4.4 + - - +
125S GLU* 3.3 12.8 + - - +
126S LEU 3.2 1.0 - - - -
127S TYR* 1.3 78.1 - - - +
129S ALA* 1.3 50.1 + - - +
130S ILE 3.5 1.5 - - - +
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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