Contacts of the helix formed by residues 122 - 128 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M VAL* 4.7 3.8 - - + +
84M ALA* 3.8 34.8 - - + +
87M CYS* 3.8 14.6 - - + -
164M TYR* 4.8 2.0 - - - +
120O ASP 3.8 8.1 - - - +
121O ILE* 1.3 79.4 - - - +
123O PHE* 1.3 66.1 + - - +
124O ASP* 2.8 23.3 + - - +
125O GLU* 2.9 41.8 + - - +
126O LEU* 3.0 11.8 + - - +
209O VAL* 4.3 3.6 - - - -
213O ARG* 4.2 4.9 - - - +
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Residues in contact with PHE 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M CYS* 4.2 11.8 - - - -
88M TYR 4.7 0.4 - - - +
89M GLY* 3.5 17.9 - - - +
90M ASP* 3.8 13.5 - - + -
166M ILE* 3.5 24.5 - - + -
167M GLY 3.4 22.9 - - - -
122O THR* 1.3 72.6 - - - +
124O ASP* 1.3 61.7 + - - +
126O LEU* 3.3 4.7 + - - +
127O TYR* 3.3 30.5 + + - -
203O HIS* 3.8 32.3 - + - -
205O LEU* 3.5 30.3 - - + +
206O ASN* 3.4 27.4 - - - -
209O VAL* 3.8 14.7 - - + +
213O ARG* 5.2 0.8 - - - +
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Residues in contact with ASP 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M CYS* 3.9 2.1 - - - -
111M VAL* 4.4 18.5 - - + +
132M TRP* 5.3 3.6 - - - -
134M LEU* 4.7 5.9 - - + +
164M TYR* 4.3 4.0 + - - -
166M ILE* 3.5 26.4 - - + +
225M GLY 5.1 4.9 - - - +
227M ILE* 3.7 33.0 - - + +
122O THR* 2.8 22.5 + - - -
123O PHE* 1.3 77.7 - - - +
125O GLU* 1.3 74.1 + - - +
127O TYR* 3.3 25.4 + - - +
128O ASN* 3.6 6.4 + - - +
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Residues in contact with GLU 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M ARG* 3.1 37.0 + - - -
57M VAL* 3.9 12.5 - - - +
225M GLY 5.5 6.8 - - - +
114O ARG* 5.7 0.9 + - - -
116O LEU* 5.5 0.2 - - - +
118O ALA* 5.4 1.2 - - - +
121O ILE* 3.5 17.8 - - + +
122O THR* 2.9 36.2 + - - +
124O ASP* 1.3 81.8 - - - +
126O LEU* 1.3 65.7 + - - +
128O ASN* 3.4 15.6 + - - +
129O ALA* 3.6 10.2 + - - +
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Residues in contact with LEU 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O LEU* 4.7 2.0 - - + -
112O LEU* 5.2 6.1 - - + -
116O LEU* 4.2 24.5 - - + -
121O ILE* 4.1 12.5 - - + +
122O THR 3.0 10.7 + - - +
123O PHE 3.6 8.3 - - - +
125O GLU* 1.3 75.8 - - - +
127O TYR* 1.3 65.4 + - - +
129O ALA* 2.8 18.9 + - + +
130O ILE* 3.4 11.5 + - + +
205O LEU* 3.8 36.6 - - + +
208O ALA* 3.4 46.7 - - + +
209O VAL* 4.1 8.7 - - + +
212O ALA* 4.4 3.1 - - + -
228O ILE* 5.6 1.3 - - + -
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Residues in contact with TYR 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M TRP* 4.4 16.0 - + + +
134M LEU* 3.7 19.1 - - + -
167M GLY 3.6 20.2 - - - -
168M GLY* 3.7 12.0 - - - -
169M PRO* 3.8 3.6 - - - +
170M ALA* 3.5 39.8 + - + -
123O PHE* 3.3 26.8 + + - -
124O ASP* 3.3 11.4 - - - +
125O GLU 3.3 0.4 - - - -
126O LEU* 1.3 78.8 - - - +
128O ASN* 1.3 62.2 + - - +
129O ALA 3.1 1.4 + - - -
130O ILE* 3.3 27.1 + - + +
173O PRO* 4.7 16.5 - - + +
176O LEU 4.7 1.6 + - - -
178O LEU* 4.3 19.5 + - + +
203O HIS* 4.5 6.4 + - - -
205O LEU* 3.6 24.6 - - + +
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Residues in contact with ASN 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M VAL* 6.0 2.7 - - + -
131M GLU* 2.8 37.4 + - - +
132M TRP* 2.8 35.0 - - + +
172M ARG* 4.8 1.6 - - - +
113O ASN* 2.6 24.4 + - - -
114O ARG* 3.1 32.2 + - - +
124O ASP 3.6 5.1 + - - +
125O GLU* 3.4 12.9 + - - +
126O LEU 3.2 1.2 - - - -
127O TYR* 1.3 79.0 - - - +
129O ALA* 1.3 50.1 + - - +
130O ILE 3.5 1.8 - - - +
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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