Contacts of the helix formed by residues 122 - 128 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 1.3 - - + -
120F ASP 3.8 7.4 - - - +
121F ILE* 1.3 80.0 - - - +
123F PHE* 1.3 64.2 + - - +
124F ASP* 2.8 25.8 + - - +
125F GLU* 2.9 39.4 + - - +
126F LEU* 3.0 12.0 + - - +
209F VAL* 4.3 3.1 - - - -
213F ARG* 4.3 4.3 - - - +
57G VAL* 4.7 3.1 - - + +
84G ALA* 3.6 37.2 - - + +
87G CYS* 3.8 13.2 - - + -
164G TYR* 4.9 1.3 - - - +
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Residues in contact with PHE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F THR* 1.3 73.3 - - - +
124F ASP* 1.3 61.7 + - - +
126F LEU* 3.4 4.3 + - - +
127F TYR* 3.3 31.9 + + - -
203F HIS* 3.9 29.2 - + - -
205F LEU* 3.5 30.5 - - + +
206F ASN* 3.3 19.5 - - - -
209F VAL* 3.8 15.8 - - + +
213F ARG* 5.2 0.6 - - - +
87G CYS* 4.2 12.0 + - - -
88G TYR 4.6 0.2 - - - +
89G GLY* 3.3 26.7 - - - +
90G ASP* 3.7 16.6 - - + -
166G ILE* 3.4 31.9 - - + -
167G GLY 3.6 15.5 - - - -
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Residues in contact with ASP 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F THR* 2.8 22.5 + - - -
123F PHE* 1.3 78.1 - - - +
125F GLU* 1.3 79.9 + - - +
127F TYR* 3.3 25.5 + - - +
128F ASN* 3.5 6.8 + - - +
57G VAL* 6.1 0.5 - - - +
87G CYS* 3.8 2.6 - - - -
111G VAL* 4.6 17.7 - - + +
132G TRP* 5.5 2.1 - - - -
134G LEU* 4.9 4.9 - - + +
164G TYR* 4.2 4.5 + - - -
166G ILE* 3.6 31.0 - - + +
225G GLY 5.2 4.2 - - - +
227G ILE* 3.8 29.9 - - + +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ARG* 5.7 0.5 + - - -
116F LEU* 5.6 0.2 - - - +
118F ALA* 5.4 1.0 - - - +
121F ILE* 3.4 17.2 - - + +
122F THR* 2.9 36.5 + - - +
124F ASP* 1.3 83.1 - - - +
126F LEU* 1.3 65.4 + - - +
128F ASN* 3.3 16.6 + - - +
129F ALA* 3.6 10.0 + - - +
55G ARG* 3.0 38.9 + - - -
57G VAL* 3.8 12.1 - - - +
225G GLY 5.6 5.4 - - - +
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 4.7 2.0 - - + -
112F LEU* 5.2 6.7 - - + -
116F LEU* 4.2 24.2 - - + -
121F ILE* 4.0 8.7 - - + +
122F THR 3.0 11.3 + - - +
123F PHE 3.6 7.4 - - - +
124F ASP 3.3 0.2 - - - -
125F GLU* 1.3 75.2 - - - +
127F TYR* 1.3 59.0 - - - +
129F ALA* 2.8 25.2 + - + +
130F ILE* 3.4 11.6 + - + +
205F LEU* 3.8 37.7 - - + +
208F ALA* 3.4 46.4 - - + +
209F VAL* 4.0 8.7 - - + +
212F ALA* 4.4 5.8 - - + -
228F ILE* 5.6 0.9 - - + -
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Residues in contact with TYR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PHE* 3.3 28.2 + + - -
124F ASP* 3.3 12.5 + - - +
125F GLU 3.3 0.4 - - - -
126F LEU* 1.3 78.3 - - - +
128F ASN* 1.3 60.7 + - - +
129F ALA 3.1 1.2 + - - -
130F ILE* 3.3 26.2 + - + +
173F PRO* 4.6 18.0 - - + +
176F LEU 4.7 1.8 + - - -
178F LEU* 4.3 18.3 + - + +
203F HIS* 4.6 7.3 + - - -
205F LEU* 3.6 23.8 - - + +
132G TRP* 4.6 15.2 - + + +
134G LEU* 3.8 21.1 - - + -
167G GLY 3.5 20.4 + - - -
168G GLY* 3.7 12.0 - - - -
169G PRO* 3.9 3.6 - - - +
170G ALA* 3.7 35.7 + - + -
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Residues in contact with ASN 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASN* 2.6 24.4 + - - -
114F ARG* 3.1 32.9 + - - +
124F ASP 3.5 6.5 + - - +
125F GLU* 3.3 12.0 + - - +
126F LEU 3.2 0.8 - - - -
127F TYR* 1.3 78.3 - - - +
129F ALA* 1.3 51.1 + - - +
130F ILE 3.5 1.2 - - - +
111G VAL* 6.0 2.7 - - + -
131G GLU* 2.9 34.6 + - - +
132G TRP* 2.8 35.7 - - + +
172G ARG* 4.9 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