Contacts of the helix formed by residues 123 - 129 (chain F) in PDB entry 1WOI
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 VAL 123 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F VAL* 3.6 36.6 - - + +
38F PHE* 4.0 27.6 - - + +
97F HIS* 6.1 0.2 - - - -
100F ILE* 4.6 3.4 - - + -
118F GLY* 4.4 9.0 - - - +
119F GLY* 4.3 0.9 - - - -
120F ASP 3.3 18.8 - - - +
121F HIS 3.0 1.2 - - - -
122F SER* 1.3 77.9 + - - +
124F SER* 1.3 65.8 + - - +
125F TYR 3.1 0.6 + - - -
126F PRO* 3.3 11.7 - - - +
127F LEU* 3.1 38.1 + - + +
273F VAL* 3.8 20.6 - - + -
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Residues in contact with SER 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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121F HIS* 3.0 37.3 + - - -
122F SER 3.1 0.6 - - - -
123F VAL* 1.3 79.4 - - - +
125F TYR* 1.3 57.0 + - - +
127F LEU* 3.6 4.2 - - - +
128F LEU* 2.9 36.5 + - - +
162F PRO* 4.2 5.8 - - - -
163F PHE* 4.4 13.9 - - - -
227F SER* 3.5 0.2 + - - -
271F ASP* 2.6 32.1 + - - -
273F VAL* 4.2 2.4 - - - +
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Residues in contact with TYR 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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97F HIS* 4.3 17.3 - + - -
122F SER 3.3 7.6 + - - +
123F VAL 3.1 0.6 - - - -
124F SER* 1.3 77.9 - - - +
126F PRO* 1.3 76.8 - - + +
128F LEU* 3.1 13.2 + - - +
129F ARG* 3.2 50.1 + - + +
157F TRP* 3.7 30.3 - + - -
162F PRO* 3.6 25.0 - - + +
165F ARG* 3.4 33.7 + - + -
166F ALA* 3.5 21.7 - - - +
169F ALA* 4.0 12.9 - - + +
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Residues in contact with PRO 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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97F HIS* 3.3 44.4 - - + +
100F ILE* 3.7 27.8 - - + -
101F THR* 2.5 32.0 + - - +
122F SER 3.2 10.8 - - - +
123F VAL* 3.3 14.8 - - - +
125F TYR* 1.3 102.4 - - + +
127F LEU* 1.3 59.9 + - - +
129F ARG* 3.5 13.8 + - - +
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Residues in contact with LEU 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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34F LEU* 5.2 1.6 - - + -
36F VAL* 4.4 9.9 - - + -
100F ILE* 3.4 24.5 - - + -
104F ALA* 3.9 13.1 - - + +
116F PHE* 3.6 51.1 - - + -
123F VAL* 3.1 37.9 + - + +
124F SER* 3.6 5.2 - - - +
125F TYR 3.1 0.4 - - - -
126F PRO* 1.3 78.8 - - - +
128F LEU* 1.3 62.0 - - - +
130F ALA* 3.1 15.2 + - - +
131F PHE* 3.2 17.8 - - - -
225F TYR* 3.7 15.5 - - - +
271F ASP* 4.1 5.8 - - + -
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Residues in contact with LEU 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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124F SER 2.9 24.4 + - - +
125F TYR 3.1 4.2 + - - +
127F LEU* 1.3 72.9 - - - +
129F ARG* 1.3 55.0 + - - +
130F ALA 3.0 5.6 - - - -
131F PHE* 2.9 28.2 + - + +
137F LEU* 4.3 15.5 - - + -
139F VAL* 4.2 10.8 - - + -
163F PHE* 4.0 28.3 - - + -
166F ALA* 3.7 20.9 - - + -
170F LEU* 3.3 22.1 - - + +
173F LEU* 4.1 8.5 - - + -
225F TYR* 3.7 43.5 - - + -
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Residues in contact with ARG 129 (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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97F HIS* 3.1 31.3 + - - +
98F ASP* 3.2 25.6 + - - +
101F THR* 2.9 41.3 + - + +
105F ARG* 4.4 12.1 + - - +
125F TYR* 3.2 50.1 + - + +
126F PRO* 3.6 5.1 - - - +
127F LEU 3.2 1.0 - - - -
128F LEU* 1.3 77.4 - - - +
130F ALA* 1.3 56.6 + - - +
131F PHE 3.1 4.4 + - - -
132F ALA* 3.7 17.0 + - - +
169F ALA* 4.8 11.7 - - + -
170F LEU* 4.0 12.3 - - + +
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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