Contacts of the helix formed by residues 135 - 141 (chain O) in PDB entry 2V16
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 PRO 135 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O SER* 3.7 21.8 - - - +
38O VAL* 5.8 1.3 - - + -
99O GLN* 3.5 4.7 - - - +
122O GLY 4.3 12.1 - - - +
124O GLY 3.9 12.3 - - - +
125O PHE 3.9 2.2 - - - +
126O ILE* 3.9 29.2 - - + -
133O VAL 3.1 4.7 - - - +
134O THR* 1.4 73.0 - - + +
136O ILE* 1.3 68.4 + - - +
137O PHE 3.4 2.0 - - - +
138O ASP* 3.1 27.2 + - - +
139O ASN* 3.0 24.1 + - - -
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Residues in contact with ILE 136 (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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18O ILE* 6.1 0.7 - - + -
38O VAL* 4.0 10.6 - - + +
89O ILE* 4.0 15.9 - - + -
91O VAL* 3.8 18.4 - - + -
96O VAL* 3.4 27.1 - - + -
99O GLN* 3.1 33.1 + - + +
121O VAL* 3.8 29.2 - - + -
122O GLY 4.3 7.4 + - - +
123O MET* 5.1 4.5 - - - -
135O PRO* 1.3 75.4 - - - +
137O PHE* 1.4 65.2 + - - +
139O ASN* 4.4 1.3 - - - -
140O ILE* 3.0 43.6 + - + +
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Residues in contact with PHE 137 (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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122O GLY 4.5 6.2 + - - +
123O MET* 4.7 17.0 - - + -
135O PRO* 3.4 2.6 - - - +
136O ILE* 1.4 81.4 - - - +
138O ASP* 1.3 67.6 + - - +
140O ILE* 3.6 9.3 - - + +
141O ILE* 3.0 64.9 + - + +
146O LEU* 3.6 18.2 - - + -
149O ASP* 4.3 4.0 - - - -
150O VAL 3.4 31.0 - - - -
151O PHE* 3.8 39.0 - + + -
167O LEU* 4.3 17.5 - - + -
315O ARG* 4.4 15.9 - - + -
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Residues in contact with ASP 138 (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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124O GLY 4.4 7.3 - - - +
125O PHE* 5.1 0.5 - - - -
126O ILE* 4.8 10.3 + - - +
134O THR* 3.8 13.3 - - + +
135O PRO* 3.1 31.4 + - - +
137O PHE* 1.3 81.8 - - - +
139O ASN* 1.3 60.7 - - - +
141O ILE* 3.6 10.0 + - - +
142O SER* 3.4 21.1 + - - -
315O ARG* 3.3 35.3 + - - +
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Residues in contact with ASN 139 (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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96O VAL* 4.0 15.2 - - + +
97O THR 4.4 9.5 + - - +
99O GLN* 2.3 36.4 - - - +
134O THR* 3.1 30.6 + - - +
135O PRO 3.0 7.5 + - - +
136O ILE* 4.0 3.1 - - - +
138O ASP* 1.3 79.4 - - - +
140O ILE* 1.3 58.8 + - - +
142O SER* 2.9 22.0 + - - -
143O GLN* 4.1 8.0 + - - -
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Residues in contact with ILE 140 (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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91O VAL* 3.9 17.0 - - + -
94O ILE* 4.2 22.0 - - + -
96O VAL* 3.6 26.0 - - + -
136O ILE* 3.0 42.6 - - + +
137O PHE* 3.2 14.6 + - + +
139O ASN* 1.3 75.7 - - - +
141O ILE* 1.4 53.0 + - - +
142O SER 2.9 4.8 + - - -
143O GLN* 2.7 41.7 + - - +
144O GLY 4.0 0.9 + - - -
145O VAL* 5.2 1.5 - - + +
146O LEU* 3.9 27.5 + - + -
167O LEU* 4.9 8.1 - - + -
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Residues in contact with ILE 141 (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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137O PHE* 3.0 47.4 + - + +
138O ASP* 3.7 7.6 - - - +
140O ILE* 1.4 59.1 - - - +
142O SER* 1.3 58.5 + - - +
144O GLY* 3.8 7.9 + - - +
146O LEU* 3.2 38.4 - - + +
148O GLU 4.2 1.3 - - - +
149O ASP* 3.3 37.2 - - - +
315O ARG* 4.8 7.6 - - - +
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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