Contacts of the helix formed by residues 138 - 149 (chain F) in PDB entry 2OV2
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 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F ARG* 3.6 10.1 - - - +
136F PRO 4.0 7.4 - - - +
137F ILE* 1.3 79.2 - - - +
139F TYR* 1.3 63.9 + - - +
140F PRO* 3.6 12.0 - - - +
141F GLN* 2.8 42.4 + - - +
142F GLY* 3.0 18.7 + - - -
154F TYR* 4.3 1.0 + - - -
156F GLU* 4.2 0.4 - - - -
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Residues in contact with TYR 139 (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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120F ARG* 3.4 11.4 - - - +
138F THR* 1.3 70.0 - - - +
140F PRO* 1.4 77.1 - - + +
142F GLY* 3.1 3.1 + - - -
143F LEU* 2.9 47.8 + - + +
154F TYR* 3.7 31.1 + + - -
156F GLU* 3.4 37.9 - - + +
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Residues in contact with PRO 140 (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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138F THR* 3.6 14.8 - - - +
139F TYR* 1.4 99.0 - - + +
141F GLN* 1.3 54.0 + - - +
143F LEU* 3.5 11.7 + - + +
144F ALA* 3.0 26.5 + - - +
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Residues in contact with GLN 141 (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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90F PHE* 3.4 20.6 - - + -
136F PRO 3.9 3.1 - - - +
137F ILE* 3.5 26.9 - - + +
138F THR* 2.8 49.5 + - - +
140F PRO* 1.3 76.5 - - - +
142F GLY* 1.3 61.4 + - - +
144F ALA* 3.3 8.7 + - - +
145F MET 3.0 22.3 + - - -
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Residues in contact with GLY 142 (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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90F PHE* 4.1 14.1 - - - -
112F LEU* 3.6 6.8 - - - +
137F ILE* 4.2 1.3 - - - +
138F THR 3.0 11.5 + - - -
139F TYR 3.1 0.4 + - - -
141F GLN* 1.3 76.3 - - - +
143F LEU* 1.3 56.9 + - - +
145F MET 3.4 0.5 + - - -
146F ALA* 2.9 28.8 + - - +
154F TYR* 3.5 33.1 - - - -
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Residues in contact with LEU 143 (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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139F TYR* 2.9 40.3 + - + +
140F PRO* 3.6 12.8 - - + +
142F GLY* 1.3 77.3 - - - +
144F ALA* 1.3 62.7 + - - +
146F ALA* 3.2 4.1 + - + +
147F ARG* 3.1 64.8 + - + +
154F TYR* 3.8 23.4 - - + +
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Residues in contact with ALA 144 (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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140F PRO 3.0 14.4 + - - +
141F GLN* 3.3 11.2 + - - +
143F LEU* 1.3 75.7 - - - +
145F MET* 1.3 61.9 + - - +
147F ARG* 3.4 12.9 + - - +
148F GLU* 3.0 22.4 + - - +
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Residues in contact with MET 145 (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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90F PHE* 3.4 64.4 - - + +
91F GLU* 4.7 0.4 - - - -
93F VAL* 3.9 17.0 - - + -
94F ARG* 3.9 53.2 - - + +
112F LEU* 3.5 17.9 - - + -
141F GLN 3.0 6.1 + - - -
142F GLY 3.7 1.8 - - - +
144F ALA* 1.3 77.0 - - - +
146F ALA* 1.3 61.2 + - - +
148F GLU* 3.1 10.2 + - - +
149F ILE* 3.1 29.5 + - - +
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Residues in contact with ALA 146 (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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112F LEU* 3.4 12.3 - - + +
142F GLY 2.9 17.2 + - - +
143F LEU* 3.2 6.7 + - + +
145F MET* 1.3 76.3 - - - +
147F ARG* 1.3 62.2 + - + +
149F ILE* 3.6 1.4 + - - +
150F GLY 3.2 3.1 + - - -
151F SER* 2.8 49.3 + - - +
153F LYS* 4.6 0.4 - - - -
154F TYR* 3.7 24.9 - - + +
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Residues in contact with ARG 147 (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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143F LEU* 3.1 48.9 + - + +
144F ALA* 3.6 12.6 - - - +
146F ALA* 1.3 75.2 - - + +
148F GLU* 1.3 64.8 + - - +
150F GLY* 3.3 12.2 + - - -
151F SER 5.1 1.3 - - - +
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Residues in contact with GLU 148 (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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94F ARG* 2.6 57.1 + - - +
98F TYR* 4.7 8.3 + - + -
144F ALA 3.0 15.3 + - - +
145F MET* 3.1 15.0 + - - +
147F ARG* 1.3 78.1 - - - +
149F ILE* 1.3 64.3 + - + +
150F GLY 3.3 0.4 + - - -
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Residues in contact with ILE 149 (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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80F ILE* 4.3 18.6 - - + -
93F VAL* 3.7 31.4 - - + +
94F ARG* 4.9 3.4 - - + -
98F TYR* 3.2 54.9 - - + -
102F ARG* 4.8 2.4 + - - -
110F ILE* 4.3 17.7 - - + +
112F LEU* 4.1 19.7 - - + -
145F MET* 3.1 28.5 + - - +
146F ALA* 3.7 7.4 - - - +
147F ARG 3.3 0.2 - - - -
148F GLU* 1.3 82.2 - - + +
150F GLY* 1.3 59.2 + - - +
151F SER* 4.1 6.1 - - - -
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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