Contacts of the helix formed by residues 138 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ARG* 3.6 8.5 - - - +
136B PRO 4.1 6.7 - - - +
137B ILE* 1.3 78.9 - - - +
139B TYR* 1.3 60.1 + - - +
140B PRO* 3.5 12.3 - - - +
141B GLN* 3.1 41.4 + - - +
142B GLY* 2.9 24.6 + - - -
156B GLU* 4.1 1.1 - - - +
150C GLY 5.5 2.3 + - - +
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 3.6 10.1 - - - +
138B THR* 1.3 69.6 - - - +
140B PRO* 1.3 78.1 - - + +
142B GLY* 3.2 1.0 + - - -
143B LEU* 2.9 54.9 + - + +
154B TYR* 3.5 40.7 + + - -
155B LEU* 5.8 0.2 - - - -
156B GLU* 3.4 27.1 - - + +
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Residues in contact with PRO 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 3.5 14.1 - - - +
139B TYR* 1.3 99.5 - - + +
141B GLN* 1.3 62.3 + - + +
143B LEU* 3.9 7.4 - - + +
144B ALA* 3.0 25.5 + - - +
98C TYR* 4.2 8.9 + - - +
147C ARG 5.4 2.2 - - - +
148C GLU 5.6 2.0 - - - +
149C ILE 5.0 2.7 - - - +
150C GLY* 4.0 31.2 - - - +
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.5 11.6 - - + -
136B PRO 4.1 2.3 - - - +
137B ILE* 3.6 15.5 - - + -
138B THR* 3.1 42.2 + - - +
140B PRO* 1.3 79.0 - - + +
142B GLY* 1.3 63.6 + - - +
144B ALA* 3.4 5.3 + - - +
145B MET 3.2 17.0 + - - -
102C ARG* 3.7 26.2 - - - +
106C PRO 3.5 18.0 - - - +
107C HIS* 3.4 38.5 + - - +
108C THR 4.0 4.0 + - - -
109C PRO* 4.6 4.0 - - - +
150C GLY 5.9 0.8 + - - +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 4.1 13.9 - - - -
112B LEU* 3.7 4.2 - - - +
137B ILE* 4.2 1.7 - - - +
138B THR 2.9 10.5 + - - -
139B TYR 3.7 0.2 - - - -
141B GLN* 1.3 77.4 - - - +
143B LEU* 1.3 61.4 + - - +
145B MET* 3.3 4.7 + - - +
146B ALA* 3.0 22.2 + - - +
154B TYR* 3.6 32.5 - - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 2.9 45.5 + - + +
140B PRO* 3.9 7.2 - - + +
142B GLY* 1.3 75.1 - - - +
144B ALA* 1.3 62.6 + - - +
146B ALA* 3.1 8.5 + - + +
147B ARG* 2.9 65.8 + - + +
154B TYR* 3.7 27.8 - - + +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PRO 3.0 18.3 + - - +
141B GLN* 3.8 4.7 - - - +
142B GLY 3.3 0.2 - - - -
143B LEU* 1.3 75.6 - - - +
145B MET* 1.3 58.0 + - - +
147B ARG* 3.4 11.4 + - - +
148B GLU* 3.0 26.7 + - - +
98C TYR* 3.9 18.4 - - + +
102C ARG* 4.1 9.9 - - + -
1203C CL 3.9 15.2 - - + +
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.6 50.3 - - + +
91B GLU* 4.9 2.0 - - - -
93B VAL* 4.1 12.1 - - + -
94B ARG* 4.0 32.1 - - + +
112B LEU* 3.9 11.4 - - + -
141B GLN 3.2 3.2 + - - +
142B GLY 3.5 9.0 - - - +
144B ALA* 1.3 75.7 - - - +
146B ALA* 1.3 65.4 + - - +
148B GLU* 3.3 13.5 - - - +
149B ILE* 3.1 31.2 + - - +
106C PRO* 3.9 32.3 - - + -
1203C CL 3.9 4.2 - - + +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 3.8 12.8 - - + +
142B GLY 3.0 12.8 + - - +
143B LEU* 3.2 13.2 - - + +
145B MET* 1.3 78.5 - - - +
147B ARG* 1.3 63.4 + - + +
149B ILE* 3.3 1.2 + - - +
150B GLY 3.2 4.0 + - - -
151B SER* 3.1 44.2 + - - +
153B LYS 5.0 0.7 - - - -
154B TYR* 3.7 26.2 - - + +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 2.9 51.4 + - + +
144B ALA* 3.6 10.7 - - - +
146B ALA* 1.3 77.5 - - + +
148B GLU* 1.3 62.4 + - - +
150B GLY* 3.3 12.1 + - - +
151B SER 5.2 2.2 - - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ARG* 3.4 35.2 + - + +
98B TYR* 4.7 6.3 + - + -
144B ALA 3.0 13.7 + - - +
145B MET* 3.3 16.6 - - - +
146B ALA 3.3 0.2 - - - -
147B ARG* 1.3 77.6 - - - +
149B ILE* 1.3 67.7 + - + +
150B GLY 3.6 0.3 + - - -
103C HIS* 2.9 37.3 + - - +
1203C CL 3.8 9.4 - - + +
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 4.5 7.9 - - + -
93B VAL* 3.8 24.5 - - + -
94B ARG* 4.8 5.6 - - + -
98B TYR* 3.1 58.8 + - + -
102B ARG* 5.0 2.6 + - - -
110B ILE* 4.2 26.4 - - + +
112B LEU* 4.5 12.3 - - + -
145B MET* 3.1 29.4 + - - +
146B ALA 3.3 11.2 + - - +
148B GLU* 1.3 80.9 - - + +
150B GLY* 1.3 60.7 + - - +
151B SER* 4.0 11.0 - - - -
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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