Contacts of the helix formed by residues 111 - 119 (chain B) in PDB entry 2OB2
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 ARG 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LYS* 5.7 2.9 - - - +
41B TYR* 5.5 5.8 - - + -
82B THR* 3.6 24.0 + - - +
85B ILE* 3.2 25.5 - - - +
86B ASP* 3.0 29.5 + - - +
89B ILE* 3.5 21.3 - - - +
103B ASN* 4.6 1.8 - - - +
109B ASP* 2.7 46.1 + - - +
110B LEU* 1.3 77.0 - - - +
112B MET* 1.3 62.7 + - - +
114B PRO* 3.1 18.7 - - + +
115B LEU* 3.3 26.6 + - + +
124B TYR* 3.3 23.1 - - + +
199B ILE* 4.0 9.6 - - - +
201B GLU* 2.7 24.4 + - - -
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Residues in contact with MET 112 (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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109B ASP 3.4 25.8 - - - +
110B LEU* 3.1 22.3 - - + -
111B ARG* 1.3 82.8 - - - +
113B LEU* 1.3 74.4 + - + +
115B LEU* 4.5 1.6 - - - -
116B LEU* 2.8 40.2 + - + +
124B TYR* 3.5 41.3 + - + -
126B ASP* 4.0 6.3 - - - +
136B LYS* 3.8 11.2 - - - -
140B LEU* 4.4 7.9 - - + -
150B LEU* 4.5 0.4 - - + -
169B TYR* 3.7 39.7 - - + +
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Residues in contact with LEU 113 (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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44B TRP* 3.5 32.7 - - + -
110B LEU* 3.0 29.2 + - + +
112B MET* 1.3 93.8 - - + +
114B PRO* 1.3 67.3 - - + +
116B LEU* 4.4 2.7 - - - +
117B GLN* 3.4 17.7 + - - +
140B LEU* 5.1 0.7 - - + -
146B LEU* 3.8 29.2 - - + -
149B SER* 3.5 23.6 - - - +
150B LEU* 3.4 37.0 - - + -
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Residues in contact with PRO 114 (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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33B LEU* 3.7 28.0 - - + -
37B LEU* 4.3 10.5 - - + +
41B TYR* 4.4 21.3 - - + -
44B TRP* 3.7 17.2 - - + -
110B LEU 3.3 10.3 - - - +
111B ARG* 3.1 20.4 - - + +
113B LEU* 1.3 92.7 - - + +
115B LEU* 1.3 57.0 + - + +
117B GLN* 3.2 4.7 + - - +
118B MET* 2.8 35.8 + - - +
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Residues in contact with LEU 115 (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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31B GLN 5.9 0.2 - - - +
86B ASP* 5.5 4.7 - - - +
89B ILE* 3.9 23.8 - - + -
90B LEU* 3.7 31.4 - - + -
93B LEU* 4.0 13.9 - - + -
101B VAL* 5.6 2.0 - - + -
111B ARG* 3.3 42.8 + - + +
112B MET* 4.1 2.0 - - - +
114B PRO* 1.3 81.9 - - + +
116B LEU* 1.3 57.6 + - - +
118B MET* 4.3 5.4 - - + -
119B PHE* 2.9 41.5 + - + +
122B LEU* 3.6 14.1 - - + +
124B TYR* 4.4 11.9 - - + -
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Residues in contact with LEU 116 (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 MET* 2.8 34.9 + - + +
113B LEU 4.4 1.8 - - - +
115B LEU* 1.3 76.5 - - - +
117B GLN* 1.3 63.1 + - - +
119B PHE 3.5 4.0 - - - +
122B LEU* 3.8 13.9 - - + +
124B TYR* 3.9 11.2 - - + -
149B SER 5.7 2.9 - - - +
150B LEU* 3.8 18.8 - - + -
168B ARG* 2.9 74.4 + - + +
169B TYR* 3.5 28.9 - - + -
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Residues in contact with GLN 117 (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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34A SER* 3.2 15.0 + - - -
35A VAL* 2.7 40.9 + - - +
36A ASP* 2.9 59.5 + - - +
37B LEU* 3.9 29.6 - - + -
44B TRP* 5.4 1.6 - - + -
113B LEU 3.4 12.3 + - - +
114B PRO 3.2 9.5 + - - +
116B LEU* 1.3 81.5 - - - +
118B MET* 1.3 56.5 + - - +
119B PHE 3.6 0.2 + - - -
149B SER 6.1 0.9 - - - +
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Residues in contact with MET 118 (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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28A SER 5.4 0.5 - - - +
33A LEU 3.6 6.2 - - - +
34A SER* 3.9 4.0 - - - -
2003A GOL 3.0 46.6 + - - +
31B GLN 3.8 6.7 - - - +
32B ARG* 3.4 21.5 - - + +
33B LEU* 4.0 20.6 - - - -
34B SER 6.1 0.2 - - - +
37B LEU* 3.8 16.8 - - + -
90B LEU* 3.6 30.7 - - + -
114B PRO* 2.8 31.9 + - - +
115B LEU* 3.2 5.1 + - + -
117B GLN* 1.3 73.9 - - - +
119B PHE* 1.3 72.9 + - + +
120B PRO* 3.5 8.1 - - - +
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Residues in contact with PHE 119 (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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2003A GOL 3.7 28.0 - - - -
90B LEU* 3.5 31.6 - - + -
93B LEU* 3.6 52.9 - - + -
94B VAL* 4.0 11.7 - - + -
97B GLU* 5.3 6.1 - - + +
115B LEU* 2.9 20.4 + - + +
116B LEU 3.5 4.8 - - - +
118B MET* 1.3 91.0 - - + +
120B PRO* 1.3 63.2 - - - +
121B HIS 3.1 2.5 - - - +
122B LEU* 3.1 22.7 + - + +
168B ARG* 2.9 20.6 + - - -
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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