Contacts of the helix formed by residues 83 - 91 (chain A) in PDB entry 1OPT
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.1 22.3 + - + +
82A THR* 1.3 87.9 - - + +
84A PRO* 1.4 69.2 - - + +
86A TRP* 4.5 0.2 - - - +
87A ALA* 3.3 26.5 + - + +
104A LEU* 5.6 3.6 - - + -
108A TYR* 3.7 44.4 - - + -
112A PHE* 5.6 0.4 - - + -
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE 3.5 7.0 - - - +
80A LEU* 3.3 39.3 - - + +
83A VAL* 1.4 90.7 - - + +
85A PHE* 1.3 55.1 + - + +
87A ALA* 3.8 4.3 + - + +
88A HIS* 3.1 31.0 + - - +
108A TYR* 3.8 27.6 - - + +
109A PHE* 3.5 35.7 - - + -
112A PHE* 3.9 7.9 - - + -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 2.7 32.0 + - - +
41A PHE* 3.7 37.0 - + + -
42A ILE* 3.8 20.2 - - + -
45A PHE* 3.9 19.1 - + - -
80A LEU* 3.5 33.5 + - + -
81A LEU* 3.6 31.6 + - + +
83A VAL 3.6 0.2 - - - -
84A PRO* 1.3 76.9 - - + +
86A TRP* 1.3 56.6 + - - +
88A HIS* 3.5 3.4 + - - +
89A TYR* 2.9 21.3 + - - +
109A PHE* 5.4 0.7 - + - -
287A MET* 3.7 39.9 - - + -
290A CYS* 5.0 2.7 - - + -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.0 1.1 - - + -
42A ILE* 3.7 37.9 - - + +
43A PHE* 4.7 16.2 - + - -
81A LEU* 3.4 26.4 + - - +
82A THR* 3.5 22.3 + - + +
83A VAL 3.8 2.2 + - - +
85A PHE* 1.3 74.3 - - - +
87A ALA* 1.3 55.9 + - - +
89A TYR* 3.8 34.0 - + - +
90A ALA* 3.0 39.3 + - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A VAL* 3.3 22.4 + - + +
84A PRO* 4.0 4.9 - - + +
86A TRP* 1.3 73.5 - - - +
88A HIS* 1.3 57.6 + - - +
90A ALA* 5.1 2.0 - - - -
91A ALA* 3.1 34.1 + - - +
104A LEU* 6.4 1.6 - - + -
105A THR* 6.1 4.7 - - + +
109A PHE* 6.1 0.9 - - + -
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Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.7 29.0 + - - -
34A PRO* 3.2 44.7 - - + +
35A PRO* 3.7 10.6 - - + +
38A SER* 3.8 13.4 + - - -
84A PRO 3.1 20.8 + - - +
85A PHE* 3.6 3.5 - - - +
86A TRP 3.5 0.2 - - - -
87A ALA* 1.3 73.5 - - - +
89A TYR* 1.3 63.8 + - - +
91A ALA* 4.0 10.6 + - - +
94A TRP* 5.3 3.6 + - - -
109A PHE* 3.8 23.1 - + + -
193A PHE* 6.1 1.8 - + - -
283A GLU* 4.5 3.4 - - - -
287A MET* 3.8 26.4 - - + -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.4 38.6 - - + +
36A LEU* 5.1 9.6 - - + -
38A SER* 4.1 5.3 + - - +
39A LEU* 3.7 39.2 - - + +
42A ILE* 4.6 3.4 - - + -
85A PHE 2.9 19.9 + - - +
86A TRP* 3.8 34.8 - + - +
88A HIS* 1.3 72.9 - - - +
90A ALA* 1.3 63.0 + - + +
91A ALA 3.9 1.0 + - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 3.0 26.3 + - + +
87A ALA* 4.8 1.6 - - - +
89A TYR* 1.3 79.9 - - + +
91A ALA* 1.4 60.2 + - - +
92A ALA* 3.3 9.0 + - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 3.1 21.6 + - - +
88A HIS* 4.0 7.2 + - - +
89A TYR 3.7 3.6 - - - +
90A ALA* 1.4 72.7 - - - +
92A ALA* 1.3 58.6 + - - +
93A GLN* 4.5 0.2 - - - -
94A TRP* 3.3 31.4 + - + -
95A ASP* 4.8 15.0 - - - +
193A PHE* 5.5 8.1 - - + -
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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