Contacts of the helix formed by residues 81 - 89 (chain A) in PDB entry 2O9C
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 GLN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.0 31.7 + - + +
79A PRO* 5.6 0.2 - - - +
80A GLU* 1.3 102.6 + - - +
82A TRP* 1.3 59.2 - - - +
83A PRO* 3.4 2.9 - - - -
84A ALA* 3.1 6.6 + - - +
85A LEU* 2.8 31.5 + - + +
99A TYR* 3.6 25.7 + - + +
101A ALA* 4.2 10.6 - - + +
102A THR 5.0 4.6 + - - -
103A LEU* 3.3 34.1 - - + +
113A LEU* 4.8 2.9 - - + -
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Residues in contact with TRP 82 (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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45A ASP 4.2 1.6 - - - -
46A GLY 4.3 4.5 - - - -
47A HIS 3.7 12.6 - - - -
48A SER 4.0 3.0 + - - -
49A GLY* 3.5 24.2 - - - -
74A LEU* 3.7 39.0 - - + +
75A ALA* 3.6 31.6 - - + +
78A LEU* 2.8 18.8 + - + +
79A PRO* 4.8 0.9 - - + +
81A GLN* 1.3 76.8 - - - +
83A PRO* 1.3 74.3 - - + +
85A LEU* 3.2 15.9 + - + +
86A GLN* 2.9 62.6 + - + +
122A LEU* 3.7 29.4 - - + -
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Residues in contact with PRO 83 (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 PRO 3.4 19.1 - - - +
80A GLU 4.7 1.3 - - - -
81A GLN 3.6 2.7 - - - +
82A TRP* 1.3 100.7 - - + +
84A ALA* 1.3 62.1 + - - +
86A GLN* 3.4 12.6 + - - +
87A ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 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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80A GLU 5.1 2.9 + - - +
81A GLN* 3.1 8.3 + - - +
83A PRO* 1.3 79.7 - - - +
85A LEU* 1.3 57.7 + - - +
87A ALA* 3.4 6.1 + - - +
88A ALA* 3.0 30.5 + - - +
99A TYR* 3.6 28.0 - - + +
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Residues in contact with LEU 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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74A LEU* 4.5 4.0 - - + -
78A LEU* 5.0 5.4 - - + -
81A GLN 2.8 17.2 + - - +
82A TRP* 3.5 21.3 - - + +
84A ALA* 1.3 75.7 - - - +
86A GLN* 1.3 66.3 + - - +
88A ALA* 3.3 3.1 + - - +
89A LEU* 3.2 23.5 + - + +
99A TYR* 4.1 27.8 - - + -
113A LEU* 4.8 4.9 - - + -
115A VAL* 4.1 30.3 - - + -
122A LEU* 3.6 34.5 - - + -
124A LEU* 4.4 15.7 - - + -
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Residues in contact with GLN 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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46A GLY 4.5 6.6 - - - +
47A HIS* 3.8 14.0 + - - +
82A TRP* 2.9 68.1 + - + +
83A PRO* 3.6 9.5 - - - +
85A LEU* 1.3 80.9 - - - +
87A ALA* 1.3 63.0 + - - +
89A LEU* 3.3 21.9 + - - +
90A PRO* 3.7 5.7 - - - +
117A ARG* 5.5 2.8 + - - +
122A LEU* 5.7 1.1 - - + -
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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 PRO 3.1 14.1 + - - +
84A ALA* 3.8 6.3 - - - +
85A LEU 3.3 0.2 - - - -
86A GLN* 1.3 80.5 - - - +
88A ALA* 1.3 61.4 + - - +
89A LEU 3.5 0.3 + - - -
90A PRO* 3.7 11.4 - - - +
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Residues in contact with ALA 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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84A ALA 3.0 19.5 + - - +
85A LEU 3.8 4.0 - - - +
86A GLN 3.2 0.2 - - - -
87A ALA* 1.3 76.5 - - - +
89A LEU* 1.3 61.0 + - + +
90A PRO* 3.4 4.5 - - - +
97A LEU* 3.4 23.9 - - - +
98A GLN 5.4 1.5 - - - +
99A TYR* 3.8 29.2 - - + -
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Residues in contact with LEU 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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85A LEU* 3.2 15.2 + - + +
86A GLN* 3.3 7.6 + - - +
88A ALA* 1.3 88.0 - - - +
90A PRO* 1.3 62.4 - - - +
93A CYS* 3.8 12.1 - - - -
97A LEU* 3.6 40.4 - - + +
98A GLN 4.1 8.7 - - - +
99A TYR* 4.2 8.5 - - + -
115A VAL* 3.6 44.4 - - + +
116A HIS* 3.8 10.3 - - - -
117A ARG* 2.8 26.7 + - + +
122A LEU* 4.1 13.8 - - + +
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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