Contacts of the helix formed by residues 81 - 90 (chain D) in PDB entry 1OHV
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 HIS 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ILE* 4.4 2.4 - - - +
11D PHE 5.9 3.2 + - - -
77D ILE* 3.2 50.4 - - + +
78D GLY 4.1 2.4 + - - +
79D TYR 3.0 4.4 + - - -
80D SER* 1.3 75.7 - - - +
82D PRO* 1.3 71.5 - - + +
83D ALA* 3.1 42.1 + - + +
84D LEU* 2.9 32.6 + - + +
85D VAL* 3.0 10.3 + - - +
370D ILE* 3.9 27.2 - - + +
374D GLU* 6.2 0.2 - - - +
451D VAL* 4.7 8.4 - - + +
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Residues in contact with PRO 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.0 36.1 - - + +
80D SER 3.2 6.0 - - - +
81D HIS* 1.3 99.4 - - + +
83D ALA* 1.3 55.3 + - - +
85D VAL* 3.4 13.8 + - + +
86D LYS* 3.1 27.4 + - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS* 3.1 23.1 + - + +
82D PRO* 1.3 78.1 - - - +
84D LEU* 1.3 62.4 + - + +
86D LYS* 3.6 8.1 + - - +
87D LEU* 3.4 24.1 + - - +
366D GLU* 3.9 29.9 - - + +
370D ILE* 4.0 9.4 - - + -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ILE* 3.8 35.0 - - + +
76D PRO* 5.8 1.1 - - + -
77D ILE* 4.3 10.5 - - + -
78D GLY 5.4 3.1 - - - +
81D HIS* 2.9 27.6 + - + +
83D ALA* 1.3 75.3 - - + +
85D VAL* 1.3 68.1 + - - +
87D LEU* 3.2 19.4 + - + +
88D VAL* 3.3 16.8 + - - +
332D MET* 4.8 10.1 - - + -
363D LEU* 3.8 29.8 - - + +
366D GLU* 4.0 19.1 - - + -
367D VAL* 4.2 18.4 - - + -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 4.1 20.8 - - + +
98C ILE* 3.6 17.5 - - + +
80D SER* 4.0 14.1 - - - +
81D HIS 3.0 15.9 + - - +
82D PRO* 3.4 13.2 - - + +
84D LEU* 1.3 77.5 - - - +
86D LYS* 1.3 62.7 + - - +
88D VAL* 3.2 6.1 + - - +
89D GLN* 3.1 47.0 + - + +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PRO 3.1 16.1 + - - +
83D ALA* 3.7 8.7 - - - +
84D LEU 3.2 0.2 - - - -
85D VAL* 1.3 76.9 - - - +
87D LEU* 1.3 63.1 + - + +
89D GLN* 3.1 21.5 + - - +
90D GLN* 2.8 32.1 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ALA 3.4 12.0 + - - +
84D LEU* 3.2 10.8 + - + +
86D LYS* 1.3 78.6 - - + +
88D VAL* 1.3 62.5 + - - +
90D GLN* 3.2 12.8 + - + -
93D ASN* 2.9 39.8 + - - +
97D PHE* 5.1 0.9 - - - -
362D LEU* 3.6 36.8 - - + +
363D LEU* 4.1 22.0 - - + -
366D GLU* 3.6 30.5 - - + +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL* 4.5 26.0 - - + +
94C VAL* 4.2 30.7 - - + +
97C PHE* 4.1 20.2 - - + -
98C ILE* 3.3 33.7 - - + -
84D LEU 3.6 3.4 - - - +
85D VAL 3.2 8.3 + - - +
87D LEU* 1.3 78.1 - - - +
89D GLN* 1.3 60.9 + - - +
90D GLN 3.4 5.0 + - - +
93D ASN* 5.3 0.3 - - - +
94D VAL* 5.7 1.4 + - - +
97D PHE* 3.9 29.5 - - + -
363D LEU* 4.8 2.2 - - + -
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Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PRO* 6.3 0.8 - - - +
94C VAL* 4.8 13.3 - - + +
85D VAL* 3.1 30.7 + - + +
86D LYS* 3.1 21.5 + - - +
88D VAL* 1.3 76.5 - - - +
90D GLN* 1.3 69.0 + - - +
91D PRO* 3.3 10.6 - - - +
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Residues in contact with GLN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LYS* 2.8 34.3 + - - +
87D LEU* 3.2 15.1 + - + +
88D VAL 4.0 3.9 - - - +
89D GLN* 1.3 84.4 + - - +
91D PRO* 1.3 72.9 - - - +
92D GLN* 3.2 26.8 + - - +
93D ASN* 3.0 30.3 + - - +
94D VAL* 3.9 4.0 + - - +
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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