Contacts of the helix formed by residues 69 - 74 (chain B) 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 TYR 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.7 29.2 - - + -
106A LEU* 5.2 2.0 - - + -
44B HIS* 4.9 9.9 - + - -
67B ASP* 2.9 7.5 + - - +
68B LEU* 1.3 80.1 - - - +
70B SER* 1.3 71.6 + - - +
71B GLN 3.4 2.2 - - - +
72B ILE* 3.2 39.9 + - + +
73B SER 2.9 18.2 + - - -
270B GLU* 4.7 1.2 + - - -
435B MET* 3.7 20.4 + - - +
436B LEU 4.4 3.6 - - - -
437B GLY* 3.4 35.4 - - - +
438B GLY 4.6 1.7 + - - -
445B ARG* 3.4 38.6 + - + -
447B ARG* 3.4 9.6 - - + +
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Residues in contact with SER 70 (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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67B ASP* 2.9 22.7 + - - -
69B TYR* 1.3 77.3 + - - +
71B GLN* 1.3 64.1 + - - +
73B SER* 3.3 13.2 - - - -
74B SER 2.9 19.9 + - - -
75B ILE* 3.2 13.4 + - - -
79B TYR* 4.1 3.1 - - - -
330B LYS* 5.0 1.2 + - - -
447B ARG 2.5 25.2 + - - -
448B PRO 4.3 1.9 + - - -
449B THR* 3.5 31.4 - - - -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG 3.9 7.4 - - - +
101A PRO* 3.9 1.8 - - - -
102A ALA* 2.7 42.9 + - - +
106A LEU* 3.5 29.2 - - - +
353A THR* 4.0 1.9 - - - +
49B TYR* 3.0 31.8 + - - -
57B LEU* 4.0 4.6 - - - +
67B ASP* 4.3 1.2 + - - -
69B TYR* 3.4 3.2 - - - +
70B SER* 1.3 72.1 - - - +
72B ILE* 1.3 75.7 + - - +
74B SER* 2.7 31.2 + - - +
75B ILE* 3.4 22.4 - - + -
79B TYR* 3.0 21.6 + - + +
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Residues in contact with ILE 72 (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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102A ALA* 4.0 15.9 - - + -
105A ILE* 3.7 13.7 - - + -
351A PHE* 4.2 26.0 - - + -
353A THR* 4.5 7.2 - - + -
69B TYR* 3.2 48.9 + - + +
71B GLN* 1.3 80.5 - - - +
73B SER* 1.3 70.5 + - - +
270B GLU* 4.1 19.3 - - - +
301B GLN* 4.7 0.9 - - - +
329B LYS* 3.3 28.6 - - - +
445B ARG* 4.3 4.3 - - - +
447B ARG* 5.2 0.2 - - - -
500B ACT 4.2 13.0 - - + +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR 2.9 10.9 + - - -
70B SER* 3.2 15.2 + - - -
72B ILE* 1.3 79.3 - - - +
74B SER* 1.3 55.8 + - - +
75B ILE 3.8 1.1 - - - -
300B VAL 5.1 0.2 - - - +
301B GLN* 3.7 29.9 + - - +
306B SER* 5.3 0.5 + - - -
329B LYS* 3.6 12.0 - - - +
330B LYS* 3.5 31.0 + - - +
411B PHE* 5.0 0.2 - - - -
447B ARG* 3.5 30.3 - - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG 4.6 1.4 + - - -
353A THR* 4.3 2.0 - - - -
354A TRP* 3.7 22.8 + - - -
70B SER 2.9 3.0 + - - -
71B GLN* 2.7 34.1 + - - +
73B SER* 1.3 77.0 - - - +
75B ILE* 1.3 64.3 + - - +
76B PRO* 3.3 11.0 - - - +
329B LYS* 3.4 36.8 - - - +
330B LYS* 3.5 9.1 - - - +
332B MET* 4.9 2.4 - - - +
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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