Contacts of the helix formed by residues 69 - 74 (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 TYR 69 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ILE* 3.8 19.3 - - + -
106C LEU* 5.3 1.3 - - + -
44D HIS* 4.8 10.3 - + - -
67D ASP* 2.8 7.3 + - - +
68D LEU* 1.3 81.3 - - - +
70D SER* 1.3 72.4 + - - +
71D GLN 4.7 2.0 - - - +
72D ILE* 3.2 50.9 + - + +
73D SER 2.9 18.4 + - - -
270D GLU* 4.7 1.6 + - - -
435D MET* 3.7 20.2 + - + +
436D LEU 4.4 4.3 - - - +
437D GLY* 3.4 34.8 - - - +
438D GLY 4.6 2.3 + - - -
445D ARG* 3.3 38.7 + - + -
447D ARG* 3.4 9.9 - - + +
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Residues in contact with SER 70 (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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67D ASP* 2.8 22.2 + - - -
69D TYR* 1.3 77.8 + - - +
71D GLN* 1.3 62.8 + - - +
73D SER* 3.3 13.2 - - - -
74D SER 2.9 23.2 + - - -
75D ILE* 3.2 11.2 + - - -
79D TYR* 4.1 3.6 - - - -
330D LYS* 4.8 1.6 + - - -
447D ARG 2.5 24.7 + - - -
448D PRO 4.2 2.3 + - - -
449D THR* 3.5 30.5 - - - -
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Residues in contact with GLN 71 (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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100C ARG 4.0 7.9 - - - +
101C PRO* 4.0 2.0 - - + -
102C ALA* 2.8 43.1 + - - +
106C LEU* 3.4 30.0 - - - +
353C THR* 4.1 1.9 - - - +
49D TYR* 3.0 32.5 + - - -
57D LEU* 4.0 4.2 - - - +
67D ASP* 4.3 1.4 + - - -
69D TYR* 3.4 2.8 - - - -
70D SER* 1.3 75.1 - - - +
72D ILE* 1.3 71.2 + - - +
74D SER* 2.7 32.6 + - - +
75D ILE* 3.4 22.7 - - + -
79D TYR* 3.0 20.1 + - + +
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Residues in contact with ILE 72 (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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102C ALA* 4.1 11.9 - - + -
105C ILE* 3.8 17.0 - - + -
351C PHE* 4.2 18.4 - - + -
353C THR* 4.5 7.4 - - + -
69D TYR* 3.2 47.9 + - + +
71D GLN* 1.3 81.8 - - - +
73D SER* 1.3 68.4 + - - +
74D SER 3.3 0.3 + - - -
270D GLU* 4.1 18.8 - - - +
301D GLN* 4.7 1.3 - - - +
329D LYS* 3.3 28.0 - - - +
445D ARG* 4.3 4.5 - - - +
447D ARG* 5.1 0.7 - - - -
500D ACT 4.2 20.2 - - + -
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR 2.9 10.5 + - - -
70D SER* 3.1 15.9 + - - -
72D ILE* 1.3 79.3 - - - +
74D SER* 1.3 56.7 + - - +
75D ILE 3.8 1.3 - - - -
301D GLN* 3.7 30.1 + - - +
306D SER* 5.3 0.7 + - - -
329D LYS* 3.5 11.8 - - - +
330D LYS* 3.4 32.1 + - - +
411D PHE* 5.0 0.2 - - - -
447D ARG* 3.5 30.4 - - - +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG 4.6 1.6 + - - -
353C THR* 4.3 1.6 - - - -
354C TRP* 3.8 23.8 + - - -
70D SER 2.9 2.8 + - - -
71D GLN* 2.7 34.0 + - - +
73D SER* 1.3 78.1 - - - +
75D ILE* 1.3 64.4 + - - +
76D PRO* 3.4 11.4 - - - +
329D LYS* 3.5 35.4 - - - +
330D LYS* 3.6 9.2 - - - +
332D MET* 4.8 3.5 - - - +
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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