Contacts of the helix formed by residues 69 - 74 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C HIS* 4.8 9.6 - - - -
67C ASP* 2.9 6.9 + - - +
68C LEU* 1.3 81.3 - - - +
70C SER* 1.3 70.8 + - - +
71C GLN* 4.8 2.0 - - - +
72C ILE* 3.2 41.3 + - + +
73C SER 2.9 18.7 + - - -
270C GLU* 4.7 1.2 + - - -
435C MET* 3.7 15.5 + - - +
436C LEU 4.4 6.7 - - - +
437C GLY* 3.4 38.1 - - - +
438C GLY 4.5 1.9 + - - -
445C ARG* 3.3 39.1 + - + -
447C ARG* 3.4 9.1 - - + +
105D ILE* 3.7 29.6 - - + -
106D LEU* 5.2 1.6 - - + -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ASP* 2.9 22.5 + - - -
69C TYR* 1.3 79.9 + - - +
71C GLN* 1.3 63.7 + - - +
73C SER* 3.3 13.5 - - - -
74C SER 2.9 19.1 + - - -
75C ILE* 3.2 12.6 + - - -
79C TYR* 4.1 3.6 - - - -
330C LYS* 5.0 1.6 + - - -
447C ARG 2.5 24.1 + - - -
448C PRO 4.3 1.7 + - - -
449C THR* 3.5 31.4 - - - -
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Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C TYR* 3.0 32.3 + - - -
57C LEU* 4.0 3.6 - - - +
67C ASP* 4.3 1.2 + - - -
69C TYR* 3.4 3.0 - - - -
70C SER* 1.3 75.2 - - - +
72C ILE* 1.3 71.3 + - - +
74C SER* 2.7 31.5 + - - +
75C ILE* 3.5 22.7 - - + -
79C TYR* 3.0 21.2 + - + +
100D ARG 4.0 7.9 - - - +
101D PRO* 4.0 1.6 - - + -
102D ALA* 2.8 39.3 + - - +
106D LEU* 3.4 32.5 - - - +
353D THR* 4.1 2.1 - - - +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TYR* 3.2 39.3 + - + +
71C GLN* 1.3 80.7 - - - +
73C SER* 1.3 69.7 + - - +
74C SER 3.4 0.5 + - - -
270C GLU* 4.1 19.1 - - - +
301C GLN* 4.7 1.1 - - - +
329C LYS* 3.4 28.2 - - - +
445C ARG* 4.3 4.5 - - - +
447C ARG* 5.2 0.4 - - - -
500C ACT 4.2 13.0 - - + -
102D ALA* 4.0 15.7 - - + -
105D ILE* 3.7 22.7 - - + -
351D PHE* 4.2 25.8 - - + -
353D THR* 4.5 7.4 - - + -
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR 2.9 10.5 + - - -
70C SER* 3.2 15.2 + - - -
72C ILE* 1.3 79.8 - - - +
74C SER* 1.3 57.5 + - - +
75C ILE 3.8 1.3 - - - -
300C VAL 5.2 0.3 - - - +
301C GLN* 3.7 32.3 + - - +
306C SER* 5.3 0.7 + - - -
329C LYS* 3.6 11.0 - - - +
330C LYS* 3.4 28.9 + - - +
411C PHE* 5.0 0.2 - - - -
447C ARG* 3.5 30.7 - - - +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C SER 2.9 1.6 + - - -
71C GLN* 2.7 33.8 + - - +
73C SER* 1.3 78.5 - - - +
75C ILE* 1.3 65.2 + - - +
76C PRO* 3.3 10.2 - - - +
329C LYS* 3.2 38.9 - - - +
330C LYS* 3.5 8.9 - - - +
332C MET* 4.7 2.4 - - - +
100D ARG 4.6 1.7 + - - -
353D THR* 4.3 1.6 - - - -
354D TRP* 3.8 22.5 + - - -
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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