Contacts of the helix formed by residues 69 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS* 4.9 9.2 - + - -
67A ASP* 2.9 6.4 + - - +
68A LEU* 1.3 80.2 - - - +
70A SER* 1.3 72.2 + - - +
71A GLN 4.8 2.5 - - - +
72A ILE* 3.1 39.7 + - + +
73A SER 2.9 18.2 + - - -
270A GLU* 4.7 1.7 + - - -
435A MET* 3.6 21.3 + - - +
436A LEU 4.4 4.3 - - - -
437A GLY* 3.4 33.7 - - - +
438A GLY 4.6 1.9 + - - -
445A ARG* 3.4 39.3 + - + -
447A ARG* 3.4 10.3 - - + +
105B ILE* 3.6 30.0 - - + +
106B LEU* 5.1 2.5 - - + -
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Residues in contact with SER 70 (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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67A ASP* 2.9 21.6 + - - -
69A TYR* 1.3 78.9 + - - +
71A GLN* 1.3 63.4 + - - +
73A SER* 3.2 13.9 - - - -
74A SER 2.9 20.6 + - - -
75A ILE* 3.2 12.8 + - - -
79A TYR* 4.2 3.1 - - - -
330A LYS* 5.1 1.0 + - - -
447A ARG 2.5 24.7 + - - -
448A PRO* 4.3 2.4 + - - -
449A THR* 3.5 30.5 - - - -
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Residues in contact with GLN 71 (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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49A TYR* 3.0 31.9 + - - -
57A LEU* 4.0 4.9 - - - +
67A ASP* 4.3 0.8 + - - -
69A TYR* 3.4 3.0 - - - +
70A SER* 1.3 74.1 - - - +
72A ILE* 1.3 71.5 + - - +
74A SER* 2.6 32.4 + - - +
75A ILE* 3.4 22.4 - - + -
79A TYR* 2.9 21.2 + - + +
100B ARG 3.9 8.5 - - - +
101B PRO* 3.9 1.8 - - - -
102B ALA* 2.8 38.8 + - - +
106B LEU* 3.5 34.2 - - - +
353B THR* 4.1 1.7 - - - +
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Residues in contact with ILE 72 (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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69A TYR* 3.1 38.8 + - + +
71A GLN* 1.3 79.1 - - - +
73A SER* 1.3 70.6 + - - +
74A SER 3.3 0.3 + - - -
270A GLU* 4.1 20.4 - - - +
301A GLN* 4.8 0.9 - - - +
329A LYS* 3.4 19.3 - - - +
445A ARG* 4.3 3.6 - - - +
447A ARG* 5.1 0.9 - - - -
500A ACT 4.2 17.9 - - + -
102B ALA* 3.9 17.0 - - + -
105B ILE* 3.6 24.0 - - + -
351B PHE* 4.2 26.0 - - + -
353B THR* 4.5 9.9 - - + -
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR 2.9 10.9 + - - -
70A SER* 3.2 16.3 + - - -
72A ILE* 1.3 78.9 - - - +
74A SER* 1.3 57.8 + - - +
75A ILE 3.8 1.1 - - - -
300A VAL 5.2 0.2 - - - +
301A GLN* 3.7 29.0 + - - +
306A SER* 5.3 0.2 + - - -
329A LYS* 3.7 10.8 - - - +
330A LYS* 3.3 34.7 + - - +
411A PHE* 5.1 0.3 - - - -
447A ARG* 3.5 28.8 - - - +
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Residues in contact with SER 74 (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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70A SER 2.9 2.8 + - - -
71A GLN* 2.6 34.6 + - - +
72A ILE 4.2 0.2 - - - -
73A SER* 1.3 78.5 - - - +
75A ILE* 1.3 64.6 + - - +
76A PRO* 3.3 10.0 - - - +
329A LYS* 3.2 38.4 - - - +
330A LYS* 3.7 9.2 - - - +
332A MET* 4.8 2.4 - - - +
100B ARG 4.5 1.7 + - - -
353B THR* 4.3 1.8 - - - -
354B TRP* 3.8 22.3 + - - -
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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