Contacts of the helix formed by residues 328 - 332 (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 SER 328 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C CYS* 3.5 5.2 - - - -
136C GLY* 3.2 32.5 + - - -
299C GLU 4.8 0.5 + - - +
300C VAL* 3.6 17.4 - - - +
303C GLY 5.3 0.9 - - - +
327C PHE* 1.3 80.4 - - - +
329C LYS* 1.3 77.4 + - - +
330C LYS* 2.9 5.2 + - - +
331C MET* 3.0 15.8 + - - +
333C THR 3.5 13.9 - - - -
334C GLY* 3.8 5.8 - - - -
600C PLP 4.4 1.1 + - - -
354D TRP* 3.6 16.5 - - - -
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Residues in contact with LYS 329 (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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72C ILE* 3.4 29.6 - - - +
73C SER 3.6 11.2 - - - +
74C SER* 3.2 21.5 - - - +
300C VAL* 3.5 24.5 - - + +
301C GLN* 3.5 11.3 - - + +
328C SER* 1.3 81.3 + - - +
330C LYS* 1.3 65.9 + - - +
332C MET* 3.0 13.2 + - - +
500C ACT 4.1 2.2 - - - +
600C PLP 1.4 82.6 + - + +
353D THR* 3.1 23.8 - - + +
354D TRP* 3.5 22.9 - - + -
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER* 5.0 1.6 + - - -
73C SER* 3.4 36.4 + - - +
74C SER* 3.5 10.0 - - - +
75C ILE 4.3 3.8 - - - +
76C PRO* 3.5 50.6 - - + +
300C VAL 5.6 0.2 - - - +
301C GLN 5.3 1.0 + - - +
303C GLY 3.9 22.4 - - - +
304C GLY* 4.1 28.3 - - - +
306C SER* 4.0 17.1 + - - -
328C SER 2.9 2.7 + - - +
329C LYS* 1.3 77.9 - - + +
331C MET* 1.3 58.9 + - - +
332C MET* 3.1 8.5 + - - +
364C LEU* 4.6 2.6 - - - +
447C ARG* 5.4 1.8 + - - +
448C PRO 3.8 19.8 + - - -
449C THR* 5.0 1.2 - - - +
450C LEU* 4.3 16.6 - - + +
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Residues in contact with MET 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 3.6 24.5 - - + -
122C VAL* 4.4 4.9 - - + -
303C GLY 5.3 1.1 - - - -
304C GLY* 4.3 12.3 - - - +
310C PHE* 3.6 41.3 - - + -
311C TRP* 3.9 17.0 - - + -
327C PHE* 3.8 21.3 - - + -
328C SER 3.0 12.4 + - - +
330C LYS* 1.3 74.7 - - + +
332C MET* 1.3 59.3 + - - +
333C THR* 2.7 30.4 + - - +
364C LEU* 3.3 37.5 - - + +
368C ILE* 4.4 1.3 - - + -
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Residues in contact with MET 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER 4.7 1.6 - - - +
76C PRO* 3.7 22.2 - - + -
84C LEU* 4.7 9.6 - - + -
134C ALA 4.9 0.2 - - - +
329C LYS 3.0 14.0 + - - +
330C LYS 3.1 15.2 - - - +
331C MET* 1.3 79.8 - - - +
333C THR* 1.3 56.9 + - - +
360C LYS* 3.8 36.8 - - + +
363C LEU* 3.9 30.5 - - + -
364C LEU* 4.1 20.6 - - + +
367C VAL* 4.3 12.6 - - + -
98D ILE 5.0 6.7 - - - +
100D ARG* 4.0 6.9 + - + -
354D TRP* 3.4 23.7 - - - -
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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