Contacts of the helix formed by residues 328 - 332 (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 SER 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A TRP* 3.6 11.8 - - - -
135B CYS* 3.4 11.6 - - - -
136B GLY* 3.2 33.6 + - - -
299B GLU 4.7 0.7 + - - +
300B VAL* 3.6 17.1 - - - +
303B GLY 5.3 0.9 - - - +
327B PHE* 1.3 81.6 - - - +
329B LYS* 1.3 78.3 + - - +
330B LYS* 3.0 4.7 + - - +
331B MET* 3.0 15.3 + - - +
333B THR 3.4 13.7 - - - -
334B GLY* 3.7 5.0 - - - -
600B PLP 4.4 0.7 + - - -
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A THR* 3.1 23.8 - - + +
354A TRP* 3.4 21.8 - - + -
72B ILE* 3.3 31.6 - - - +
73B SER 3.6 10.1 - - - +
74B SER* 3.4 20.3 - - - +
300B VAL* 3.4 24.9 - - + +
301B GLN* 3.5 12.4 - - + +
328B SER* 1.3 80.7 + - - +
330B LYS* 1.3 66.0 + - - +
332B MET* 2.9 14.6 + - - -
500B ACT 4.2 2.2 - - - +
600B PLP 1.5 80.4 + - + +
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Residues in contact with LYS 330 (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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70B SER* 5.0 1.8 + - - -
73B SER* 3.5 36.6 + - - +
74B SER* 3.5 11.7 - - - +
75B ILE 4.3 5.0 + - - +
76B PRO* 3.5 51.5 - - + +
300B VAL 5.6 0.2 - - - +
301B GLN 5.2 1.7 + - - -
303B GLY 3.9 22.7 - - - +
304B GLY* 4.2 26.5 - - - +
306B SER* 4.0 18.2 + - - -
328B SER 3.0 2.7 + - - +
329B LYS* 1.3 78.4 - - + +
331B MET* 1.3 59.7 + - - +
332B MET* 3.1 6.5 + - - +
364B LEU* 4.6 2.3 - - - +
367B VAL* 4.9 0.2 - - - +
371B ILE* 6.3 0.2 - - + -
447B ARG* 5.4 1.8 + - - +
448B PRO 3.9 18.6 + - - -
450B LEU* 4.4 15.7 - - + +
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Residues in contact with MET 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.7 24.5 - - + -
122B VAL* 4.4 1.3 - - + -
299B GLU 6.1 0.2 - - - +
303B GLY 5.3 1.3 - - - -
304B GLY* 4.2 12.6 - - - +
310B PHE* 3.6 42.0 - - + -
311B TRP* 3.9 16.2 - - + -
327B PHE* 3.8 21.1 - - + -
328B SER 3.0 11.1 + - - +
329B LYS 3.0 0.8 + - - -
330B LYS* 1.3 75.0 - - + +
332B MET* 1.3 62.1 + - - +
333B THR* 2.6 31.1 + - - +
364B LEU* 3.3 36.3 - - + +
368B ILE* 4.4 4.7 - - + -
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Residues in contact with MET 332 (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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98A ILE 5.0 7.6 - - - +
100A ARG* 3.9 6.9 + - + -
354A TRP* 3.2 24.8 - - - -
74B SER 4.9 2.5 - - - +
76B PRO* 3.8 28.5 - - + -
84B LEU* 4.6 10.3 - - + -
134B ALA 4.8 0.3 - - - +
329B LYS 2.9 12.5 + - - -
330B LYS 3.1 3.3 - - - +
331B MET* 1.3 80.2 - - - +
333B THR* 1.3 57.1 + - - +
360B LYS* 3.8 36.1 - - + +
363B LEU* 3.6 33.4 - - + -
364B LEU* 4.1 19.5 - - + -
367B VAL* 4.3 12.6 - - + -
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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