Contacts of the helix formed by residues 387 - 397 (chain A) in PDB entry 1OH7
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 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A GLN* 4.5 3.8 + - - +
327A THR* 4.1 6.9 + - - -
330A ALA* 3.6 15.3 - - - +
385A VAL* 3.1 3.6 + - - -
386A ASP* 1.3 81.1 + - - +
388A ALA* 1.3 63.6 + - - +
389A PRO* 3.3 18.6 - - - +
390A VAL* 3.3 29.7 + - - +
391A GLN* 3.2 25.5 + - - +
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Residues in contact with ALA 388 (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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386A ASP* 5.2 0.4 + - - -
387A SER* 1.3 71.5 - - - +
389A PRO* 1.3 65.7 - - + +
391A GLN* 3.3 9.3 + - - +
392A ALA* 3.0 28.5 + - - +
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Residues in contact with PRO 389 (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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323A GLU* 3.3 40.2 - - + +
326A GLN* 3.7 19.1 - - + +
327A THR* 3.2 19.7 - - - +
387A SER* 3.3 11.0 - - - +
388A ALA* 1.3 93.9 - - + +
390A VAL* 1.3 62.5 + - - +
392A ALA* 3.4 7.8 + - + +
393A LEU* 3.3 29.7 + - + +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 3.5 26.2 - - + +
331A LEU* 4.0 11.2 - - + -
382A LEU* 3.8 36.0 - - + +
385A VAL* 3.8 24.9 - - + +
387A SER* 3.3 30.1 + - - +
389A PRO* 1.3 76.3 - - - +
391A GLN* 1.3 58.5 + - - +
393A LEU* 3.3 9.7 + - - +
394A ARG* 2.8 25.3 + - - +
552A LEU* 5.0 3.6 - - + -
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Residues in contact with GLN 391 (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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382A LEU 2.8 29.7 + - - -
383A GLU* 3.7 12.1 + - - +
385A VAL 3.1 17.6 + - - +
387A SER 3.2 16.5 + - - +
388A ALA* 3.6 10.5 - - - +
389A PRO 3.2 0.2 - - - -
390A VAL* 1.3 76.7 - - - +
392A ALA* 1.3 59.3 + - - +
394A ARG* 3.4 27.3 + - - +
395A GLU* 3.0 27.4 + - - +
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Residues in contact with ALA 392 (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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388A ALA 3.0 15.0 + - - +
389A PRO* 3.8 8.5 - - + +
390A VAL 3.3 0.2 - - - -
391A GLN* 1.3 76.1 - - - +
393A LEU* 1.3 59.2 + - + +
395A GLU* 3.3 7.2 + - - +
396A LYS* 2.9 30.4 + - - +
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Residues in contact with LEU 393 (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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327A THR* 4.8 4.5 - - + +
389A PRO* 3.3 18.5 + - + +
390A VAL* 3.6 10.5 - - - +
391A GLN 3.3 0.4 - - - -
392A ALA* 1.3 75.1 - - + +
394A ARG* 1.3 63.4 + - - +
395A GLU 3.2 1.6 - - - -
396A LYS* 4.3 10.8 - - + +
397A MET* 3.3 21.0 + - - +
548A ALA* 3.9 18.9 - - + +
551A GLU* 3.7 39.3 - - + +
552A LEU* 3.8 29.9 - - + +
555A LEU* 3.8 28.7 - - + -
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Residues in contact with ARG 394 (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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379A ARG* 2.8 88.0 + - + +
382A LEU* 3.5 44.2 - - + -
383A GLU* 3.4 30.5 + - - +
390A VAL 2.8 14.3 + - - +
391A GLN* 3.4 30.8 + - - +
393A LEU* 1.3 77.3 - - - +
395A GLU* 1.3 60.2 + - - +
397A MET* 3.4 24.1 - - + +
398A GLY 4.0 3.5 + - - +
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Residues in contact with GLU 395 (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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379A ARG* 5.2 9.2 + - - +
391A GLN 3.0 16.5 + - - +
392A ALA* 3.5 8.7 - - - +
393A LEU 3.2 0.4 - - - -
394A ARG* 1.3 78.0 - - - +
396A LYS* 1.3 63.3 + - - +
398A GLY* 3.5 10.2 + - - -
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Residues in contact with LYS 396 (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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392A ALA 2.9 17.2 + - - +
393A LEU* 4.3 8.3 - - + +
394A ARG 3.4 0.2 - - - -
395A GLU* 1.3 76.1 - - - +
397A MET* 1.3 64.8 + - - +
398A GLY* 3.1 3.2 + - - -
541A ALA 4.6 2.1 - - - +
544A GLN* 3.4 43.9 - - + +
545A SER* 3.6 12.6 + - - -
547A SER* 3.0 27.8 + - - -
548A ALA* 3.8 13.8 - - + +
551A GLU* 3.3 21.4 + - - -
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Residues in contact with MET 397 (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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375A LEU* 3.7 24.8 - - + +
378A LEU* 3.6 37.7 - - + -
379A ARG* 4.7 4.3 - - - -
382A LEU* 3.4 22.9 - - + -
393A LEU 3.3 10.3 + - - +
394A ARG* 3.4 14.4 - - + +
396A LYS* 1.3 76.5 - - - +
398A GLY* 1.3 63.3 + - - +
400A PHE* 3.7 0.7 - - - -
545A SER* 2.7 26.0 + - - -
548A ALA* 3.5 9.7 - - + +
549A LEU* 3.6 22.0 - - + -
552A LEU* 3.3 30.1 - - + -
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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