Contacts of the helix formed by residues 387 - 398 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B GLN* 4.6 10.8 - - - -
327B THR* 4.7 2.7 + - - -
330B ALA* 3.9 18.3 - - - +
385B VAL* 3.1 3.3 + - - +
386B ASP* 1.3 78.7 - - - +
388B ALA* 1.3 63.7 + - - +
389B PRO* 3.8 8.9 - - - +
390B VAL* 3.2 32.6 + - - +
391B GLN* 3.3 22.7 + - - +
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Residues in contact with ALA 388 (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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387B SER* 1.3 71.9 - - - +
389B PRO* 1.3 65.9 - - + +
391B GLN* 3.4 9.5 + - - +
392B ALA* 3.0 26.0 + - - +
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Residues in contact with PRO 389 (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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323B GLU* 3.6 35.7 - - + +
326B GLN* 5.6 7.0 - - + +
327B THR* 3.6 19.5 - - + +
387B SER* 3.3 12.3 - - - +
388B ALA* 1.3 92.7 - - + +
390B VAL* 1.3 59.2 + - - +
392B ALA* 3.1 8.2 + - + +
393B LEU* 2.9 35.5 + - + +
555B LEU* 6.4 0.4 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR* 3.6 26.9 - - + +
331B LEU* 3.9 13.5 - - + -
382B LEU* 3.7 31.5 - - + +
385B VAL* 3.7 30.1 - - + -
387B SER* 3.2 22.9 + - - +
389B PRO* 1.3 75.5 - - - +
391B GLN* 1.3 62.3 - - - +
393B LEU* 3.5 10.8 + - + +
394B ARG* 3.0 24.4 + - - +
552B LEU* 5.0 2.5 - - + -
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Residues in contact with GLN 391 (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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382B LEU 2.8 24.8 + - - -
383B GLU* 3.8 13.3 + - - +
385B VAL* 2.8 28.0 + - - +
386B ASP* 5.7 0.4 - - - -
387B SER 3.3 14.9 + - - +
388B ALA* 3.7 10.5 - - - +
389B PRO 3.2 0.6 - - - -
390B VAL* 1.3 76.3 - - - +
392B ALA* 1.3 60.2 + - - +
394B ARG* 3.6 26.2 + - - +
395B GLU* 3.2 23.9 + - - +
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Residues in contact with ALA 392 (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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388B ALA 3.0 13.9 + - - +
389B PRO* 3.1 11.9 + - + +
391B GLN* 1.3 74.3 - - - +
393B LEU* 1.3 59.0 + - - +
394B ARG 3.1 1.9 + - - -
395B GLU* 3.2 4.9 + - - +
396B LYS* 2.9 33.1 + - - +
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Residues in contact with LEU 393 (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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327B THR* 5.1 3.1 - - + -
389B PRO* 2.9 19.2 + - + +
390B VAL* 3.7 12.8 - - - +
392B ALA* 1.3 75.6 - - + +
394B ARG* 1.3 56.3 + - - +
396B LYS* 4.3 10.1 - - + -
397B MET* 3.1 30.9 + - - +
548B ALA* 3.8 30.1 - - + +
551B GLU* 3.7 24.7 - - + +
552B LEU* 3.7 37.1 - - + +
555B LEU* 4.0 26.2 - - + -
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Residues in contact with ARG 394 (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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379B ARG* 3.0 76.4 + - + +
380B ALA* 5.5 0.2 - - - +
382B LEU* 4.0 24.2 - - + +
383B GLU* 3.9 23.3 + - - +
390B VAL 3.0 17.7 + - - +
391B GLN* 3.6 29.9 + - - +
392B ALA 3.1 0.2 - - - -
393B LEU* 1.3 75.8 - - - +
395B GLU* 1.3 69.7 + - - +
397B MET* 3.3 30.1 - - + +
398B GLY 3.8 2.6 + - - -
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Residues in contact with GLU 395 (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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379B ARG* 4.6 17.5 + - - +
391B GLN 3.2 13.8 + - - +
392B ALA* 3.2 7.4 + - - +
394B ARG* 1.3 77.2 + - - +
396B LYS* 1.3 68.3 + - - +
398B GLY* 3.0 17.0 + - - -
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Residues in contact with LYS 396 (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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392B ALA 2.9 21.3 + - - +
393B LEU* 4.1 8.1 - - + +
395B GLU* 1.3 73.1 - - - +
397B MET* 1.3 63.2 + - - +
398B GLY* 3.3 1.9 + - - -
400B PHE* 5.5 0.9 - - - -
541B ALA 4.7 1.7 - - - +
544B GLN* 3.3 51.2 - - + +
545B SER* 3.8 12.1 + - - -
547B SER* 3.7 20.8 + - - -
548B ALA* 3.6 18.2 - - + +
551B GLU* 5.5 4.2 + - - -
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Residues in contact with MET 397 (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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375B LEU* 4.0 12.9 - - + +
378B LEU* 3.7 26.9 - - + -
379B ARG* 3.9 20.9 - - + -
382B LEU* 3.6 30.1 - - + -
393B LEU 3.1 17.4 + - - +
394B ARG* 3.3 17.7 - - + +
396B LYS* 1.3 75.0 - - - +
398B GLY* 1.3 63.8 + - - +
400B PHE* 3.7 1.2 - - - -
545B SER* 2.6 32.4 + - - +
548B ALA* 3.9 6.7 - - - +
549B LEU* 3.5 37.9 - - + +
552B LEU* 5.3 4.7 - - + -
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Residues in contact with GLY 398 (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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375B LEU* 3.3 17.7 - - - +
379B ARG* 3.9 14.0 - - - +
394B ARG 3.8 2.2 + - - -
395B GLU 3.0 14.4 + - - -
396B LYS 4.1 1.6 - - - -
397B MET* 1.3 86.1 - - - +
399B GLU* 1.3 61.4 + - - +
400B PHE* 4.0 10.3 - - - -
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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