Contacts of the helix formed by residues 385 - 394 (chain B) in PDB entry 2OKC
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 LEU 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PRO 4.2 10.5 - - - +
158B LEU* 4.4 12.3 - - + -
161B ALA* 3.8 30.3 - - + -
334B LEU* 4.4 22.0 - - + -
336B LEU* 5.2 4.0 - - + -
365B TYR* 5.8 0.2 - - + -
367B TYR* 4.1 26.7 - - + -
380B LEU* 4.3 29.4 - - + -
381B GLU 5.0 2.7 - - - +
382B ARG* 3.0 12.7 + - - +
384B HIS* 1.3 79.5 - - - +
386B ASP* 1.3 62.6 + - - +
387B ASP 3.4 1.6 - - - -
388B PHE* 3.1 17.7 + - + +
389B VAL* 3.0 22.3 + - + +
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Residues in contact with ASP 386 (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 ARG* 3.0 24.0 + - - +
383B HIS* 3.2 30.6 + - - +
384B HIS 3.4 0.4 - - - -
385B LEU* 1.3 75.7 - - - +
387B ASP* 1.3 57.8 + - - +
389B VAL* 3.1 6.4 + - - +
390B SER* 3.0 30.4 + - - -
501B IPA 3.4 19.8 + - - +
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Residues in contact with ASP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TYR* 2.7 31.0 + - - +
383B HIS 4.9 0.2 + - - -
384B HIS 4.8 5.5 + - - +
385B LEU 3.4 0.4 - - - -
386B ASP* 1.3 77.9 - - - +
388B PHE* 1.3 57.5 + - - +
390B SER* 3.9 6.6 - - - -
391B CYS* 3.1 39.9 + - - -
398B ILE* 6.0 2.4 - - - +
408B ARG* 5.2 3.8 - - - +
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Residues in contact with PHE 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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161B ALA* 5.3 5.4 - - + -
165B CYS* 3.7 20.0 - - - -
332B THR* 4.2 13.2 - - + -
334B LEU* 3.8 32.3 - - + -
352B PHE* 3.8 29.8 - + - -
365B TYR* 3.5 54.6 + + + -
384B HIS 5.4 0.4 + - - -
385B LEU* 3.1 25.5 + - + +
387B ASP* 1.3 77.9 - - - +
389B VAL* 1.3 66.9 + - + +
390B SER 3.1 0.2 - - - -
391B CYS* 3.3 0.7 + - - +
392B TYR* 2.8 38.2 + + - +
409B TRP* 4.4 5.2 - + - -
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA* 4.3 11.9 - - + +
164B ASP* 4.5 11.4 - - + -
165B CYS* 4.2 26.2 - - - +
382B ARG* 3.5 34.8 - - - +
385B LEU 3.0 15.7 + - - +
386B ASP* 3.1 6.5 + - - +
388B PHE* 1.3 77.7 - - + +
390B SER* 1.3 60.4 + - - +
392B TYR* 3.4 7.1 + - - +
393B ASN* 3.0 35.7 + - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ASP 3.0 16.0 + - - -
387B ASP* 3.9 8.7 - - - -
389B VAL* 1.3 75.4 - - - +
391B CYS* 1.3 59.8 + - - +
393B ASN* 3.0 7.9 + - - +
394B ASN* 2.9 30.1 + - - +
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Residues in contact with CYS 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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365B TYR* 3.9 14.1 - - + -
387B ASP* 3.1 30.6 + - - +
388B PHE* 3.4 8.1 - - - +
390B SER* 1.3 78.7 + - - +
392B TYR* 1.3 61.8 + - - +
394B ASN* 3.0 17.5 + - - +
395B ARG* 4.1 0.2 + - - -
398B ILE* 4.5 11.9 - - - -
409B TRP* 3.0 62.5 + - + +
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Residues in contact with TYR 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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165B CYS* 3.2 48.8 + - + -
166B ILE* 4.7 6.6 - - - +
331B HIS* 3.3 20.8 - + - -
332B THR* 3.7 8.7 - - + -
352B PHE* 3.6 37.2 - + - +
388B PHE* 2.8 30.7 + + + +
389B VAL 3.4 10.1 - - - +
390B SER 3.2 0.2 - - - -
391B CYS* 1.3 71.8 - - - +
393B ASN* 1.3 71.0 + - - +
395B ARG* 3.0 50.3 + - - +
409B TRP* 4.0 4.5 - - - -
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Residues in contact with ASN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASP 5.5 2.0 + - - -
165B CYS* 5.1 5.1 - - - +
389B VAL* 3.0 29.9 + - - +
390B SER* 3.0 8.6 + - - +
392B TYR* 1.3 98.2 - - - +
394B ASN* 1.3 59.5 + - - +
395B ARG* 4.1 2.5 - - - -
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Residues in contact with ASN 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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390B SER* 2.9 16.2 + - - +
391B CYS* 3.0 15.2 + - - +
393B ASN* 1.3 80.5 - - - +
395B ARG* 1.3 57.8 + - - +
396B VAL* 2.9 44.7 + - - +
409B TRP* 3.3 6.9 + - - -
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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