Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 2O8C
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 THR 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A CYS* 4.0 0.2 - - - +
334A LYS* 1.3 82.3 - - - +
336A PRO* 1.4 67.1 - - - +
337A GLN* 3.9 14.5 + - - +
338A GLY* 3.2 11.8 + - - -
339A GLN* 2.9 30.5 + - - +
381A LEU* 3.3 28.7 - - + +
382A ARG* 5.2 0.7 - - - -
384A PHE* 3.5 25.1 - - + +
599A LEU 5.2 0.7 + - - -
603A ASP* 2.5 29.5 + - + +
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Residues in contact with PRO 336 (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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139A ASN 5.2 7.9 - - - +
334A LYS 4.4 3.1 - - - +
335A THR* 1.4 86.7 - - - +
337A GLN* 1.3 61.9 + - + +
339A GLN* 3.7 17.3 - - + +
340A ARG* 3.2 40.6 + - - +
384A PHE 5.0 2.0 - - - +
385A PRO* 5.7 0.4 - - + -
386A ASP* 3.8 41.1 - - + +
389A ARG* 4.2 19.3 - - - +
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Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 3.9 11.4 - - - +
336A PRO* 1.3 79.3 - - - +
338A GLY* 1.3 58.6 + - - +
340A ARG* 3.8 7.7 + - - +
341A LEU* 3.7 15.4 + - - +
384A PHE* 3.9 13.2 - - - +
385A PRO 2.9 28.9 - - - +
386A ASP* 3.9 16.8 - - - +
387A LEU* 4.0 7.1 - - - +
596A ASN* 2.9 53.6 + - - +
599A LEU* 4.1 15.6 - - - +
600A ALA* 3.4 23.8 - - + +
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Residues in contact with GLY 338 (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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333A CYS* 3.4 21.1 - - - -
335A THR* 3.1 10.5 + - - -
337A GLN* 1.3 78.8 - - - +
339A GLN* 1.3 62.0 + - - +
340A ARG 3.3 0.7 - - - -
341A LEU* 3.3 10.7 + - - +
342A VAL* 3.4 10.7 + - - +
600A ALA* 3.7 20.1 - - - +
603A ASP* 3.8 13.2 - - - -
604A ALA* 4.5 0.5 - - - +
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Residues in contact with GLN 339 (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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139A ASN 5.4 7.3 - - - -
331A ASN* 2.9 37.8 + - - +
333A CYS* 3.8 22.8 + - - +
334A LYS 4.9 3.8 + - - -
335A THR 2.9 19.5 + - - +
336A PRO* 3.4 17.8 + - - +
338A GLY* 1.3 76.9 - - - +
340A ARG* 1.3 62.5 + - + +
341A LEU 3.5 0.2 + - - -
343A ASN* 3.1 18.4 + - - +
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Residues in contact with ARG 340 (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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139A ASN* 3.6 36.5 + - - +
169A ILE* 3.6 42.2 - - - +
336A PRO* 3.2 21.3 + - - +
337A GLN* 4.1 7.1 - - - +
338A GLY 3.3 0.4 - - - -
339A GLN* 1.3 77.2 - - + +
341A LEU* 1.3 60.5 + - + +
343A ASN* 3.6 9.6 + - - +
344A GLN* 2.9 29.0 + - - +
386A ASP* 3.7 26.5 + - - -
388A ASN* 4.7 5.9 - - - +
389A ARG* 5.9 0.8 - - - +
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Residues in contact with LEU 341 (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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170A GLN* 5.4 9.6 - - - +
337A GLN 3.7 11.5 + - - +
338A GLY 3.3 8.8 + - - +
339A GLN 3.3 0.8 - - - -
340A ARG* 1.3 78.5 - - + +
342A VAL* 1.3 59.8 + - - +
344A GLN* 3.4 19.3 - - + +
345A TRP* 2.8 49.7 + - + +
597A ASP* 4.6 1.6 - - - +
600A ALA* 3.6 35.0 - - + +
601A GLN* 3.6 22.4 - - + +
604A ALA* 4.4 7.9 - - + -
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Residues in contact with VAL 342 (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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330A LEU* 4.1 7.9 - - + +
331A ASN* 3.5 43.1 - - + +
333A CYS* 3.7 12.6 - - - -
338A GLY 3.4 16.7 + - - +
340A ARG 3.4 0.2 - - - -
341A LEU* 1.3 76.2 - - - +
343A ASN* 1.3 59.4 + - - +
345A TRP* 3.4 7.6 + - - +
346A ILE* 3.0 52.2 + - + +
604A ALA* 4.4 8.7 - - + -
607A SER* 4.2 9.6 - - - +
608A PHE* 4.2 15.9 - - + -
691A ILE* 5.4 0.2 - - - +
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Residues in contact with ASN 343 (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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313A PHE* 4.1 27.8 - - + -
327A ALA* 4.7 5.9 - - - +
331A ASN* 3.1 23.7 + - - +
339A GLN* 3.3 13.0 + - - +
340A ARG* 3.6 9.3 + - - +
341A LEU 3.3 0.4 - - - -
342A VAL* 1.3 75.2 - - - +
344A GLN* 1.3 65.8 + - - +
346A ILE* 4.5 1.8 - - - +
347A LYS* 3.2 38.0 + - + +
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Residues in contact with GLN 344 (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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145A ILE* 5.7 5.7 - - - +
167A ASP* 5.8 1.8 + - - -
193A GLN 5.5 1.1 - - - -
194A ILE* 6.1 0.2 - - - +
340A ARG 2.9 20.4 + - - +
341A LEU* 3.4 24.5 - - + +
342A VAL 3.2 0.2 - - - -
343A ASN* 1.3 77.3 - - - +
345A TRP* 1.3 63.9 + - + +
347A LYS* 4.0 9.7 + - - +
348A GLN* 3.1 65.7 + - - +
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Residues in contact with TRP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 2.8 40.2 + - + +
342A VAL* 4.0 3.1 - - - +
343A ASN 3.3 0.4 - - - -
344A GLN* 1.3 84.9 - - + +
346A ILE* 1.3 62.6 + - - +
348A GLN* 3.1 27.8 - - + +
349A PRO* 3.6 6.1 - - - +
350A LEU* 6.1 0.4 - - + -
359A ARG* 3.1 58.1 - - + +
601A GLN* 4.4 25.8 - - + -
604A ALA* 3.5 33.2 - - + -
605A VAL* 5.0 6.7 - - + -
608A PHE* 3.8 24.2 - + - -
691A ILE* 3.8 15.0 - - + +
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Residues in contact with ILE 346 (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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302A LEU* 4.9 6.1 - - - +
312A LEU* 4.1 29.6 - - + +
313A PHE* 4.2 18.4 - - + -
326A LEU* 4.3 9.9 - - + +
327A ALA* 3.8 31.2 - - + +
330A LEU* 4.4 11.0 - - + -
342A VAL* 3.0 35.2 + - + +
343A ASN* 4.2 3.4 - - - +
344A GLN 3.4 0.4 - - - -
345A TRP* 1.3 75.9 - - - +
347A LYS* 1.3 63.0 + - - +
348A GLN 3.5 0.2 + - - -
349A PRO* 3.8 14.2 - - - +
687A LEU* 4.2 9.4 - - + +
691A ILE* 4.0 24.2 - - + -
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Residues in contact with LYS 347 (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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145A ILE* 5.7 2.8 - - - +
192A ILE* 3.4 29.8 - - + +
193A GLN* 3.3 42.9 + - - +
194A ILE 3.5 16.2 + - - -
195A GLY* 3.5 19.7 + - - -
300A MET 4.7 0.7 - - - +
302A LEU* 5.1 3.4 - - - +
312A LEU* 6.3 0.7 - - - -
313A PHE* 3.5 30.7 - - + -
343A ASN* 3.2 25.0 + - + +
344A GLN* 4.0 10.5 + - - +
346A ILE* 1.3 75.9 - - - +
348A GLN* 1.3 57.7 - - - +
349A PRO* 3.4 6.4 - - - +
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Residues in contact with GLN 348 (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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193A GLN* 3.3 36.1 + - + +
194A ILE* 4.6 10.5 - - - +
299A TYR* 3.2 52.8 + - + -
344A GLN* 3.1 47.8 + - - +
345A TRP* 3.1 20.8 - - + +
347A LYS* 1.3 79.4 - - - +
349A PRO* 1.3 64.4 - - - +
350A LEU* 3.6 5.5 + - - +
359A ARG* 5.5 0.5 + - - -
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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