Contacts of the helix formed by residues 376 - 391 (chain B) in PDB entry 2C31
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 ASN 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LYS 4.8 3.7 + - - +
368B ALA* 5.1 5.9 - - - +
370B THR* 3.7 17.9 - - + +
374B MET 3.9 0.6 + - - +
375B MET* 1.3 75.0 - - - +
377B TYR* 1.3 54.1 + - + +
378B SER* 3.0 13.6 - - - +
379B ASN* 2.7 52.2 + - - +
380B SER* 2.6 26.7 + - - -
545B ILE* 4.2 4.2 - - - +
546B ASP* 5.5 0.9 - - + -
549B ALA* 3.9 20.9 - - + -
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Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 1.3 77.9 - - - +
378B SER* 1.3 57.7 + - - +
380B SER* 3.6 2.5 - - - -
381B LEU* 3.0 40.8 + - + +
402B ASN* 3.3 27.1 - - + +
403B ALA* 3.8 12.3 - - + -
406B ASN* 3.3 35.4 - - + +
410B ILE* 4.4 0.7 - - - -
477B MET* 3.6 31.0 + - + -
479B ASN* 3.3 23.7 + - - +
545B ILE* 4.2 15.7 - - + -
549B ALA* 4.1 13.9 - - + -
550B GLY* 3.7 20.6 - - - -
1554B TZD 2.8 19.8 + - - -
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 4.7 3.0 - - - +
365B LYS* 3.5 47.2 + - - +
366B MET* 3.4 16.7 - - - +
376B ASN* 3.0 10.3 - - - +
377B TYR* 1.3 78.2 - - - +
379B ASN* 1.3 57.9 + - - -
382B GLY 3.0 21.8 + - - -
406B ASN* 5.5 1.6 + - - -
410B ILE* 3.8 15.9 - - - +
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Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS 4.2 3.6 - - - +
366B MET 3.6 24.6 - - - +
368B ALA 3.7 20.5 + - - +
369B GLU* 5.1 0.2 - - - +
370B THR* 3.0 28.3 + - - +
375B MET* 3.8 3.7 - - - +
376B ASN* 2.7 54.7 + - - +
378B SER* 1.3 71.5 - - - +
380B SER* 1.3 65.6 + - - +
382B GLY* 3.8 6.1 + - - +
383B VAL* 3.9 14.6 + - - +
522B PRO* 3.4 30.3 - - + +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B MET* 4.1 19.1 - - - -
376B ASN 2.6 22.7 + - - -
377B TYR 3.2 4.9 + - - -
379B ASN* 1.3 83.6 + - - +
381B LEU* 1.3 68.9 + - - +
383B VAL* 3.3 20.7 + - - +
384B VAL* 3.9 3.3 + - - +
477B MET* 3.5 19.2 - - - +
525B LEU* 3.4 21.2 - - - +
543B ALA* 5.7 0.7 - - - -
545B ILE* 3.8 15.3 - - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.0 23.4 + - + +
380B SER* 1.3 76.7 + - - +
382B GLY* 1.3 60.3 + - - +
383B VAL 3.1 2.0 - - - -
384B VAL* 3.1 17.6 + - + +
385B ARG* 2.9 27.9 + - - +
403B ALA 4.8 0.7 - - - +
406B ASN* 3.4 34.1 - - + +
407B THR* 3.4 34.3 - - + +
410B ILE* 3.8 17.9 - - + +
411B VAL* 4.2 5.0 - - + +
449B VAL* 4.1 11.4 - - + -
477B MET* 3.8 26.9 - - + -
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Residues in contact with GLY 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B MET* 3.6 32.3 - - - +
378B SER 3.0 12.6 + - - -
379B ASN 3.8 3.1 + - - -
380B SER 3.2 1.2 - - - -
381B LEU* 1.3 77.0 - - - +
383B VAL* 1.3 56.1 + - - +
385B ARG* 3.3 4.9 - - - +
386B ASP* 3.0 36.2 + - - +
410B ILE* 4.1 0.2 - - - +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ASN 3.9 14.3 + - - +
380B SER 3.4 9.4 - - - +
381B LEU 3.1 0.4 - - - -
382B GLY* 1.3 74.9 - - - +
384B VAL* 1.3 65.8 + - - +
386B ASP* 3.4 8.1 + - - +
387B PHE* 3.0 21.8 + - + +
522B PRO* 3.6 31.0 - - + +
525B LEU* 4.0 13.0 - - + -
526B LYS* 3.6 41.1 - - + +
529B LEU* 4.4 10.1 - - + -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER 4.1 11.9 - - - +
381B LEU* 3.1 19.4 + - + +
383B VAL* 1.3 75.1 - - + +
385B ARG* 1.3 61.6 + - - +
387B PHE* 3.2 1.7 + - - +
388B MET* 2.9 40.6 + - + +
396B LEU* 4.6 5.6 - - + -
411B VAL* 4.0 17.5 - - + -
447B ILE* 4.8 9.0 - - + -
449B VAL* 4.4 15.7 - - + -
475B ILE* 4.0 24.2 - - + -
525B LEU* 5.0 6.5 - - + -
529B LEU* 4.2 14.6 - - + -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 5.7 3.0 - - - +
366B MET* 3.8 37.8 - - - +
381B LEU 2.9 12.8 + - - +
382B GLY 3.3 7.0 - - - +
384B VAL* 1.3 77.4 - - - +
386B ASP* 1.3 82.6 + - - +
388B MET* 3.3 1.9 + - - +
389B LEU* 3.1 43.2 + - + +
410B ILE* 3.3 29.7 + - + +
411B VAL* 4.1 14.5 - - - +
412B ASP* 4.2 20.7 + - - +
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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
----------------------------------------------------------
366B MET* 5.9 0.2 - - - +
382B GLY 3.0 22.3 + - - +
383B VAL* 3.8 7.4 - - - +
385B ARG* 1.3 99.6 + - - +
387B PHE* 1.3 61.6 + - - +
389B LEU* 3.6 8.7 + - - +
390B ALA* 3.4 22.0 + - - +
526B LYS* 6.0 6.3 - - - -
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Residues in contact with PHE 387 (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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383B VAL* 3.0 17.5 + - + +
384B VAL 3.2 4.5 + - - +
386B ASP* 1.3 78.7 - - - +
388B MET* 1.3 60.8 + - - +
390B ALA* 3.3 3.0 + - + +
391B ASN* 2.8 59.0 + - + +
394B ILE* 3.8 17.3 - - + -
447B ILE* 3.7 32.3 - - + -
529B LEU* 3.9 19.7 - - + -
530B GLU* 4.1 33.7 - - + -
533B VAL* 3.8 27.6 - - + -
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Residues in contact with MET 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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384B VAL* 2.9 27.7 + - + +
385B ARG 3.9 2.9 - - - +
387B PHE* 1.3 76.1 - - + +
389B LEU* 1.3 61.0 + - - +
391B ASN 3.0 14.0 - - - +
392B PRO* 3.0 40.1 - - + +
394B ILE* 3.4 31.2 - - - +
396B LEU* 4.2 13.7 - - + -
411B VAL* 3.8 23.1 - - + -
412B ASP 4.1 9.7 - - - +
413B MET* 3.7 26.5 - - + -
414B LEU* 4.9 0.3 - - - +
447B ILE* 4.2 23.1 - - - -
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Residues in contact with LEU 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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257B ASN* 4.3 9.9 - - + +
385B ARG* 3.1 55.0 + - + +
386B ASP* 3.9 9.2 - - - +
388B MET* 1.3 76.3 - - - +
390B ALA* 1.3 60.1 + - - +
392B PRO* 3.8 4.2 - - - +
412B ASP* 3.9 29.8 - - + +
414B LEU* 3.6 41.2 - - + +
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Residues in contact with ALA 390 (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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386B ASP 3.4 10.6 + - - +
387B PHE* 3.3 10.0 + - - +
388B MET 3.2 0.2 - - - -
389B LEU* 1.3 81.9 - - - +
391B ASN* 1.3 71.1 + - - +
392B PRO* 3.5 5.8 - - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 2.8 49.6 + - + +
388B MET* 3.0 17.2 - - - +
390B ALA* 1.3 92.5 - - - +
392B PRO* 1.3 62.7 - - - +
393B ASP 3.4 3.3 + - - -
394B ILE* 3.7 30.4 - - + +
533B VAL* 6.2 0.2 - - - -
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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
------------------------------------------------------------
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