Contacts of the helix formed by residues 487 - 502 (chain A) in PDB entry 2C0L
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 ASP 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A TRP* 4.9 1.7 - - - -
433A THR* 5.2 1.9 - - - +
436A TYR* 2.5 41.1 + - - +
479A VAL* 6.6 0.2 - - - -
485A SER 3.8 3.8 + - - +
486A ILE* 1.3 72.1 - - - +
488A PRO* 1.3 70.1 - - - +
489A ASP* 3.3 19.5 + - - +
490A VAL* 3.1 19.0 + - + +
491A GLN* 3.0 25.0 + - - +
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Residues in contact with PRO 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ILE* 3.3 13.2 - - + +
487A ASP* 1.3 89.3 - - - +
489A ASP* 1.3 62.1 + - - +
491A GLN* 3.6 0.6 - - + +
492A CYS* 3.0 23.4 + - - +
514A ALA* 3.2 43.6 - - + +
517A VAL* 3.9 24.0 - - + -
518A ARG* 4.1 27.6 - - - +
524A LEU* 5.0 0.7 - - - +
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Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 3.1 19.6 - - + +
429A TRP* 3.5 25.7 - - + -
487A ASP* 3.1 8.6 + - - +
488A PRO* 1.3 77.5 - - - +
490A VAL* 1.3 64.3 + - - +
491A GLN 3.2 0.2 - - - -
492A CYS* 3.3 7.3 + - - +
493A GLY* 3.1 17.5 + - - -
518A ARG* 3.2 36.0 + - - -
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TRP* 3.7 16.6 - - + -
436A TYR* 3.4 44.9 - - + +
475A PHE* 3.3 24.4 - - + +
478A ALA* 4.0 7.9 - - + -
479A VAL* 3.5 32.8 - - + +
487A ASP* 3.1 16.6 + - + +
489A ASP* 1.3 76.1 - - - +
491A GLN* 1.3 57.9 + - + +
493A GLY 3.3 0.9 + - - -
494A LEU* 3.0 24.7 + - + +
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Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A VAL* 3.6 38.0 - - - +
486A ILE* 3.8 25.6 - - + +
487A ASP 3.0 17.7 + - - +
488A PRO 3.6 8.5 - - - +
490A VAL* 1.3 75.5 - - + +
492A CYS* 1.3 59.3 + - - +
494A LEU* 3.3 7.1 + - - +
495A GLY* 2.8 24.1 + - - -
509A ASP 4.5 0.2 - - - +
510A CYS* 3.2 53.8 - - - +
513A ALA* 3.7 14.5 - - + +
514A ALA* 3.9 2.7 - - + -
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Residues in contact with CYS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 3.9 23.1 - - + -
488A PRO 3.0 15.8 + - - +
489A ASP* 3.4 15.9 - - - +
490A VAL 3.3 0.4 - - - -
491A GLN* 1.3 76.1 - - - +
493A GLY* 1.3 57.3 + - - +
495A GLY* 3.0 3.5 + - - -
496A VAL* 2.9 34.0 + - - +
511A PHE* 3.6 11.7 - - - -
514A ALA* 4.5 1.1 - - - +
518A ARG* 5.9 0.9 - - - +
524A LEU* 4.5 11.7 - - + -
527A LYS* 3.9 35.0 - - - -
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Residues in contact with GLY 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 3.6 19.0 - - - +
426A LEU* 3.9 11.5 - - - +
475A PHE* 3.8 15.5 - - - -
489A ASP 3.1 7.9 + - - -
490A VAL 3.3 3.1 + - - -
492A CYS* 1.3 78.8 - - - +
494A LEU* 1.3 56.8 + - - +
496A VAL* 3.5 4.8 + - - +
497A LEU* 3.1 32.1 + - - +
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Residues in contact with LEU 494 (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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472A LYS* 4.1 21.5 - - + +
475A PHE* 4.0 21.7 - - + +
476A LEU* 4.0 24.2 - - + -
479A VAL* 4.0 24.2 - - + -
490A VAL 3.0 12.2 + - - +
491A GLN* 3.5 16.2 - - - +
493A GLY* 1.3 75.3 - - - +
495A GLY* 1.3 58.4 + - - +
497A LEU* 3.4 9.3 + - + +
498A PHE* 3.1 47.1 + - + -
510A CYS* 3.6 19.3 - - - -
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Residues in contact with GLY 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN 2.8 14.3 + - - -
492A CYS 3.0 4.0 + - - -
494A LEU* 1.3 74.5 - - - +
496A VAL* 1.3 55.4 + - - +
499A ASN* 2.6 34.7 + - - -
507A ALA* 3.4 11.4 - - - +
510A CYS* 3.6 13.9 - - - +
511A PHE* 3.5 18.6 - - - -
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 4.9 2.5 - - - -
410A ALA* 4.2 8.5 - - + +
411A VAL* 3.9 24.7 - - + -
414A THR* 3.0 33.4 - - + +
426A LEU* 4.1 16.4 - - + -
492A CYS* 2.9 23.3 + - - +
493A GLY* 3.7 11.0 - - - +
494A LEU 3.3 0.2 - - - -
495A GLY* 1.3 75.0 - - - +
497A LEU* 1.3 65.2 + - - +
499A ASN* 3.1 18.6 + - - +
500A LEU* 3.2 13.8 + - + +
511A PHE* 4.3 9.9 - - + -
527A LYS* 5.1 1.1 - - + -
143B LEU* 4.6 7.0 - - + -
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Residues in contact with LEU 497 (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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423A CYS* 3.9 15.0 - - - -
426A LEU* 3.7 19.1 - - + -
468A PHE* 3.0 55.0 - - + +
471A VAL* 3.8 27.1 - - + -
472A LYS* 3.8 24.2 - - + +
475A PHE* 4.1 15.3 - - + -
493A GLY 3.1 21.4 + - - +
494A LEU* 3.4 11.4 + - + +
496A VAL* 1.3 74.6 - - - +
498A PHE* 1.3 58.7 + - - +
500A LEU* 3.1 15.6 + - + -
501A SER 3.2 1.2 + - - -
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Residues in contact with PHE 498 (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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468A PHE* 5.3 0.2 - + - -
472A LYS* 3.7 23.6 - - + -
476A LEU* 4.9 8.7 - - + -
494A LEU* 3.1 39.9 + - + +
496A VAL 3.2 0.4 - - - -
497A LEU* 1.3 76.3 - - - +
499A ASN* 1.3 59.4 + - - +
501A SER* 3.6 3.4 - - - -
502A GLY 3.1 4.5 + - - -
503A GLU* 2.8 69.4 + - + +
504A TYR 3.9 0.2 + - - -
506A LYS* 3.5 54.7 - - + -
507A ALA* 3.6 12.3 - - + -
510A CYS* 3.6 19.5 - - - -
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Residues in contact with ASN 499 (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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414A THR* 4.5 4.5 - - + -
495A GLY 2.6 27.3 + - - -
496A VAL 3.1 9.0 + - - +
498A PHE* 1.3 77.0 - - - +
500A LEU* 1.3 64.1 + - - +
502A GLY* 3.4 7.1 + - - -
504A TYR* 3.4 39.0 + - + -
507A ALA* 3.6 5.3 - - - +
511A PHE* 3.6 5.5 - - - -
531A THR* 3.2 33.1 + - - -
534A ASN* 4.6 5.9 + - - -
143B LEU* 3.9 26.1 - - + +
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Residues in contact with LEU 500 (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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414A THR* 3.5 43.3 - - + +
417A SER* 5.8 2.0 - - - -
418A LEU 5.6 0.4 - - - +
419A GLN* 4.1 39.9 + - + +
422A ALA* 4.0 15.5 - - + -
423A CYS* 4.2 12.1 - - - +
426A LEU* 4.9 1.1 - - + -
468A PHE* 3.8 7.9 - - + -
496A VAL* 3.2 17.2 + - + +
497A LEU* 3.1 28.3 + - + +
499A ASN* 1.3 78.5 - - - +
501A SER* 1.3 59.7 + - - +
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Residues in contact with SER 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLN* 6.0 0.4 - - - -
468A PHE* 3.3 25.9 - - - -
497A LEU 3.2 8.9 + - - -
498A PHE* 3.4 10.7 + - - -
500A LEU* 1.3 75.3 - - - +
502A GLY* 1.3 60.8 + - - +
503A GLU* 2.7 31.8 + - - +
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Residues in contact with GLY 502 (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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498A PHE 3.1 5.8 + - - -
499A ASN 3.4 5.4 + - - -
500A LEU 3.4 3.2 - - - -
501A SER* 1.3 78.5 - - - +
503A GLU* 1.3 57.8 + - - +
504A TYR* 3.0 39.7 + - - -
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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