Contacts of the helix formed by residues 497 - 514 (chain A) in PDB entry 2CEA
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 ALA 497 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A HIS* 3.6 23.3 - - + -
483A ARG* 3.8 38.4 - - + +
486A GLU* 4.6 1.3 + - - +
494A THR 3.8 3.2 + - - -
495A SER 3.1 1.2 - - - -
496A GLY* 1.3 75.3 - - - +
498A ALA* 1.3 64.2 + - - +
499A ASN* 3.3 7.4 - - - +
500A ASP* 3.3 8.9 + - + +
501A ILE* 3.0 28.3 + - + +
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ARG* 5.3 0.4 - - - +
495A SER* 3.0 18.4 + - - +
496A GLY 3.3 1.6 - - - -
497A ALA* 1.3 77.7 - - - +
499A ASN* 1.3 63.2 + - - +
501A ILE* 3.3 11.1 + - - +
502A GLU* 3.1 22.1 + - - +
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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
----------------------------------------------------------
496A GLY 3.5 20.8 + - - -
497A ALA 3.8 0.2 - - - -
498A ALA* 1.3 74.4 - - - +
500A ASP* 1.3 81.2 + - - +
502A GLU* 3.3 11.1 + - - +
503A ARG* 2.9 31.8 + - + +
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Residues in contact with ASP 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A HIS* 3.0 7.6 + - - -
427A HIS* 2.7 17.7 + - - -
479A LEU* 3.3 27.9 - - + +
480A LEU* 5.2 2.5 - - + -
482A GLY* 5.0 0.2 - - - -
483A ARG* 5.3 1.2 + - + +
497A ALA* 3.6 12.1 - - + +
499A ASN* 1.3 91.6 + - - +
501A ILE* 1.3 62.3 + - + +
503A ARG* 3.3 6.4 + - - +
504A ALA* 2.7 31.6 + - - +
1603A ZN 2.0 37.9 - - - -
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Residues in contact with ILE 501 (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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480A LEU* 4.9 14.1 - - + -
483A ARG* 3.9 36.1 - - + +
497A ALA* 3.0 22.7 + - + +
498A ALA* 3.5 10.1 - - - +
500A ASP* 1.3 74.8 - - + +
502A GLU* 1.3 65.3 + - - +
504A ALA* 3.7 4.7 - - - +
505A THR* 2.8 38.7 + - - +
561A VAL* 6.5 1.3 - - + -
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ALA 3.1 14.3 + - - +
499A ASN* 3.6 12.2 - - - +
500A ASP 3.3 0.2 - - - -
501A ILE* 1.3 78.1 - - - +
503A ARG* 1.3 65.0 + - + +
505A THR* 3.7 5.1 - - - -
506A GLU* 2.9 30.9 + - + +
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Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LYS* 5.9 7.3 - - - +
479A LEU* 3.6 27.6 - - + -
499A ASN* 2.9 18.4 + - + +
500A ASP* 3.5 5.4 - - - +
502A GLU* 1.3 77.8 - - + +
504A ALA* 1.3 63.6 + - - +
506A GLU* 3.0 50.2 + - - +
507A ILE* 3.1 27.6 + - - +
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Residues in contact with ALA 504 (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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476A LEU* 3.2 35.4 - - + +
479A LEU* 3.8 8.3 - - + +
480A LEU* 4.0 24.9 - - + -
500A ASP 2.7 21.5 + - - +
501A ILE* 3.7 4.3 - - - +
503A ARG* 1.3 74.2 - - - +
505A THR* 1.3 63.2 + - - +
508A ALA* 3.1 18.2 + - - +
561A VAL* 4.5 8.3 - - + -
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Residues in contact with THR 505 (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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501A ILE* 2.8 29.5 + - - +
502A GLU* 3.7 6.1 - - - -
504A ALA* 1.3 77.1 - - - +
506A GLU* 1.3 59.2 + - - +
508A ALA* 3.2 2.4 + - - +
509A ARG* 2.9 46.7 + - + +
557A VAL* 4.7 10.3 - - + -
561A VAL* 4.4 16.1 - - + +
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Residues in contact with GLU 506 (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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502A GLU* 2.9 20.9 + - + +
503A ARG* 3.0 44.3 + - - +
505A THR* 1.3 79.1 - - - +
507A ILE* 1.3 62.7 + - - +
509A ARG* 3.3 8.2 + - - +
510A ASN* 3.1 22.7 + - - +
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 3.6 30.3 - - + +
475A LYS* 4.1 28.7 - - + +
476A LEU* 3.1 36.3 - - + -
479A LEU* 3.6 25.4 - - + -
503A ARG* 3.1 20.3 + - - +
506A GLU* 1.3 74.1 - - - +
508A ALA* 1.3 58.8 + - - +
510A ASN* 2.9 22.4 + - + +
511A MET* 2.9 24.4 + - + +
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Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 4.0 10.1 - - + +
504A ALA 3.1 11.1 + - - +
505A THR 3.6 6.5 - - - +
507A ILE* 1.3 77.0 - - - +
509A ARG* 1.3 66.3 + - - +
511A MET* 3.1 19.1 + - - +
512A VAL* 3.1 19.8 + - - +
557A VAL* 4.1 15.0 - - + +
560A ILE* 4.1 11.9 - - + -
561A VAL* 3.8 21.1 - - + -
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Residues in contact with ARG 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A THR* 2.9 35.9 + - + +
506A GLU* 3.8 7.0 - - - +
508A ALA* 1.3 75.2 - - - +
510A ASN* 1.3 58.3 + - - +
512A VAL 3.3 0.3 + - - -
513A CYS* 2.8 44.2 + - - +
514A GLN* 4.9 1.6 - - - -
545A TYR* 3.9 18.8 + - - -
553A ILE* 4.2 18.7 - - - +
554A ASP* 3.6 22.0 + - - -
557A VAL* 3.7 21.7 - - + +
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Residues in contact with ASN 510 (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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506A GLU 3.1 13.2 + - - +
507A ILE* 2.9 14.5 + - - +
509A ARG* 1.3 75.5 - - - +
511A MET* 1.3 63.4 + - - +
512A VAL 3.1 1.8 - - - -
514A GLN* 2.5 57.9 + - - +
515A LEU* 3.0 52.5 + - + +
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Residues in contact with MET 511 (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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469A ARG* 3.8 46.4 - - + +
472A LEU* 4.0 30.1 - - + -
473A LEU* 4.0 21.8 - - + -
476A LEU* 4.8 1.8 - - - -
507A ILE* 2.9 24.4 + - + +
508A ALA* 3.1 15.0 + - - +
510A ASN* 1.3 79.0 - - - +
512A VAL* 1.3 65.9 + - + +
515A LEU* 3.5 9.5 + - + -
516A GLY 3.3 6.1 + - - -
517A MET* 3.0 43.0 + - + +
560A ILE* 4.6 13.5 - - + -
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Residues in contact with VAL 512 (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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508A ALA 3.1 15.8 + - - +
509A ARG 3.8 3.1 - - - +
511A MET* 1.3 81.3 - - + +
513A CYS* 1.3 59.2 + - - +
514A GLN 3.7 0.2 - - - -
515A LEU 4.9 0.2 - - - -
516A GLY* 4.7 5.4 + - - -
518A SER* 4.0 21.2 - - - -
521A LEU* 3.7 31.4 - - + +
522A GLY 5.1 1.4 - - - +
524A LEU 4.5 2.4 - - - +
526A TRP* 4.0 11.6 - - - -
553A ILE* 4.0 19.5 - - + +
556A GLU* 4.1 9.4 - - + -
557A VAL* 4.0 13.9 - - + -
560A ILE* 4.0 23.8 - - + -
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Residues in contact with CYS 513 (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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509A ARG* 2.8 32.4 + - - +
512A VAL* 1.3 78.5 - - - +
514A GLN* 1.3 63.1 + - + +
524A LEU 4.2 2.2 - - - -
525A ALA* 3.3 8.3 - - - +
526A TRP* 2.9 49.2 + - + +
527A GLY 5.5 0.2 - - - +
528A LYS* 4.5 8.5 + - - +
545A TYR* 5.5 0.7 - - - -
553A ILE* 3.6 44.9 - - - -
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Residues in contact with GLN 514 (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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509A ARG* 4.6 2.3 - - - +
510A ASN* 2.5 44.4 + - - +
513A CYS* 1.3 82.0 - - - +
515A LEU* 1.3 70.3 - - + +
516A GLY 3.5 2.2 + - - -
524A LEU 5.1 1.1 - - - -
525A ALA* 5.0 4.8 - - + +
528A LYS* 3.1 39.0 + - - +
498B ALA* 3.8 21.7 - - + +
501B ILE* 3.8 10.0 - - - +
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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