Contacts of the helix formed by residues 483 - 499 (chain A) in PDB entry 2CG2
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 ARG 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A ASP 2.9 11.5 + - - +
482A ASN* 1.3 73.3 + - - +
484A ALA* 1.3 57.7 + - - +
486A ARG* 3.5 16.2 + - + +
487A GLU* 3.0 57.6 + - + +
516A LEU 5.8 1.3 - - - -
517A ARG 5.2 9.7 + - - -
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Residues in contact with ALA 484 (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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450A GLU* 5.4 3.4 - - - +
453A LEU* 4.0 13.6 - - + +
457A ARG* 3.8 23.2 + - - +
482A ASN* 3.3 9.3 + - - +
483A ARG* 1.3 78.6 - - - +
485A ALA* 1.3 61.7 + - - +
487A GLU* 3.5 7.5 + - - +
488A LEU* 3.1 24.9 + - - +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.8 11.6 - - + +
472A VAL* 3.4 7.3 - - + +
475A LEU* 3.6 32.1 - - + -
476A VAL* 3.9 15.5 - - + +
482A ASN* 3.0 25.5 + - + +
484A ALA* 1.3 74.1 - - - +
486A ARG* 1.3 60.3 + - - +
488A LEU* 3.4 0.7 + - - +
489A GLN* 2.9 31.7 + - - +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 4.1 15.7 - - + -
479A GLU 5.2 0.2 - - - +
480A PRO* 2.7 40.6 + - - +
481A ASP* 4.7 4.2 + - - +
482A ASN 3.1 17.8 + - - +
483A ARG* 3.8 17.2 - - + +
485A ALA* 1.3 78.9 - - - +
487A GLU* 1.3 58.3 + - + +
489A GLN* 3.5 1.2 + - - +
490A ALA* 2.8 31.1 + - - +
515A GLU 3.0 27.1 + - - -
516A LEU* 2.8 45.0 + - + +
519A GLY* 4.0 12.3 - - - +
650A VAL* 5.7 0.4 - - - +
651A THR* 3.6 25.2 - - - +
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Residues in contact with GLU 487 (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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20A THR* 3.6 36.8 + - - +
21A THR* 4.0 18.9 - - + +
24A LYS* 5.9 0.4 - - - +
483A ARG* 3.0 42.3 + - + +
484A ALA* 4.1 6.8 - - - +
486A ARG* 1.3 77.7 - - + +
488A LEU* 1.3 58.9 + - - +
490A ALA* 3.6 5.9 + - - +
491A ASP* 2.9 37.8 + - - +
517A ARG* 5.0 8.5 + - + -
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.9 19.3 - - + -
456A ALA* 3.8 28.9 - - + -
457A ARG* 4.0 27.1 - - + +
460A TYR* 3.8 36.8 - - + -
468A VAL* 4.4 7.6 - - + -
472A VAL* 3.9 6.5 - - + -
484A ALA 3.1 18.5 + - - +
485A ALA 3.9 2.9 - - - +
487A GLU* 1.3 71.7 - - - +
489A GLN* 1.3 67.5 + - - +
491A ASP* 3.1 10.4 + - + +
492A ALA* 3.0 21.7 + - - +
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A VAL 4.2 0.3 - - - -
469A VAL* 2.8 44.3 + - - +
472A VAL* 3.2 26.7 - - + +
473A ASN* 3.2 23.4 + - - +
476A VAL* 4.0 12.6 - - + -
485A ALA 2.9 18.8 + - - +
486A ARG 3.6 4.0 - - - +
488A LEU* 1.3 75.7 - - - +
490A ALA* 1.3 65.1 + - - +
492A ALA* 3.2 4.0 + - - +
493A LEU* 2.9 37.8 + - + +
516A LEU* 3.4 21.3 - - + -
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ARG 2.8 19.6 + - - +
487A GLU 3.6 5.2 - - - +
489A GLN* 1.3 77.0 - - - +
491A ASP* 1.3 57.1 + - - +
493A LEU* 3.3 1.5 + - - +
494A GLU* 2.8 31.2 + - - +
513A ALA* 3.4 36.9 - - - +
516A LEU* 3.8 7.4 - - + +
517A ARG* 3.7 22.0 - - + +
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Residues in contact with ASP 491 (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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24A LYS* 3.0 32.0 + - + +
460A TYR* 3.8 21.8 + - + +
487A GLU* 2.9 26.1 + - - +
488A LEU* 3.1 11.9 + - + +
490A ALA* 1.3 75.4 - - - +
492A ALA* 1.3 61.9 + - - +
494A GLU* 3.3 4.3 + - - +
495A GLN* 3.1 27.2 + - - +
517A ARG* 2.8 25.3 + - - +
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Residues in contact with ALA 492 (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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460A TYR* 3.6 17.2 - - + -
465A TYR* 3.8 10.0 - - + +
468A VAL* 3.7 29.6 - - + -
469A VAL* 3.6 19.3 - - + -
488A LEU 3.0 10.2 + - - +
489A GLN 3.8 1.3 - - - +
491A ASP* 1.3 73.3 - - - +
493A LEU* 1.3 66.4 + - - +
495A GLN* 3.3 4.3 + - - +
496A LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 3.5 26.7 - - + +
489A GLN* 2.9 31.5 + - + +
490A ALA* 3.7 4.7 - - - +
492A ALA* 1.3 76.6 - - - +
494A GLU* 1.3 57.1 + - - +
496A LEU* 3.1 3.4 + - - +
497A GLY 2.9 23.4 + - - -
509A TYR* 3.3 46.3 - - + +
512A ALA* 3.8 21.1 - - + -
513A ALA* 4.6 0.4 - - + -
516A LEU* 3.5 32.3 - - + -
650A VAL* 5.4 2.0 - - + -
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.1 14.9 - - - +
24A LYS* 2.8 30.3 + - - +
232A GLN 5.0 1.6 - - - +
490A ALA 2.8 18.1 + - - +
491A ASP 3.5 4.6 - - - +
492A ALA 3.2 0.4 - - - -
493A LEU* 1.3 78.0 - - - +
495A GLN* 1.3 63.2 + - - +
497A GLY* 3.1 2.3 + - - -
498A TYR* 2.9 53.7 + - + -
510A LEU* 3.7 17.6 - - + +
513A ALA* 4.2 7.1 - - + +
517A ARG* 2.7 35.5 + - - -
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Residues in contact with GLN 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 4.4 9.9 - - - +
25A PRO 3.0 24.4 + - - -
26A PRO* 3.6 1.9 - - - +
27A SER* 2.9 22.8 + - - +
30A THR* 2.5 32.2 + - - +
460A TYR* 3.5 18.9 + - - +
465A TYR* 3.5 28.0 - - + -
491A ASP 3.1 19.9 + - - +
492A ALA 3.3 3.8 + - - +
494A GLU* 1.3 76.2 + - - +
496A LEU* 1.3 63.2 + - - +
498A TYR* 3.3 17.1 + - - +
499A GLN* 3.0 30.2 + - - +
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Residues in contact with LEU 496 (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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465A TYR* 3.6 41.1 - - + +
466A ARG* 3.8 24.2 - - + +
469A VAL* 3.8 21.8 - - + -
492A ALA 3.1 12.6 + - - +
493A LEU 3.1 7.2 + - - +
495A GLN* 1.3 77.0 - - - +
497A GLY* 1.3 54.7 + - - +
499A GLN* 3.4 15.3 + - + +
500A ALA* 3.1 27.7 + - - +
509A TYR* 3.7 40.3 - - + +
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Residues in contact with GLY 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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493A LEU 2.9 10.9 + - - -
494A GLU 3.1 4.2 + - - -
496A LEU* 1.3 73.7 - - - +
498A TYR* 1.4 65.8 + - - +
500A ALA* 3.2 12.1 + - - +
506A ARG* 3.4 29.0 + - - +
509A TYR* 3.5 23.7 - - - +
510A LEU* 4.0 8.1 - - - -
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Residues in contact with TYR 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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23A PRO* 3.6 0.7 - - - +
24A LYS 2.6 29.8 + - - -
26A PRO* 3.9 24.5 - - + -
30A THR* 3.6 11.0 - - + -
34A GLN* 2.9 16.9 + - - -
90A SER* 3.3 36.1 - - - +
91A ILE* 3.7 0.7 - - - -
92A ASN* 3.1 17.3 + - - +
232A GLN* 3.1 34.4 + - + +
494A GLU* 2.9 46.0 + - + -
495A GLN* 3.5 25.6 - - - +
497A GLY* 1.4 76.1 - - - +
499A GLN* 1.3 59.2 + - - +
500A ALA 3.4 0.7 + - - +
506A ARG* 4.0 3.4 - - - +
510A LEU* 4.2 8.5 - - + -
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Residues in contact with GLN 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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29A PHE* 4.2 3.8 + - - +
30A THR* 3.2 40.0 + - + +
33A ALA* 3.7 22.4 - - + +
34A GLN* 4.0 7.8 - - - +
37A VAL* 5.3 0.3 - - - +
92A ASN* 3.0 24.7 + - - +
463A GLY 5.3 0.8 + - - -
465A TYR* 3.5 26.4 - - - -
495A GLN 3.0 17.0 + - - +
496A LEU* 3.6 16.6 - - + +
497A GLY 3.2 0.2 - - - -
498A TYR* 1.3 77.9 - - - +
500A ALA* 1.3 56.1 - - - +
501A GLU 3.5 0.3 + - - -
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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