Contacts of the helix formed by residues 465 - 478 (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 TYR 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER* 2.5 31.4 + - - -
29A PHE* 3.9 12.7 - - + +
30A THR* 3.8 2.9 - - - -
460A TYR* 3.5 57.1 + + - -
463A GLY* 2.9 25.0 + - - -
464A GLU* 1.3 73.4 - - - +
466A ARG* 1.3 57.8 + - - +
468A VAL* 4.2 5.2 - - - -
469A VAL* 2.9 35.2 + - - +
492A ALA* 3.8 9.0 - - + +
495A GLN* 3.5 21.7 - - + +
496A LEU* 3.6 23.8 - - + -
499A GLN* 3.5 31.6 - - - -
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Residues in contact with ARG 466 (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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386A HIS* 4.3 10.9 + - - -
387A ASN* 2.8 36.1 + - - +
464A GLU 3.3 1.2 - - - -
465A TYR* 1.3 76.7 - - - +
467A TRP* 1.3 60.2 + - - +
469A VAL* 3.4 19.4 - - - +
470A GLU* 3.6 11.8 + - - +
496A LEU* 3.8 23.1 - - + -
509A TYR* 5.6 2.7 - - - +
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Residues in contact with TRP 467 (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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446A MET* 4.8 9.6 - - + -
456A ALA* 5.6 1.0 - - - +
459A SER* 3.7 32.7 + - - -
464A GLU* 3.2 23.8 + - + +
466A ARG* 1.3 75.6 - - - +
468A VAL* 1.3 69.0 + - - +
470A GLU* 3.0 37.0 + - + +
471A VAL* 3.0 50.5 + - + +
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Residues in contact with VAL 468 (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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456A ALA* 3.7 10.1 - - - +
459A SER* 3.7 10.8 - - - -
460A TYR* 3.5 35.9 - - + +
464A GLU 2.9 25.0 + - - +
465A TYR* 3.3 5.1 + - - +
467A TRP* 1.3 74.0 - - - +
469A VAL* 1.3 58.8 + - - +
471A VAL* 4.0 6.5 - - - -
472A VAL* 2.8 48.0 + - + +
488A LEU* 4.4 14.8 - - + +
489A GLN* 5.0 0.4 - - - +
492A ALA* 3.7 22.0 - - + -
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Residues in contact with VAL 469 (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 2.9 23.8 + - - +
466A ARG* 3.4 10.8 - - - +
468A VAL* 1.3 75.3 - - - +
470A GLU* 1.3 61.0 + - - +
473A ASN* 2.9 15.9 + - - +
489A GLN* 2.8 33.8 + - - +
492A ALA* 3.6 10.1 - - + -
493A LEU* 3.5 46.7 - - + +
496A LEU* 3.8 16.6 - - + -
509A TYR* 5.3 2.5 - - + +
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Residues in contact with GLU 470 (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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466A ARG 3.8 11.6 - - - +
467A TRP* 3.0 31.0 + - + +
469A VAL* 1.3 86.1 - - + +
471A VAL* 1.3 61.4 + - - +
473A ASN* 3.6 13.2 + - - +
474A ARG* 3.6 35.3 + - - +
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Residues in contact with VAL 471 (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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446A MET* 3.5 39.7 - - + -
452A LEU* 4.0 11.7 - - + +
456A ALA* 4.5 10.3 - - + -
467A TRP* 3.0 49.8 + - + +
468A VAL* 3.6 11.0 - - - +
470A GLU* 1.3 75.8 - - - +
472A VAL* 1.3 77.6 + - + +
474A ARG* 3.1 27.9 - - + +
475A LEU 3.6 2.4 + - - -
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Residues in contact with VAL 472 (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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452A LEU* 4.2 8.7 - - + -
453A LEU* 4.8 2.9 - - + -
456A ALA* 3.4 33.4 - - + -
468A VAL* 2.8 28.0 + - + +
471A VAL* 1.3 71.7 - - + +
473A ASN* 1.3 60.4 + - - +
475A LEU* 2.9 4.9 + - + -
476A VAL* 2.9 26.3 + - - +
485A ALA* 3.4 37.2 - - + +
488A LEU* 3.9 8.7 - - + -
489A GLN* 3.2 24.7 - - + +
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Residues in contact with ASN 473 (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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435A PRO* 5.6 5.7 - - - +
469A VAL 2.9 20.6 + - - +
470A GLU* 3.6 8.2 + - - +
472A VAL* 1.3 77.4 - - - +
474A ARG* 1.3 61.4 + - - +
476A VAL* 3.3 5.1 + - - +
477A PHE* 2.9 58.0 + - - +
489A GLN* 3.2 20.2 + - - +
650A VAL* 4.4 6.2 - - - +
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Residues in contact with ARG 474 (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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435A PRO* 5.3 10.3 + - - +
438A SER* 4.3 7.7 + - - -
439A ALA* 3.2 17.5 - - + +
442A TYR* 3.3 70.0 + - + -
443A VAL* 4.3 3.4 - - + -
446A MET* 5.7 0.4 - - + -
452A LEU* 5.0 2.5 - - + -
470A GLU* 3.6 33.8 + - - +
471A VAL* 3.1 23.5 + - + +
473A ASN* 1.3 83.9 - - - +
475A LEU* 1.3 57.6 + - - +
477A PHE* 3.4 1.6 + - - -
478A ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 475 (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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443A VAL* 3.8 19.5 - - + +
449A ALA* 3.7 24.2 - - + +
452A LEU* 4.0 22.6 - - + +
453A LEU* 3.7 28.5 - - + -
471A VAL 3.6 1.2 + - - -
472A VAL* 2.9 9.0 + - + +
474A ARG* 1.3 77.0 - - - +
476A VAL* 1.3 57.0 + - - +
478A ALA 3.2 0.3 + - - -
479A GLU* 2.7 65.9 + - + +
482A ASN* 4.2 2.2 - - - +
485A ALA* 3.6 24.7 - - + -
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Residues in contact with VAL 476 (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 VAL 2.9 18.2 + - - +
473A ASN* 3.3 8.9 + - - +
475A LEU* 1.3 76.2 - - - +
477A PHE* 1.3 58.2 + - + +
479A GLU 4.1 4.9 - - - -
480A PRO* 2.9 35.6 - - + +
485A ALA* 3.9 30.7 - - + +
486A ARG* 4.0 12.3 - - + +
489A GLN* 4.0 17.9 - - + -
516A LEU* 3.9 8.3 - - + -
650A VAL 3.6 24.5 - - - +
651A THR* 3.8 16.4 - - + -
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Residues in contact with PHE 477 (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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435A PRO* 3.7 37.2 - - + +
436A GLU* 3.9 18.1 - - + +
439A ALA* 3.7 16.6 - - + -
473A ASN* 2.9 42.4 + - - +
474A ARG* 4.8 0.7 - - - -
476A VAL* 1.3 77.7 - - + +
478A ALA* 1.3 57.7 + - - +
480A PRO* 4.1 2.8 - - - +
649A ILE 3.8 14.1 - - - -
650A VAL* 3.4 26.0 - - - -
651A THR* 3.6 15.3 - - - -
652A PRO* 3.4 45.3 - - + +
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Residues in contact with ALA 478 (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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436A GLU 5.5 1.3 - - - -
439A ALA* 3.4 16.7 - - - +
440A GLY* 4.0 8.7 - - - +
443A VAL* 3.6 24.0 - - + -
474A ARG 3.0 17.9 + - - +
475A LEU 3.6 1.6 - - - +
477A PHE* 1.3 75.3 - - - +
479A GLU* 1.3 72.2 + - + +
480A PRO* 3.6 5.7 - - - +
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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