Contacts of the helix formed by residues 503 - 518 (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 ALA 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.1 21.1 - - + -
236A ASP 3.5 23.8 - - - +
237A MET* 3.9 7.2 - - + -
238A ALA* 3.9 18.6 - - + +
404A TYR 2.8 14.4 + - - +
501A GLU 3.5 2.8 + - - -
502A ASN* 1.3 71.2 - - - +
504A GLY* 1.3 57.9 + - - +
506A ARG* 3.6 2.2 - - - +
507A ASN* 2.9 38.7 + - - +
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Residues in contact with GLY 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLN* 3.6 29.1 - - - +
237A MET* 4.5 6.1 - - - +
311A LEU* 4.7 5.4 - - - -
404A TYR 4.2 1.2 + - - -
405A HIS* 5.2 2.3 + - - +
502A ASN* 2.9 8.0 + - - -
503A ALA* 1.3 76.9 - - - +
505A TRP* 1.3 59.0 + - - +
507A ASN* 4.0 0.9 - - - +
508A SER* 2.7 37.7 + - - -
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Residues in contact with TRP 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 3.6 21.0 - - + +
386A HIS* 5.9 0.4 - + - -
407A SER* 3.5 16.0 + - - -
409A SER* 3.4 23.6 - - - -
410A HIS* 3.1 22.4 + + + +
413A ARG* 3.5 24.2 - - - -
500A ALA* 4.0 11.4 - - + -
502A ASN* 2.7 41.9 + - + +
504A GLY* 1.3 70.9 - - - +
506A ARG* 1.3 60.3 + - - +
508A SER* 3.2 6.6 + - - -
509A TYR* 2.8 67.1 + + + -
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 2.7 22.4 + - - -
91A ILE* 3.7 13.7 - - - +
92A ASN 4.8 0.4 - - - +
95A LEU* 3.7 22.6 - - + +
231A PRO 2.7 32.3 + - - -
232A GLN* 3.8 0.8 - - - +
233A GLY 2.8 30.7 + - - +
235A VAL* 3.7 21.2 - - - +
236A ASP 6.0 0.4 - - - -
497A GLY* 3.4 30.6 + - - +
498A TYR* 4.0 2.2 + - - +
500A ALA* 3.6 6.0 + - + +
502A ASN 2.8 19.8 + - - +
503A ALA* 3.6 6.3 - - - +
505A TRP* 1.3 73.9 - - - +
507A ASN* 1.3 71.1 + - - +
509A TYR* 3.7 0.9 - - - +
510A LEU* 3.0 42.9 + - + +
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Residues in contact with ASN 507 (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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221A TYR 3.1 6.7 - - - +
222A GLN 2.9 29.4 + - - +
223A TYR 3.5 12.4 + - - -
224A GLY* 3.5 11.7 - - - +
227A LEU* 3.8 8.8 - - - +
234A GLN* 3.7 26.9 - - - +
236A ASP 3.9 10.1 + - - +
237A MET* 3.5 18.6 - - - -
503A ALA 2.9 20.5 + - - +
504A GLY 4.0 0.2 - - - +
506A ARG* 1.3 80.6 - - - +
508A SER* 1.3 54.3 + - - +
511A SER* 2.7 37.8 + - - -
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.1 34.1 + - - +
222A GLN* 3.7 4.5 + - - +
311A LEU* 4.7 11.0 - - - +
504A GLY 2.7 25.1 + - - -
505A TRP* 3.4 6.3 - - - -
507A ASN* 1.3 71.7 - - - +
509A TYR* 1.3 60.7 + - - +
511A SER* 3.2 2.1 + - - -
512A ALA* 2.9 31.6 + - - +
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Residues in contact with TYR 509 (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* 5.6 2.8 - - - +
469A VAL* 5.3 2.3 - - + +
493A LEU* 3.3 50.5 - - + +
496A LEU* 3.7 38.5 - - + +
497A GLY* 3.5 20.0 - - - -
500A ALA* 4.7 1.3 - - + -
505A TRP* 2.8 64.0 + + + +
508A SER* 1.3 73.9 - - - +
510A LEU* 1.3 59.0 + - - +
512A ALA* 3.4 6.7 + - + +
513A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 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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227A LEU* 3.6 20.9 - - + +
232A GLN* 3.7 19.5 - - - +
233A GLY* 3.5 26.7 - - - +
494A GLU* 3.7 44.4 - - + +
497A GLY* 4.0 7.4 - - - -
498A TYR* 4.2 6.1 - - + -
506A ARG* 3.0 43.4 + - + +
509A TYR* 1.3 71.9 - - - +
511A SER* 1.3 60.2 + - - +
513A ALA* 3.4 5.3 + - + +
514A TYR* 2.9 27.2 + - - +
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR 3.8 2.5 + - - -
221A TYR* 3.7 28.4 + - - -
224A GLY* 3.5 20.8 - - - -
226A GLN* 5.1 9.3 + - - +
227A LEU* 3.8 12.0 - - - +
507A ASN 2.7 25.7 + - - -
508A SER 3.7 3.1 - - - -
510A LEU* 1.3 74.4 - - - +
512A ALA* 1.3 66.7 + - - +
514A TYR* 3.2 4.1 + - - +
515A GLU* 3.0 28.9 + - - +
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Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.9 17.4 - - + -
493A LEU* 3.8 17.5 - - + -
508A SER 2.9 17.6 + - - +
509A TYR* 3.6 7.0 - - - +
511A SER* 1.3 75.8 - - - +
513A ALA* 1.3 64.7 + - - +
515A GLU* 3.3 2.1 + - - +
516A LEU* 3.0 29.6 + - - +
650A VAL* 3.7 22.4 - - + +
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Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ALA* 3.4 38.5 - - + +
493A LEU* 4.4 1.3 - - + +
494A GLU* 4.2 10.1 - - + +
509A TYR 3.0 16.1 + - - +
510A LEU* 3.7 7.2 - - - +
512A ALA* 1.3 76.1 - - - +
514A TYR* 1.3 62.4 + - - +
516A LEU* 3.4 0.4 + - - -
517A ARG* 3.0 45.3 + - - +
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Residues in contact with TYR 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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226A GLN* 3.7 54.5 + - + +
227A LEU* 4.4 8.7 - - + -
228A PRO* 5.3 7.6 - - + -
510A LEU 2.9 17.3 + - - +
511A SER* 3.4 10.5 - - - +
513A ALA* 1.3 78.4 - - - +
515A GLU* 1.3 62.0 + - + +
517A ARG* 3.4 3.9 + - - +
518A HIS* 2.8 71.1 + + + +
519A GLY 4.8 3.4 - - - -
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Residues in contact with GLU 515 (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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217A ARG* 2.7 38.8 + - - -
221A TYR* 2.5 32.3 + - - +
226A GLN* 2.7 33.1 + - - +
486A ARG* 3.0 11.1 + - - -
511A SER 3.0 17.0 + - - +
514A TYR* 1.3 76.3 - - + +
516A LEU* 1.3 60.3 + - - +
519A GLY* 2.6 42.3 + - - +
520A VAL* 3.7 11.7 - - + +
521A PRO* 4.6 0.5 - - - +
646A TRP* 4.2 1.0 - - - -
649A ILE* 4.8 0.9 + - - +
650A VAL* 4.1 11.6 - - + +
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Residues in contact with LEU 516 (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 VAL* 3.9 30.3 - - + -
483A ARG* 5.8 1.9 - - - -
486A ARG* 2.8 59.0 + - + +
487A GLU* 5.6 0.5 - - - +
489A GLN* 3.4 29.2 - - + -
490A ALA* 3.8 9.2 - - + +
493A LEU* 3.5 20.6 - - + -
512A ALA 3.0 17.3 + - - +
513A ALA 3.8 3.1 - - - +
515A GLU* 1.3 76.5 - - - +
517A ARG* 1.3 62.3 + - - +
650A VAL* 3.8 25.4 - - + +
651A THR* 4.3 4.3 - - + -
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Residues in contact with ARG 517 (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 4.5 8.2 + - - +
21A THR* 3.5 49.4 - - + +
22A ALA 3.8 8.7 + - - -
23A PRO* 3.6 14.1 - - - +
24A LYS* 3.8 5.7 - - - +
483A ARG* 5.2 9.4 + - - -
487A GLU* 5.0 9.6 + - + -
490A ALA* 3.7 18.6 + - + +
491A ASP* 2.8 34.8 + - - +
494A GLU* 2.7 44.4 + - - -
513A ALA* 3.0 27.2 + - - +
514A TYR* 3.9 4.0 - - - +
516A LEU* 1.3 79.8 - - - +
518A HIS* 1.3 67.9 + - + +
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Residues in contact with HIS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 2.9 39.5 + - - +
22A ALA* 5.6 0.2 - - - -
23A PRO* 6.2 0.6 - - - +
514A TYR* 2.8 70.1 + + + +
517A ARG* 1.3 83.1 + - + +
519A GLY* 1.3 60.9 + - - +
520A VAL 5.3 0.3 - - - +
522A ARG* 5.4 4.5 + - - -
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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