Contacts of the helix formed by residues 501 - 514 (chain O) in PDB entry 6CNB
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 GLY 501 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496O ILE 4.4 0.7 - - - +
497O ALA* 2.9 19.2 + - - +
498O SER* 3.7 4.1 + - - -
499O THR 3.6 1.4 - - - -
500O LEU* 1.3 82.8 - - - +
502O PRO* 1.3 76.0 - - - +
503O SER 3.3 2.5 - - - -
504O ALA* 3.3 17.1 + - - +
505O MET 4.2 0.9 + - - -
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Residues in contact with PRO 502 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497O ALA* 3.3 8.5 - - + +
501O GLY* 1.3 83.1 - - - +
503O SER* 1.3 65.7 + - - +
504O ALA 3.0 1.2 + - - -
505O MET* 3.0 43.0 + - + +
506O ARG 4.0 2.3 + - - -
250P ASP* 4.2 6.0 - - - +
296P TYR* 6.4 3.4 - - + -
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Residues in contact with SER 503 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501O GLY 3.3 1.5 - - - -
502O PRO* 1.3 81.8 - - - +
504O ALA* 1.3 62.5 + - - +
506O ARG* 3.4 36.2 + - - +
507O LEU* 4.1 7.1 + - - +
528O MET* 5.3 0.5 - - - +
532O ASP* 3.0 28.1 + - - -
533O ILE* 5.6 2.1 - - - +
536O THR* 3.9 9.5 + - - +
250P ASP* 5.0 1.8 - - - -
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Residues in contact with ALA 504 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496O ILE* 4.7 10.3 - - + -
500O LEU* 4.0 24.4 + - + -
501O GLY 3.3 14.8 + - - +
502O PRO 3.0 1.0 + - - -
503O SER* 1.3 75.1 - - - +
505O MET* 1.3 68.9 + - - +
507O LEU* 3.0 19.4 + - - +
508O SER* 3.2 11.1 + - - -
536O THR* 3.1 25.5 + - - +
540O LEU* 5.2 5.4 - - + -
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Residues in contact with MET 505 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493O GLU 6.1 0.2 - - - -
494O TYR* 4.9 21.5 - - + +
496O ILE* 3.1 30.7 - - + +
497O ALA* 4.1 18.4 - - + -
502O PRO* 3.0 31.9 + - + +
504O ALA* 1.3 75.8 - - - +
506O ARG* 1.3 56.1 - - - +
508O SER* 2.9 9.5 + - - -
509O ARG* 2.4 39.0 + - + -
249P TYR 4.8 5.4 - - - +
250P ASP* 4.6 19.1 - - - +
251P ASP* 5.5 7.2 - - + +
296P TYR* 5.9 5.4 - - + -
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Residues in contact with ARG 506 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502O PRO 4.0 0.2 + - - -
503O SER* 3.4 29.2 + - - +
505O MET* 1.3 78.4 - - - +
507O LEU* 1.3 57.5 + - + +
509O ARG* 3.8 0.4 - - - -
510O CYS* 2.5 34.7 + - - +
526O ALA* 5.3 7.6 - - + +
527O LEU* 2.5 33.0 + - - +
528O MET* 3.8 18.0 - - - +
533O ILE* 6.0 2.8 - - - +
179P LEU* 5.3 7.1 - - - +
246P VAL* 3.5 25.2 - - - +
249P TYR* 3.3 31.9 - - + +
250P ASP* 3.0 42.0 + - - +
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Residues in contact with LEU 507 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503O SER 4.3 4.7 - - - +
504O ALA* 3.0 16.6 + - - +
506O ARG* 1.3 79.8 - - + +
508O SER* 1.3 68.4 + - - +
510O CYS* 2.9 9.1 + - - +
511O ILE* 2.6 45.4 + - + +
522O ILE* 5.2 9.9 - - + -
526O ALA* 4.8 13.7 - - + -
533O ILE* 4.0 19.3 - - + -
536O THR* 3.5 40.2 - - + +
537O LEU* 4.5 22.0 - - + +
540O LEU* 3.9 22.2 - - + -
546O VAL* 5.3 1.8 - - + -
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Residues in contact with SER 508 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492O TYR* 6.1 0.5 - - - -
496O ILE* 5.8 4.8 - - - +
504O ALA 3.2 4.6 + - - -
505O MET* 2.9 14.7 + - - -
507O LEU* 1.3 79.3 - - - +
509O ARG* 1.3 51.0 + - - -
511O ILE* 2.8 14.9 + - - +
512O ARG* 2.8 36.7 + - - +
540O LEU* 3.9 24.3 - - - +
545O SER* 5.7 3.1 - - - -
546O VAL* 5.1 4.5 - - - +
568O CYS* 4.8 3.6 - - - -
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Residues in contact with ARG 509 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303O ARG* 5.7 4.9 - - - +
493O GLU* 5.4 10.4 + - - -
505O MET* 2.4 33.9 + - + +
506O ARG 3.6 3.8 - - - +
508O SER* 1.3 68.0 + - - +
510O CYS* 1.3 55.9 + - - +
512O ARG* 2.6 54.5 + - - +
513O ASP* 3.5 11.0 + - - -
248P VAL* 4.3 11.5 + - - +
249P TYR* 3.3 40.4 - - + +
251P ASP* 3.9 23.5 + - - -
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Residues in contact with CYS 510 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506O ARG 2.5 23.6 + - - +
507O LEU* 2.9 13.9 + - - +
509O ARG* 1.3 68.4 - - - +
511O ILE* 1.3 56.8 + - + +
512O ARG 2.8 5.4 + - - -
513O ASP* 3.1 10.6 + - - +
514O ASN* 2.6 30.1 + - - +
522O ILE* 4.2 17.9 - - + -
525O THR* 3.6 22.7 - - - -
526O ALA* 4.6 7.2 - - + -
249P TYR* 3.6 36.3 - - + -
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Residues in contact with ILE 511 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507O LEU* 2.6 31.7 + - + +
508O SER* 2.8 11.4 + - - +
510O CYS* 1.3 70.7 - - - +
512O ARG* 1.3 55.8 + - - +
514O ASN* 2.6 22.6 - - - +
515O LYS* 4.3 2.4 - - - +
516O LEU 5.3 1.8 - - - +
517O VAL* 3.5 28.7 - - + -
522O ILE* 3.7 19.5 - - + -
537O LEU* 6.3 0.7 - - + -
546O VAL* 5.1 9.9 - - + -
566O PHE* 4.8 15.7 - - + -
567O ARG* 3.4 35.4 - - - +
568O CYS* 3.2 16.9 - - - -
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Residues in contact with ARG 512 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492O TYR* 4.2 25.7 - - - +
508O SER* 2.8 13.6 + - - +
509O ARG* 2.6 48.7 - - - +
510O CYS 2.8 0.8 + - - -
511O ILE* 1.3 80.1 - - - +
513O ASP* 1.3 76.7 + - - +
514O ASN 3.0 1.7 - - - +
515O LYS* 5.0 3.8 - - - +
568O CYS* 4.0 19.3 - - - +
570O GLU* 4.4 16.4 - - - +
574O TYR* 4.1 18.7 + - - -
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Residues in contact with ASP 513 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509O ARG* 4.6 9.2 + - - -
510O CYS 3.1 6.3 + - - +
512O ARG* 1.3 93.8 - - - +
514O ASN* 1.3 62.7 + - - +
515O LYS* 4.1 12.1 - - - -
245P GLU* 5.5 2.1 - - - +
248P VAL* 4.9 8.7 - - - +
249P TYR* 3.5 30.2 + - - +
255P LYS* 6.1 1.0 - - - -
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Residues in contact with ASN 514 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 4.9 20.0 - - + +
510O CYS* 2.6 44.3 - - - +
511O ILE* 2.6 29.8 - - - +
512O ARG 3.0 2.1 - - - +
513O ASP* 1.3 81.5 - - - +
515O LYS* 1.3 58.2 + - - +
517O VAL* 3.5 31.7 - - + +
521O ILE* 5.5 1.2 - - - +
522O ILE* 4.7 0.4 - - - +
525O THR* 4.8 10.1 + - - +
249P TYR* 4.8 4.2 + - - -
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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