Contacts of the helix formed by residues 496 - 511 (chain C) in PDB entry 6DBV
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 SER 496 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C ARG* 5.5 0.7 - - - -
494C PHE 3.2 3.2 + - - -
495C LEU* 1.3 71.9 - - - +
497C CYS* 1.3 64.9 + - - +
498C SER 3.8 2.3 + - - -
499C GLN* 2.2 51.0 + - - +
500C TYR* 2.9 20.0 + - - +
996C MET* 4.3 15.9 - - - -
997C ASN* 4.3 5.4 - - - +
22E T 3.1 24.2 + - - -
23E G 3.9 10.0 + - - -
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Residues in contact with CYS 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C ARG* 4.1 26.2 - - - +
495C LEU 4.1 0.2 + - - -
496C SER* 1.3 74.8 - - - +
498C SER* 1.3 64.1 + - - +
500C TYR* 3.1 6.5 + - - +
501C HIS* 2.9 25.5 + - - +
519C LEU* 3.8 22.9 - - + +
997C ASN* 5.4 0.2 - - - -
22E T 5.8 0.2 - - + -
23E G 3.1 54.4 + - + +
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Residues in contact with SER 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C SER* 3.4 6.0 + - - -
497C CYS* 1.3 78.9 - - - +
499C GLN* 1.3 65.2 + - - +
501C HIS* 3.4 5.7 + - - +
502C LYS* 3.0 32.1 + - - +
21E G 5.4 5.6 - - - -
22E T 4.8 14.8 - - - +
23E G 4.7 1.4 + - - -
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Residues in contact with GLN 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A THR* 3.1 36.5 + - - +
494A PHE* 5.1 10.9 + - + +
495A LEU* 5.4 2.9 - - - +
992A ARG* 5.9 3.2 - - - +
996A MET* 5.8 6.3 - - - +
494C PHE 5.0 2.0 + - - -
495C LEU* 3.1 23.5 - - + +
496C SER* 2.2 51.2 + - - +
498C SER* 1.3 75.9 + - - +
500C TYR* 1.3 64.3 + - - +
502C LYS* 2.8 19.8 + - - +
503C MET* 2.9 16.9 + - - +
996C MET* 6.0 4.8 - - - +
22E T 4.9 2.9 + - - +
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Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C CYS* 2.5 36.4 - - - -
489C ILE* 6.0 1.8 - - + -
490C ARG* 3.8 28.5 - - + -
495C LEU* 3.3 20.1 - - + +
496C SER 2.9 10.7 + - - +
497C CYS* 3.4 12.1 - - - +
499C GLN* 1.3 73.5 - - - +
501C HIS* 1.3 63.1 + - - +
503C MET* 3.3 11.6 - - + +
504C TYR* 2.9 28.4 + - + +
516C PHE* 4.1 23.1 - + + -
517C GLN 3.5 17.6 + - - -
519C LEU* 4.3 18.8 - - + -
522C LEU* 3.4 32.0 - - + +
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Residues in contact with HIS 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C CYS 2.9 14.4 + - - +
498C SER* 3.8 6.3 - - - +
500C TYR* 1.3 76.0 - - - +
502C LYS* 1.3 65.0 + - - +
504C TYR* 3.3 10.5 + + - +
505C ARG* 3.0 52.8 + - + +
518C PRO* 6.3 0.2 - - - +
519C LEU* 3.5 26.5 - - + +
24F G 3.4 49.3 + - + +
25F T 3.9 17.2 + + + +
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Residues in contact with LYS 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 3.7 40.3 + - - +
493A THR* 5.2 7.0 - - - +
494A PHE* 5.7 6.9 - - - -
1025A MET* 4.6 8.5 - - + -
498C SER* 3.0 20.3 + - - +
499C GLN* 2.8 18.2 + - - +
501C HIS* 1.3 78.0 - - - +
503C MET* 1.3 57.0 + - - +
505C ARG* 3.2 14.5 + - + +
506C THR* 2.4 34.6 + - - +
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Residues in contact with MET 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 3.8 28.9 - - + +
493A THR* 5.3 9.9 - - + +
495A LEU* 6.2 2.0 - - + -
503A MET* 5.3 9.4 - - + +
516A PHE* 4.3 16.8 - - + -
495C LEU* 5.3 6.1 - - + -
499C GLN* 2.9 16.4 + - + +
500C TYR* 3.3 26.2 - - - +
502C LYS* 1.3 74.6 - - - +
504C TYR* 1.3 59.4 + - - +
506C THR* 3.2 9.8 - - - -
507C VAL* 2.9 36.0 + - + +
516C PHE* 3.3 43.5 - - + -
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Residues in contact with TYR 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C TYR* 2.9 24.2 + + + +
501C HIS* 3.4 18.4 - + - +
502C LYS 3.0 0.2 - - - -
503C MET* 1.3 80.9 - - - +
505C ARG* 1.3 73.0 + - + +
506C THR 3.0 0.7 - - - -
507C VAL* 3.3 6.6 + - + +
508C LYS* 3.0 59.2 + - + +
514C GLN* 4.4 7.2 - - + +
515C ILE 6.0 0.2 - - - -
516C PHE* 3.1 36.1 + - + -
517C GLN 3.5 14.4 - - - -
518C PRO* 3.1 44.4 - - + +
519C LEU* 5.8 1.8 - - + -
23F T 5.4 0.5 + - - -
24F G 4.0 15.7 + - - -
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Residues in contact with ARG 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A MET* 5.1 13.0 - - - +
1026A GLU 5.7 1.3 - - - -
1029A LYS 5.1 13.2 + - - -
501C HIS* 3.0 41.2 + - + +
502C LYS* 3.3 18.4 + - + +
504C TYR* 1.3 82.6 - - + +
506C THR* 1.3 70.6 + - - +
508C LYS* 4.6 4.7 - - - +
509C ALA* 3.0 31.3 + - + +
24F G 4.3 3.0 + - - +
25F T 1.7 50.0 + - - -
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Residues in contact with THR 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 4.6 5.2 - - + -
489A ILE* 3.5 26.7 - - + -
1024A PHE 4.7 0.2 - - - +
1025A MET* 3.5 46.7 - - + +
1027A ALA* 4.6 1.3 - - - +
502C LYS* 2.4 29.9 + - - +
503C MET* 3.2 12.3 - - - -
504C TYR 3.0 0.2 - - - -
505C ARG* 1.3 80.0 - - - +
507C VAL* 1.3 54.3 + - - +
509C ALA* 3.7 1.7 - - - +
510C THR* 2.1 45.4 + - - +
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Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 3.8 26.7 - - + -
489A ILE* 4.4 10.8 - - + -
515A ILE* 5.5 1.8 - - + -
516A PHE* 4.5 10.8 - - + -
503C MET* 2.9 32.7 + - + +
504C TYR* 3.4 11.2 - - + +
506C THR* 1.3 73.7 - - - +
508C LYS* 1.3 67.7 + - + +
510C THR* 3.2 13.6 + - - -
511C SER* 3.2 17.8 + - - +
513C ARG 4.5 0.6 - - - +
515C ILE* 4.1 30.1 - - + +
516C PHE* 4.6 13.7 - - + +
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Residues in contact with LYS 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C TYR* 3.0 53.7 + - + +
505C ARG* 3.9 4.3 - - - +
507C VAL* 1.3 80.1 - - + +
509C ALA* 1.3 63.3 + - - +
510C THR 3.2 1.0 + - - -
512C GLY* 3.5 15.4 + - - -
513C ARG 3.3 30.1 + - - +
514C GLN* 4.1 21.1 - - + +
515C ILE 5.5 1.1 - - - +
24F G 4.3 11.0 + - - -
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Residues in contact with ALA 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A GLU 4.4 3.8 - - - +
1027A ALA* 3.1 41.0 - - + +
1028A HIS* 5.1 2.3 - - - +
1029A LYS 5.1 6.5 - - - +
505C ARG* 3.0 19.1 + - + +
506C THR* 5.3 0.4 - - - -
508C LYS* 1.3 77.9 - - - +
510C THR* 1.3 63.2 + - - +
512C GLY 4.9 1.4 + - - -
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Residues in contact with THR 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ARG* 5.7 1.6 - - - +
481A LEU* 3.5 26.0 - - + -
485A VAL* 3.7 38.8 - - + +
489A ILE* 5.1 0.3 - - - +
1024A PHE 4.6 0.6 + - - +
1027A ALA* 4.2 9.5 - - + +
506C THR* 2.1 34.3 + - - +
507C VAL* 3.3 10.6 - - - -
508C LYS 3.1 0.8 - - - -
509C ALA* 1.3 81.2 - - - +
511C SER* 1.3 59.2 + - - +
512C GLY 3.8 1.5 + - - -
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Residues in contact with SER 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ARG* 4.8 9.4 - - - -
478A GLY* 3.6 32.5 + - - +
479A PHE 5.4 0.7 + - - -
481A LEU* 3.5 27.8 - - - +
507C VAL* 3.2 10.8 + - - +
508C LYS 3.9 1.8 - - - -
510C THR* 1.3 77.0 - - - +
512C GLY* 1.3 51.0 + - - +
513C ARG* 2.4 33.5 + - - +
515C ILE* 5.1 4.9 - - - +
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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
------------------------------------------------------------
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