Contacts of the helix formed by residues 498 - 510 (chain A) in PDB entry 5W6V
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 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A PHE* 3.5 14.0 - - - -
493A ALA* 3.8 11.3 - - - +
494A GLN 3.5 13.4 + - - -
495A GLY 2.7 22.2 + - - -
496A ALA 3.1 0.2 - - - -
497A ASP* 1.3 78.4 - - - +
499A VAL* 1.3 62.9 + - - +
500A GLU 3.4 1.3 - - - -
501A PRO* 3.7 6.6 - - - +
502A MET* 3.2 27.0 + - - +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PHE* 3.4 31.0 - - + -
495A GLY 4.2 1.3 - - - +
496A ALA* 3.6 10.5 - - - +
498A SER* 1.3 77.7 - - - +
500A GLU* 1.3 57.8 + - - +
502A MET* 4.2 7.6 - - - -
503A PHE* 2.6 48.4 + - + +
526A VAL* 4.1 15.7 - - + -
529A GLU* 3.4 43.7 - - + +
530A VAL* 4.1 11.4 - - + -
533A VAL* 3.8 9.2 - - + -
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Residues in contact with GLU 500 (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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496A ALA 4.9 0.2 + - - -
497A ASP 4.6 1.3 + - - +
499A VAL* 1.3 82.2 - - + +
501A PRO* 1.3 61.1 - - + +
504A ARG* 2.7 69.1 + - + +
529A GLU* 4.6 2.9 - - - +
532A ARG* 3.5 17.0 + - - -
533A VAL* 3.8 18.6 - - + -
537A LEU* 3.5 25.7 - - + +
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Residues in contact with PRO 501 (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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497A ASP 3.4 23.6 - - - +
498A SER* 3.7 8.3 - - - +
500A GLU* 1.3 93.4 - - + +
502A MET* 1.3 55.7 + - - +
504A ARG* 3.8 6.3 - - + +
505A HIS* 3.0 28.2 + - - +
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Residues in contact with MET 502 (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 ALA* 3.8 15.0 - - + -
454A PHE* 3.5 31.6 - - + -
489A PHE* 4.0 37.0 - - + -
491A LYS* 5.4 4.5 - - - +
493A ALA* 4.3 12.8 - - + -
498A SER* 3.2 22.1 + - - +
499A VAL* 4.2 1.8 - - - -
501A PRO* 1.3 74.0 - - - +
503A PHE* 1.3 81.4 + - + +
505A HIS* 3.2 8.5 + - - +
506A LEU* 2.8 32.3 + - + +
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Residues in contact with PHE 503 (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 ALA* 4.6 1.1 - - + -
454A PHE* 5.5 0.4 - + - -
499A VAL* 2.6 27.2 + - + +
502A MET* 1.3 92.2 - - + +
504A ARG* 1.3 66.0 + - - +
506A LEU* 3.8 9.3 - - + +
507A LYS* 3.1 19.2 + - - +
516A ILE* 4.0 29.8 - - + -
518A VAL* 3.9 25.1 - - + -
530A VAL* 4.2 27.1 - - + -
533A VAL* 3.6 21.1 - - + -
534A GLY* 4.6 6.1 - - - -
538A LEU* 3.5 17.4 - - + +
540A MET* 3.6 15.3 - - + +
542A THR* 4.0 17.5 - - + -
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Residues in contact with ARG 504 (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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500A GLU* 2.7 59.9 + - + +
501A PRO* 3.8 7.2 - - + +
503A PHE* 1.3 72.5 - - - +
505A HIS* 1.3 60.5 + - - +
507A LYS* 3.5 3.6 + - - +
508A ASN* 3.3 34.9 + - - +
537A LEU* 3.8 22.6 + - - +
538A LEU* 3.5 32.1 - - + +
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Residues in contact with HIS 505 (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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489A PHE* 4.3 27.9 - + - -
491A LYS* 5.7 2.5 - - - -
501A PRO 3.0 20.3 + - - +
502A MET* 3.4 9.0 + - - +
503A PHE 3.2 0.2 - - - -
504A ARG* 1.3 74.5 - - - +
506A LEU* 1.3 61.8 + - - +
508A ASN* 3.1 7.2 + - + +
509A THR* 2.8 68.4 + - + +
510A TYR* 4.7 2.9 - + - -
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Residues in contact with LEU 506 (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 ALA* 4.2 7.9 - - + -
452A ALA* 5.8 0.4 - - + -
489A PHE* 3.4 47.8 - - + -
502A MET* 2.8 30.8 + - + +
503A PHE* 3.3 16.6 + - + +
505A HIS* 1.3 72.9 - - - +
507A LYS* 1.3 62.5 + - - +
510A TYR* 3.1 49.3 + - + +
513A LEU* 4.1 12.8 - - + +
516A ILE* 3.6 32.8 - - + -
540A MET* 4.3 4.5 - - + -
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Residues in contact with LYS 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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503A PHE 3.1 16.5 + - - +
504A ARG* 3.9 5.8 - - - +
506A LEU* 1.3 76.6 - - - +
508A ASN* 1.3 65.2 + - - +
510A TYR 4.2 9.9 - - - +
511A SER* 5.6 1.0 - - - -
513A LEU* 5.2 1.3 - - - -
538A LEU* 3.3 40.9 + - + +
539A GLY 5.2 1.8 - - - -
540A MET* 3.7 22.8 - - + +
847A HIS* 4.3 14.6 + - - -
849A ASP* 4.9 8.1 + - - -
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Residues in contact with ASN 508 (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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504A ARG* 3.3 24.1 + - - +
505A HIS* 3.1 8.0 + - + +
507A LYS* 1.3 87.0 - - - +
509A THR* 1.3 63.1 + - - +
510A TYR 5.2 0.2 - - - -
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Residues in contact with THR 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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505A HIS* 2.8 48.7 + - + +
508A ASN* 1.3 76.9 - - - +
510A TYR* 1.3 96.6 + - + +
511A SER* 3.7 3.0 + - - -
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Residues in contact with TYR 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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448A VAL* 4.5 5.4 - - + -
488A CYS* 3.1 53.3 + - + -
489A PHE* 3.6 19.3 - + + -
505A HIS* 4.7 4.3 - + - -
506A LEU* 3.1 47.2 + - + +
507A LYS* 4.2 8.8 - - - +
508A ASN 5.2 0.2 - - - -
509A THR* 1.3 103.7 - - + +
511A SER* 1.3 63.7 + - - +
512A GLY 3.8 0.2 + - - -
513A LEU* 3.6 24.4 + - + +
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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