Contacts of the helix formed by residues 500 - 506 (chain A) in PDB entry 5FWP
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 VAL 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A ILE* 3.8 24.9 - - + -
494A VAL 3.4 18.8 - - - +
495A ALA 4.3 0.7 - - - +
497A SER 3.2 17.0 - - - +
499A PHE* 1.3 78.0 - - - +
501A GLU* 1.3 64.2 + - + +
502A ARG 3.6 1.1 - - - -
503A VAL* 3.7 8.5 - - - +
504A ARG* 3.1 50.4 + - - +
510A VAL* 3.8 34.5 - - + -
512A TYR* 4.5 2.2 - - + +
536A VAL* 4.0 5.6 - - + -
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Residues in contact with GLU 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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496A ASN 5.3 2.5 - - - +
497A SER 3.7 14.2 - - - +
498A ALA* 3.3 24.1 + - - +
499A PHE 3.5 0.4 - - - -
500A VAL* 1.3 81.5 - - + +
502A ARG* 1.3 65.2 + - - +
504A ARG* 3.2 11.0 + - - +
505A LYS* 3.1 23.1 + - - +
583A ARG 4.0 0.4 - - - +
585A VAL* 2.9 40.6 + - + -
586A SER* 2.6 35.2 + - - -
587A SER 4.1 2.1 + - - -
674B GLN* 5.2 3.3 - - - +
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Residues in contact with ARG 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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501A GLU* 1.3 76.0 - - - +
503A VAL* 1.3 60.4 + - - +
505A LYS* 2.9 25.2 + - - +
506A ARG* 2.8 58.0 + - + +
543A LEU* 3.7 16.4 - - + -
582A ASN* 2.6 50.4 + - - +
583A ARG* 3.1 17.2 + - - +
584A LEU 3.9 11.3 + - - -
585A VAL* 3.8 14.6 - - + +
629A ASN* 5.9 0.4 + - - -
631A ASP* 4.7 11.7 + - - -
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Residues in contact with VAL 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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484A TYR* 4.5 9.0 - - + -
499A PHE 3.5 23.1 - - - +
500A VAL* 3.7 9.9 - - - +
501A GLU 3.2 0.4 - - - -
502A ARG* 1.3 77.3 - - + +
504A ARG* 1.3 58.3 + - - +
506A ARG* 3.2 7.6 + - - +
508A PHE* 3.0 46.6 + - + +
510A VAL* 3.4 27.1 - - + -
536A VAL* 3.9 9.2 - - + -
541A LEU* 3.8 13.7 - - + -
543A LEU* 3.8 25.6 - - + -
583A ARG* 5.7 0.2 - - + -
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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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460A SER* 4.2 17.0 + - - +
461A GLN* 5.4 4.9 - - - +
495A ALA* 2.6 37.4 + - - +
496A ASN* 5.2 1.2 + - - +
500A VAL* 3.1 24.9 + - + +
501A GLU* 3.5 11.7 - - - +
503A VAL* 1.3 79.3 - - - +
505A LYS* 1.3 59.2 + - + +
507A GLY* 2.9 20.0 + - - -
508A PHE 4.2 9.0 - - - +
510A VAL* 5.2 1.8 - - + -
512A TYR* 2.7 29.9 + - - -
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Residues in contact with LYS 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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501A GLU* 3.1 20.9 + - - +
502A ARG* 2.9 34.4 + - - +
504A ARG* 1.3 77.1 - - + +
506A ARG* 1.3 61.7 + - - +
507A GLY 3.2 1.0 + - - -
585A VAL* 4.3 25.4 - - + -
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A LYS* 2.9 21.4 + - - -
502A ARG* 2.8 43.9 + - + +
503A VAL 3.2 0.4 + - - -
504A ARG 3.1 0.4 - - - -
505A LYS* 1.3 79.8 + - - +
507A GLY* 1.3 59.3 + - - +
508A PHE* 3.3 31.3 + - + -
543A LEU* 4.1 11.6 - - + +
544A PRO 3.6 14.8 - - - +
545A GLU* 2.8 43.7 + - - +
546A ASP* 4.8 1.2 - - - +
549A GLU* 2.7 35.5 + - - +
582A ASN* 3.8 9.9 - - - +
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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
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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