Contacts of the strand formed by residues 497 - 502 (chain B) in PDB entry 1FVU
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 GLU 497 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LYS* 2.9 38.0 + - - +
470B ASP* 2.9 27.0 + - - +
471B VAL* 3.1 13.9 + - - +
472B TRP* 2.8 36.1 + - + +
495B GLU* 3.3 22.9 + - + +
496B TYR* 1.3 76.7 - - - +
498B CYS* 1.3 57.8 + - - +
510B ILE* 3.4 13.9 - - + +
511B ILE* 3.3 16.5 - - - +
512B PRO* 3.8 23.5 - - + +
513B CYS* 3.0 5.6 - - - -
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Residues in contact with CYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TRP* 3.4 37.9 - - + -
465B TRP* 3.6 11.4 - - + -
468B LEU 3.5 5.4 - - - +
469B SER* 3.5 20.9 - - - -
471B VAL* 4.7 0.4 - - - -
496B TYR* 4.5 0.9 - - - -
497B GLU* 1.3 72.9 - - - +
499B VAL* 1.3 66.8 + - - +
509B TRP 3.7 0.2 - - - +
510B ILE* 3.4 4.0 - - - -
511B ILE* 2.8 33.0 + - - +
513B CYS* 2.0 44.0 - - - -
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 5.2 4.3 - - + -
95A VAL* 5.6 1.1 - - + -
465B TRP* 3.4 7.6 - - - -
466B ILE* 3.1 48.0 + - + +
468B LEU* 3.0 41.1 + - + -
471B VAL* 4.0 14.1 - - + -
498B CYS* 1.3 75.7 - - - +
500B ALA* 1.3 63.2 + - - +
508B TRP* 3.7 31.6 - - + -
509B TRP 3.5 5.6 - - - +
510B ILE* 4.3 15.3 - - + -
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Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B VAL* 3.4 29.4 - - + -
464B VAL 3.1 14.6 - - - +
465B TRP* 3.8 19.1 - - + -
466B ILE* 4.3 0.7 - - - +
498B CYS 4.0 0.2 + - - -
499B VAL* 1.3 77.3 - - - +
501B SER* 1.3 59.9 + - - +
507B LYS 4.0 0.2 - - - +
508B TRP* 3.5 1.9 - - - -
509B TRP* 2.8 37.1 + - + +
511B ILE* 4.0 7.9 - - + -
517B LYS* 5.2 0.9 - - + -
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Residues in contact with SER 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PHE* 4.1 8.4 - - - -
463B VAL* 3.2 4.3 - - - -
464B VAL* 2.7 40.8 + - - +
466B ILE* 3.9 21.0 - - - +
500B ALA* 1.3 74.3 - - - +
502B LYS* 1.3 66.4 + - - +
503B PRO* 3.1 12.1 - - - +
506B ASN* 3.7 22.0 + - - -
507B LYS 3.6 4.1 + - - -
508B TRP* 3.8 14.1 - - - -
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Residues in contact with LYS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B GLY* 3.1 37.4 - - - +
462B ASP 4.0 6.7 + - - +
463B VAL* 3.7 12.7 - - + +
501B SER* 1.3 71.2 + - - +
503B PRO* 1.3 63.3 - - + +
504B THR* 3.3 29.4 + - + +
505B ASN* 3.3 23.9 - - - +
506B ASN* 2.8 28.2 + - - -
507B LYS 2.9 13.8 + - - +
509B TRP* 4.5 7.6 - - + +
310C LEU* 3.9 23.8 - - + -
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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