Contacts of the strand formed by residues 491 - 496 (chain B) in PDB entry 5FS9
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 491 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484B SER 3.4 8.5 - - - -
485B ASP* 3.6 11.0 - - - -
490B VAL* 1.3 74.8 - - - +
492B TYR* 1.3 61.8 + - - -
517B PRO* 3.6 7.1 - - - +
529B ARG* 3.7 4.5 - - - -
579B TRP* 3.7 7.6 - - - -
580B ASN* 2.8 38.3 + - - +
582B PHE* 4.0 5.6 - - - -
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Residues in contact with TYR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 4.0 24.7 - + + -
340B MET* 4.1 7.6 - - + -
344B LEU* 4.0 23.8 - - + -
348B LEU* 4.1 10.5 - - + -
351B TRP* 3.8 14.4 - - - -
352B THR* 2.6 36.0 + - - +
482B PHE* 5.5 2.0 - - + -
483B TRP* 3.2 1.6 - - - -
484B SER* 2.8 42.8 + - - +
486B LEU* 4.0 19.1 - - + +
490B VAL* 3.7 21.7 - - + +
491B GLY* 1.3 72.8 - - - -
493B GLU* 1.3 66.2 + - - +
529B ARG* 3.1 9.1 + - - +
577B VAL* 4.9 4.9 - - + -
578B LEU 3.3 8.1 - - - +
579B TRP* 3.7 22.9 - + + -
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Residues in contact with GLU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B MET* 3.8 16.5 - - + +
482B PHE* 3.3 7.6 - - - +
483B TRP* 4.1 1.1 - - + +
492B TYR* 1.3 80.8 - - - +
494B ALA* 1.3 60.6 + - - +
529B ARG* 2.7 39.6 + - - +
577B VAL* 3.2 7.0 - - - +
578B LEU* 2.8 44.3 + - + +
581B ILE 4.1 15.7 - - - +
582B PHE* 3.7 10.0 - - + -
583B ASN 4.8 5.8 + - - -
585B MET* 3.4 36.7 + - + +
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 6.3 2.0 - - + -
343B ILE* 6.1 1.6 - - + -
454B HIS* 5.6 1.7 - - + -
481B MET* 3.3 4.3 - - - +
482B PHE* 2.8 53.7 + - + +
493B GLU* 1.3 77.3 - - - +
495B ILE* 1.3 65.5 + - - +
498B VAL* 4.3 11.0 - - + -
576B ILE 3.1 10.3 - - - +
577B VAL* 4.0 15.5 - - + -
585B MET* 4.2 2.2 - - - -
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Residues in contact with ILE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B HIS* 6.4 1.1 - - - -
479B GLN* 3.7 32.3 - - + +
480B SER 3.6 14.1 - - - +
481B MET* 4.6 0.2 - - - -
494B ALA* 1.3 78.1 - - - +
496B GLY* 1.3 67.2 + - - +
498B VAL* 3.5 2.4 - - - +
575B GLY* 3.2 3.3 - - - -
576B ILE* 2.8 39.9 + - + +
585B MET* 3.6 31.0 - - + -
588B ALA* 3.9 14.8 - - + -
589B ARG* 3.9 30.3 - - + +
592B ILE* 3.9 17.5 - - + -
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Residues in contact with GLY 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 4.1 14.1 - - - -
450B ARG* 3.7 21.2 + - - +
454B HIS* 5.7 4.3 - - - -
479B GLN* 4.7 3.3 + - - -
480B SER 4.5 3.4 + - - -
495B ILE* 1.3 83.3 - - - +
497B LEU* 1.3 63.9 + - - +
498B VAL* 3.5 6.8 + - - +
574B VAL 3.4 10.1 - - - -
592B ILE* 4.3 3.8 - - - -
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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