Contacts of the strand formed by residues 536 - 540 (chain B) in PDB entry 4YFF
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 ALA 536 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B LEU* 4.7 10.8 - - + -
463B ILE* 4.8 6.5 - - + -
489B ILE* 4.0 16.6 - - + -
490B LYS 3.3 11.7 - - - +
491B ARG* 4.5 6.5 - - + -
492B TYR* 5.0 0.4 - - - +
506B PHE* 3.7 4.6 - - - -
527B ALA* 3.2 8.4 - - - +
528B CYS* 2.9 37.7 + - + +
534B GLN 3.3 7.6 + - - +
535B PHE* 1.3 77.1 - - - +
537B ILE* 1.3 64.7 + - - +
538B VAL* 5.0 0.9 - - - -
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Residues in contact with ILE 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 3.2 3.5 - - - -
490B LYS* 2.6 47.0 + - + +
492B TYR* 4.2 5.8 - - + -
506B PHE* 3.8 24.9 - - + -
509B GLU* 3.6 35.4 - - + +
510B VAL* 3.9 21.1 - - + -
513B LEU* 3.6 25.1 - - + -
524B PHE* 4.6 2.5 - - + -
526B GLY 3.9 2.5 - - - -
527B ALA* 4.2 2.7 - - + -
536B ALA* 1.3 78.9 - - - +
538B VAL* 1.3 66.2 + - - +
539B THR* 4.4 3.4 - - + -
801B 4CV 3.5 19.8 - - - +
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU* 3.5 26.7 - - + -
463B ILE* 4.1 18.4 - - + -
482B CYS* 4.5 5.6 - - + -
487B VAL* 3.6 39.0 - - + -
488B ALA 3.4 4.3 - - - +
489B ILE* 4.4 10.3 - - + -
524B PHE* 3.5 2.9 - - - -
525B VAL* 2.9 31.1 + - + -
526B GLY 2.9 17.2 + - - +
527B ALA* 5.0 1.6 - - - -
536B ALA 5.0 0.7 - - - -
537B ILE* 1.3 79.6 - - - +
539B THR* 1.3 69.4 + - - +
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Residues in contact with THR 539 (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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487B VAL* 3.2 10.9 - - - +
488B ALA* 2.9 22.0 + - - +
513B LEU* 4.7 5.2 - - + -
522B ILE* 3.7 20.8 - - + +
523B GLN 3.2 15.0 - - - +
524B PHE* 4.3 9.6 - - + -
525B VAL* 3.8 7.4 - - - -
537B ILE* 4.4 7.6 - - + -
538B VAL* 1.3 81.0 - - - +
540B GLN* 1.3 73.4 + - - +
801B 4CV 2.8 42.5 + - - +
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Residues in contact with GLN 540 (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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486B ILE 4.5 3.8 - - - -
487B VAL* 4.7 1.1 - - - +
488B ALA* 3.8 1.4 - - - +
521B VAL 4.2 2.8 - - - +
522B ILE* 3.5 23.8 - - + +
523B GLN* 2.9 57.5 + - + +
525B VAL* 3.9 6.5 - - + +
539B THR* 1.3 88.9 + - - +
541B TYR* 1.3 63.3 + - - +
542B ILE* 4.0 12.8 - - + +
597B TYR* 3.2 30.6 + - - -
603B VAL* 4.8 2.1 - - - +
801B 4CV 3.6 10.6 - - - -
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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