Contacts of the strand formed by residues 466 - 473 (chain F) in PDB entry 2W3S
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 GLN 466 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463F HIS* 2.7 26.1 + - - +
464F LEU 2.7 12.4 + - - +
465F ASN* 1.3 72.6 - - - +
467F ALA* 1.3 63.5 + - - +
523F ASN* 4.5 7.4 - - - +
524F THR* 5.6 1.2 - - - -
525F SER* 3.8 19.9 + - - +
535F MET* 3.4 13.5 - - - +
601F PHE* 3.8 25.9 - - + -
602F TYR 3.2 11.7 - - - +
603F ALA* 4.7 0.2 - - - -
590H TYR* 3.3 51.4 + - - -
593H ARG* 3.3 16.7 - - - +
594H ILE 5.0 1.9 + - - +
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Residues in contact with ALA 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F GLN* 1.3 77.5 - - - +
468F GLY* 1.3 59.8 + - - +
524F THR* 6.0 3.4 - - - +
535F MET* 3.2 41.7 - - + +
536F ASN* 3.8 18.4 - - - +
539F ALA* 3.9 1.8 - - - -
601F PHE* 3.0 12.4 - - - -
602F TYR 2.8 32.1 + - - +
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Residues in contact with GLY 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467F ALA* 1.3 77.0 - - - +
469F ALA* 1.3 62.2 + - - +
483F HIS* 3.5 0.3 - - - +
484F GLY* 3.1 23.7 + - - +
521F VAL* 3.7 21.0 - - - +
524F THR* 5.3 2.8 - - - +
536F ASN* 3.5 7.7 + - - +
539F ALA* 3.8 4.8 - - - +
600F GLY 3.0 10.5 - - - -
601F PHE* 4.2 4.7 - - - -
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Residues in contact with ALA 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F GLY* 1.3 74.7 - - - +
470F LEU* 1.3 63.0 + - - +
471F VAL* 4.9 2.2 - - + -
482F ASN 3.2 13.7 - - - +
483F HIS* 4.0 1.1 - - + -
521F VAL* 4.0 7.3 - - - +
539F ALA 3.8 18.4 - - - +
540F VAL* 3.8 26.2 - - + +
543F ALA* 4.8 3.8 - - + -
599F THR* 3.1 6.9 - - - +
600F GLY 2.6 36.1 + - - +
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Residues in contact with LEU 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F ALA* 1.3 75.9 - - - +
471F VAL* 1.3 62.2 + - - +
472F GLN* 3.8 28.1 - - + +
480F ALA 4.0 1.0 - - - +
481F LEU 4.0 0.3 - - - -
482F ASN* 2.7 43.3 + - + +
520F LYS* 4.0 39.0 - - + +
521F VAL* 4.2 8.5 - - + +
597F SER* 4.4 3.8 - - - +
598F ALA 3.4 7.9 - - - +
599F THR* 3.9 23.8 - - + -
470H LEU* 4.0 22.7 - - + -
519H SER 4.5 2.7 - - - +
520H LYS 4.8 0.2 - - - +
599H THR* 4.1 9.4 - - + -
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Residues in contact with VAL 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F ALA* 4.9 2.2 - - + -
470F LEU* 1.3 80.1 - - - +
472F GLN* 1.3 70.2 + - - +
479F VAL* 3.7 21.8 - - + -
480F ALA 3.5 10.1 - - - +
481F LEU* 4.1 20.6 - - + -
500F ALA* 6.0 0.4 - - + -
504F LEU* 5.0 1.1 - - + -
540F VAL* 4.6 2.0 - - - +
543F ALA* 3.7 21.8 - - + -
544F CYS* 4.3 19.7 - - - -
547F LEU* 3.8 25.5 - - + +
596F LEU 4.0 0.3 - - - +
597F SER* 3.6 1.9 - - - -
598F ALA 2.8 31.8 + - - +
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Residues in contact with GLN 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470F LEU* 3.8 20.5 - - + +
471F VAL* 1.3 79.3 - - - +
473F ILE* 1.3 63.6 + - - +
474F TYR* 3.9 20.3 + - + +
478F SER 4.0 0.2 - - - +
479F VAL* 3.3 5.5 - - - +
480F ALA* 2.8 51.9 + - + +
596F LEU 3.7 1.8 - - - -
597F SER* 2.6 24.9 + - - -
519H SER 2.6 29.2 + - - +
520H LYS* 2.9 20.9 + - - +
522H PRO* 3.4 17.7 - - + +
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Residues in contact with ILE 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471F VAL 4.3 0.2 - - - -
472F GLN* 1.3 74.4 - - - +
474F TYR* 1.3 74.8 + - - +
477F GLY* 4.0 7.0 - - - +
478F SER 3.4 11.4 - - - +
479F VAL* 3.5 21.5 - - + -
504F LEU* 4.5 8.7 - - + -
547F LEU* 3.7 37.7 - - + -
551F LEU* 4.9 8.1 - - + -
582F PHE* 4.4 17.7 - - + -
586F VAL* 3.8 22.7 - - + -
596F LEU* 3.1 27.8 + - + +
522H PRO* 4.6 0.2 - - - +
523H ASN* 2.8 22.8 + - - -
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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