Contacts of the strand formed by residues 466 - 473 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590F TYR* 3.1 51.2 + - + +
593F ARG* 3.4 17.3 - - + +
594F ILE 4.9 2.1 + - - +
463H HIS* 2.9 25.7 + - - +
464H LEU 2.9 10.2 + - - +
465H ASN* 1.3 75.0 - - - +
467H ALA* 1.3 62.9 + - - +
523H ASN* 4.3 9.0 - - - +
524H THR* 5.6 1.0 - - - -
525H SER* 3.9 15.6 + - - +
535H MET* 3.6 9.0 - - - +
601H PHE* 3.6 28.5 - - + -
602H TYR 3.0 11.7 - - - +
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Residues in contact with ALA 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466H GLN* 1.3 77.2 - - - +
468H GLY* 1.3 60.2 + - - +
484H GLY* 6.3 0.2 - - - -
524H THR* 5.6 5.2 - - - +
535H MET* 3.6 40.6 - - + +
536H ASN* 3.8 17.5 - - - +
539H ALA* 3.3 2.1 - - - +
601H PHE* 3.2 9.2 - - - -
602H TYR 2.7 38.6 + - - +
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Residues in contact with GLY 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467H ALA* 1.3 77.0 - - - +
469H ALA* 1.3 60.1 + - - +
483H HIS* 3.6 1.0 - - - -
484H GLY 3.1 26.2 + - - -
521H VAL* 3.3 23.3 - - - +
524H THR* 4.9 4.6 - - - +
536H ASN* 3.7 3.7 + - - +
539H ALA* 3.7 2.9 - - - -
600H GLY 3.1 9.2 - - - -
601H PHE* 4.2 6.1 - - - -
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Residues in contact with ALA 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468H GLY* 1.3 75.2 - - - +
470H LEU* 1.3 61.2 + - - +
471H VAL* 5.3 0.2 - - + -
481H LEU* 5.1 1.6 - - + -
482H ASN 3.3 12.3 - - - +
483H HIS* 4.2 2.5 - - + -
521H VAL* 4.1 4.2 - - - +
539H ALA* 3.5 29.8 - - + +
540H VAL* 3.6 19.7 - - + +
543H ALA* 4.8 3.6 - - + -
599H THR* 3.3 5.5 - - - -
600H GLY 2.7 33.7 + - - +
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Residues in contact with LEU 470 (chain H).
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* 4.0 25.6 - - + -
519F SER 4.6 0.7 - - - +
520F LYS* 4.9 1.1 - - - +
599F THR* 4.0 6.3 - - + -
469H ALA* 1.3 75.7 - - - +
471H VAL* 1.3 62.4 + - - +
472H GLN* 4.1 22.7 - - - +
480H ALA 4.0 1.6 - - - +
481H LEU 3.9 0.3 - - - -
482H ASN* 2.8 38.2 + - + +
520H LYS* 4.0 46.2 - - + +
521H VAL* 4.2 4.4 - - + +
597H SER* 4.5 7.0 - - - +
598H ALA 3.5 17.9 - - - +
599H THR* 3.7 21.3 - - + -
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Residues in contact with VAL 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469H ALA* 5.3 1.8 - - + -
470H LEU* 1.3 77.4 - - - +
472H GLN* 1.3 69.5 + - - +
479H VAL* 3.4 28.3 - - + -
480H ALA 3.5 7.9 - - - +
481H LEU* 4.4 17.7 - - + -
500H ALA* 5.7 0.9 - - + -
504H LEU* 5.4 1.1 - - + -
540H VAL* 4.6 2.0 - - - +
543H ALA* 3.6 24.5 - - + -
544H CYS* 4.2 22.7 - - - +
547H LEU* 3.7 19.2 - - + +
597H SER* 3.4 2.4 - - - -
598H ALA 3.0 30.9 + - - +
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Residues in contact with GLN 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519F SER 2.7 30.6 + - - +
520F LYS* 2.9 23.3 + - - +
522F PRO* 3.3 21.4 - - + +
470H LEU* 4.1 14.1 - - + +
471H VAL* 1.3 78.0 - - - +
473H ILE* 1.3 62.9 + - - +
474H TYR* 3.8 12.8 + - + +
479H VAL* 3.2 8.9 - - - +
480H ALA* 3.0 47.5 + - + +
520H LYS* 5.8 0.9 - - - +
596H LEU 3.5 3.1 - - - -
597H SER* 3.2 28.3 + - - -
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Residues in contact with ILE 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F PRO* 4.6 0.7 - - - +
523F ASN* 2.9 23.0 + - - -
472H GLN* 1.3 75.9 - - - +
474H TYR* 1.3 66.5 + - - +
477H GLY 4.0 2.5 - - - +
478H SER 3.7 8.3 - - - +
479H VAL* 4.1 11.0 - - + -
504H LEU* 4.9 5.8 - - + -
547H LEU* 4.0 38.6 - - + -
551H LEU* 4.5 11.7 - - + -
582H PHE* 3.8 33.2 - - + -
586H VAL* 3.6 22.2 - - + -
596H LEU* 2.9 34.1 + - + +
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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