Contacts of the strand formed by residues 495 - 502 (chain A) in PDB entry 3SHW
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 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A LYS* 3.3 37.4 + - - +
427A PHE 3.5 19.7 - - - +
428A ARG* 4.1 26.9 + - - +
471A ASN* 4.0 9.2 + - - +
490A LEU* 5.8 0.3 - - - +
494A GLU* 1.3 86.6 - - + +
496A VAL* 1.3 70.7 + - - +
497A THR* 4.4 3.4 + - - +
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A VAL 3.6 1.6 - - - +
426A LYS* 3.3 5.2 - - - -
427A PHE* 2.8 53.9 + - + +
429A LYS* 4.1 22.9 - - + +
433A VAL* 5.1 1.8 - - + -
470A VAL* 4.0 14.1 - - + -
471A ASN* 3.4 11.0 - - - +
487A LEU* 5.4 1.3 - - + -
490A LEU* 3.7 34.3 - - + -
491A PRO* 6.0 0.7 - - + +
494A GLU 4.3 1.3 - - - +
495A GLU* 1.3 80.7 - - - +
497A THR* 1.3 65.3 + - - +
498A ILE* 4.0 14.1 - - + -
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Residues in contact with THR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A LEU* 3.7 28.0 - - + -
425A VAL 3.3 3.4 - - - +
426A LYS* 3.1 33.4 + - + +
469A ARG 3.6 1.2 - - - +
470A VAL* 3.4 2.4 - - - -
471A ASN* 2.7 49.2 + - - +
495A GLU* 4.4 3.3 + - - +
496A VAL* 1.3 73.7 - - - +
498A ILE* 1.3 61.6 + - - +
499A LEU 4.1 0.8 + - - +
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Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LYS 3.7 1.0 - - - +
424A LEU* 3.4 6.2 - - - -
425A VAL* 2.7 52.4 + - + +
427A PHE* 3.6 32.1 - - + -
433A VAL* 6.1 0.4 - - + -
435A LEU* 4.6 10.1 - - + -
461A LEU* 4.2 19.7 - - + -
467A ILE* 4.3 14.8 - - + -
469A ARG 3.3 4.7 - - - +
470A VAL* 4.1 19.3 - - + -
487A LEU* 5.2 5.4 - - + -
496A VAL* 4.0 11.9 + - + -
497A THR* 1.3 75.3 - - - +
499A LEU* 1.3 73.5 + - - +
500A ALA* 4.2 11.4 - - + +
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A MET* 3.8 33.9 - - + -
423A LYS 3.6 17.5 - - - +
424A LEU* 4.5 19.1 - - + +
468A LEU* 2.9 41.3 + - + -
469A ARG* 2.8 36.7 + - + +
497A THR* 4.1 1.2 + - - +
498A ILE* 1.3 73.5 - - - +
500A ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A MET* 3.3 9.5 - - - +
423A LYS* 2.7 52.8 + - + +
425A VAL* 6.0 0.2 - - + -
461A LEU* 3.9 27.8 - - + -
465A ASP* 4.4 8.3 - - + -
466A GLN 3.4 13.5 - - - +
467A ILE* 4.6 2.0 - - + -
468A LEU* 4.3 1.8 - - - +
498A ILE* 3.8 6.7 + - + -
499A LEU* 1.3 75.6 - - - +
501A GLN* 1.3 60.4 + - - +
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Residues in contact with GLN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A SER 3.6 17.3 + - - +
422A MET* 3.7 30.8 - - + +
423A LYS* 4.7 0.7 - - - +
465A ASP* 4.2 3.8 - - - -
466A GLN* 2.7 37.3 + - + +
468A LEU* 3.6 19.3 - - + +
500A ALA* 1.3 77.9 - - - +
502A LYS* 1.3 70.8 + - - +
503A LYS* 3.0 33.4 + - + +
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Residues in contact with LYS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A SER* 3.3 27.5 + - - +
423A LYS* 4.9 9.6 - - - +
462A GLU* 2.9 31.3 + - - +
463A GLU 4.4 8.9 + - - -
464A GLY* 5.3 0.4 - - - +
465A ASP* 3.4 17.5 + - - +
501A GLN* 1.3 76.2 - - - +
503A LYS* 1.3 70.1 + - - +
504A LYS* 3.5 29.9 - - + +
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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