Contacts of the strand formed by residues 457 - 465 (chain B) in PDB entry 4KSP
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 THR 457 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B GLN 4.5 2.9 + - - -
456B ILE* 1.3 74.6 - - - +
458B VAL* 1.3 72.8 + - - +
459B GLY* 3.5 2.1 + - - +
473B GLY* 3.1 6.4 - - - -
474B LYS* 3.0 49.7 + - + +
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Residues in contact with VAL 458 (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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456B ILE* 3.8 16.9 + - + +
457B THR* 1.3 79.0 - - - +
459B GLY* 1.3 62.7 + - - +
471B TYR* 3.4 46.7 - - + -
472B LYS 4.5 1.6 - - - -
473B GLY* 4.6 2.0 - - - -
481B VAL* 4.6 7.0 - - + -
483B MET* 3.7 29.8 - - + -
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Residues in contact with GLY 459 (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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457B THR* 3.5 4.7 + - - -
458B VAL* 1.3 79.1 - - - +
460B GLN* 1.3 64.4 + - - -
461B ARG 3.9 0.9 + - - -
471B TYR* 4.1 8.1 - - - -
472B LYS 2.9 17.9 + - - -
473B GLY* 4.9 0.2 - - - -
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Residues in contact with GLN 460 (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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459B GLY* 1.3 73.8 - - - -
461B ARG* 1.3 73.7 + - - +
462B ILE* 4.0 14.3 - - - +
471B TYR* 3.3 4.2 - - - -
472B LYS* 2.9 42.8 + - + +
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Residues in contact with ARG 461 (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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459B GLY 3.9 1.2 + - - -
460B GLN* 1.3 87.1 + - - +
462B ILE* 1.3 67.7 + - - +
463B GLY* 4.4 7.6 - - - +
464B SER* 3.4 36.7 + - - +
469B THR* 4.0 14.8 - - + +
470B VAL 4.4 0.2 - - - +
471B TYR* 3.7 28.7 - - + -
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Residues in contact with ILE 462 (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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460B GLN* 4.0 19.1 - - - +
461B ARG* 1.3 82.2 + - - +
463B GLY* 1.3 56.2 + - - +
470B VAL* 2.8 25.4 + - + +
471B TYR 4.2 1.3 - - - -
472B LYS* 3.9 18.6 - - + +
530B TRP* 3.7 32.3 - - + -
596B LEU 4.4 13.5 - - - +
901B 1SU 3.7 26.9 - - + +
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Residues in contact with GLY 463 (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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461B ARG* 3.8 9.4 - - - +
462B ILE* 1.3 82.9 - - - +
464B SER* 1.3 63.6 + - - -
469B THR* 3.4 3.4 - - - +
470B VAL* 2.8 28.4 + - - +
596B LEU* 3.4 25.9 + - - -
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Residues in contact with SER 464 (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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461B ARG* 3.4 26.8 + - - +
463B GLY* 1.3 75.8 - - - -
465B GLY* 1.3 61.4 + - - +
468B GLY 4.1 4.7 - - - -
469B THR* 2.8 29.2 + - - +
596B LEU* 3.9 17.4 - - - +
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Residues in contact with GLY 465 (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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464B SER* 1.3 79.3 + - - +
466B SER* 1.3 58.7 + - - -
467B PHE* 3.2 8.6 + - - -
468B GLY 2.7 23.3 + - - +
469B THR* 4.5 0.9 + - - -
596B LEU* 4.9 8.9 - - - +
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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