Contacts of the strand formed by residues 453 - 462 (chain A) in PDB entry 4U7C
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 GLY 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LYS* 1.3 74.2 - - - +
454A ARG* 1.3 59.9 + - - -
477A VAL* 4.0 2.5 - - - -
478A VAL* 2.6 41.9 + - - +
513A ILE* 3.7 17.8 - - - +
514A SER 3.5 13.0 - - - -
515A SER 3.7 8.3 - - - -
516A PHE* 4.3 4.2 - - - -
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Residues in contact with ARG 454 (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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453A GLY* 1.3 76.5 - - - +
455A THR* 1.3 60.6 + - - +
456A VAL* 4.2 2.7 - - - -
472A SER 3.6 1.2 - - - +
473A THR* 3.2 31.9 - - - +
474A VAL* 2.8 53.9 + - + +
475A SER* 3.9 13.1 + - - +
476A SER 3.8 11.4 - - - +
477A VAL* 4.0 13.7 - - + -
478A VAL* 5.1 1.3 - - - -
487A ILE* 6.0 0.4 - - - -
514A SER 3.1 3.4 + - - -
515A SER* 3.4 26.6 + - - +
5C G 3.5 23.6 + - - -
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Residues in contact with THR 455 (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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453A GLY 3.8 0.4 - - - -
454A ARG* 1.3 77.0 - - - +
456A VAL* 1.3 63.9 + - - +
457A THR* 4.0 14.1 - - - +
471A ALA* 4.3 11.4 - - + -
472A SER 3.3 5.4 - - - +
473A THR* 2.8 28.8 + - - +
512A ARG 3.6 0.2 - - - +
513A ILE* 3.1 8.9 - - - +
514A SER* 3.0 38.6 + - - +
515A SER* 2.7 26.1 + - - -
5C G 5.1 0.5 + - - -
6C C 4.4 4.0 - - - +
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Residues in contact with VAL 456 (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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454A ARG 5.5 0.9 - - - -
455A THR* 1.3 77.5 - - - +
457A THR* 1.3 66.4 + - - +
471A ALA* 3.2 1.9 - - - -
472A SER 2.9 31.7 + - - -
478A VAL* 4.9 3.6 - - + -
484A ILE* 4.2 22.4 - - + +
487A ILE* 3.7 38.1 - - + -
488A ALA* 4.3 20.2 - - + +
491A LEU* 3.7 5.4 - - + +
511A VAL* 4.2 18.6 - - + -
512A ARG 3.3 6.7 - - - +
513A ILE* 4.4 12.8 - - + -
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Residues in contact with THR 457 (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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455A THR* 4.0 9.0 + - - +
456A VAL* 1.3 76.2 - - - +
458A ILE* 1.3 75.8 + - - +
459A LYS* 5.6 0.4 - - + +
469A THR* 3.8 20.4 - - + +
470A ARG 3.3 15.5 - - - +
471A ALA* 3.5 14.2 - - + +
511A VAL* 3.4 3.3 - - - +
512A ARG* 2.7 61.6 + - + +
514A SER* 4.9 2.1 + - - -
7C G 5.6 0.2 - - - +
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Residues in contact with ILE 458 (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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435A CYS* 5.0 2.9 - - - -
456A VAL* 4.9 0.4 - - + -
457A THR* 1.3 79.2 - - - +
459A LYS* 1.3 61.4 + - - +
460A LEU* 3.8 30.3 - - + -
468A LYS 4.1 0.2 - - - +
469A THR* 3.2 8.2 - - - -
470A ARG* 2.9 49.1 + - + +
488A ALA* 3.6 38.1 - - + +
491A LEU* 3.9 12.6 - - + +
492A LEU* 3.7 31.9 - - + +
495A GLU* 4.7 0.9 - - + -
509A MET* 5.3 3.8 - - + -
510A GLY 3.3 9.6 - - - +
511A VAL* 4.4 5.4 - - + -
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Residues in contact with LYS 459 (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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419A GLU* 3.3 38.2 + - - +
457A THR* 5.9 0.2 - - + -
458A ILE* 1.3 74.5 - - - +
460A LEU* 1.3 70.1 + - - +
461A LYS* 4.4 0.4 - - - -
467A VAL* 3.9 13.5 - - + -
468A LYS 3.7 3.1 - - - -
469A THR* 4.1 17.5 - - + -
508A LEU* 4.2 14.6 - - + -
509A MET* 3.4 5.8 - - - +
510A GLY* 2.9 39.2 + - - +
512A ARG* 6.5 0.9 - - + -
603A PEG 3.5 42.9 + - - -
7D T 4.4 8.7 - - - +
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Residues in contact with LEU 460 (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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458A ILE* 3.8 17.7 - - + -
459A LYS* 1.3 84.0 - - - +
461A LYS* 1.3 62.5 + - - +
462A ASN 4.1 0.4 - - - -
466A GLU 3.6 1.9 - - - +
467A VAL* 3.3 3.4 - - - +
468A LYS* 2.9 51.2 + - + +
470A ARG* 5.6 1.3 - - + -
492A LEU* 4.2 16.6 - - + -
495A GLU* 3.8 33.7 - - + -
504A LEU* 4.8 7.4 - - + -
506A LEU* 3.5 34.3 - - + -
508A LEU 3.9 2.0 - - - -
509A MET* 4.3 16.2 - - + -
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Residues in contact with LYS 461 (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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49A PHE* 5.9 1.2 - - - -
421A THR* 5.5 0.2 + - - -
460A LEU* 1.3 74.7 - - - +
462A ASN* 1.3 62.9 + - - +
465A PHE* 3.6 33.0 - - - -
466A GLU 3.4 3.4 - - - -
467A VAL* 3.6 24.0 - - + -
506A LEU* 3.7 4.8 - - - -
507A ARG* 2.8 37.9 + - + +
508A LEU* 3.2 48.8 + - + +
603A PEG 3.2 31.4 + - - +
5D VKJ 4.1 24.4 + - - +
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Residues in contact with ASN 462 (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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460A LEU 4.1 0.8 - - - -
461A LYS* 1.3 76.5 - - - +
463A VAL* 1.3 60.8 + - + +
464A ASN* 3.3 14.2 + - - +
465A PHE* 2.8 20.8 + - - -
466A GLU* 2.9 58.1 + - - +
468A LYS* 6.1 3.0 - - - +
504A LEU* 6.6 0.2 - - + -
505A ARG* 3.2 20.6 - - + +
506A LEU* 4.2 7.4 - - + +
507A ARG* 3.5 8.6 - - - -
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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