Contacts of the strand formed by residues 455 - 465 (chain A) in PDB entry 4HXG
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 ALA 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A LYS* 3.7 2.8 - - - +
380A VAL* 3.7 6.7 - - + -
409A TYR* 3.3 25.3 - - + -
448A PHE* 3.6 31.2 - - + -
449A LEU* 4.0 8.1 - - + +
452A GLU 3.0 14.9 + - - +
453A PRO 3.6 9.7 - - - +
454A GLN* 1.3 78.1 - - - +
456A ASP* 1.3 61.6 + - - +
457A ARG* 3.4 7.3 + - - +
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Residues in contact with ASP 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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377A LYS* 3.8 25.9 - - + +
378A ALA 3.0 18.3 + - - +
379A PRO* 4.7 0.4 - - + -
380A VAL* 4.3 1.6 - - - +
454A GLN 3.5 0.8 + - - -
455A ALA* 1.3 71.0 - - - +
457A ARG* 1.3 63.5 + - - +
458A GLU* 2.7 27.3 + - - +
459A ARG* 2.9 58.4 + - - +
460A ILE* 3.7 3.6 - - - +
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU* 3.7 16.6 + - - -
449A LEU* 3.4 52.5 + - + +
453A PRO* 6.4 0.4 - - - +
455A ALA 3.4 7.8 + - - +
456A ASP* 1.3 73.2 + - - +
458A GLU* 1.3 77.4 + - + +
459A ARG 3.5 0.2 - - - -
460A ILE* 3.4 24.8 - - + +
481A LEU* 4.5 13.6 - - + +
483A LYS* 4.7 1.2 + - - -
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Residues in contact with GLU 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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456A ASP* 2.7 17.0 + - - +
457A ARG* 1.3 94.2 - - + +
459A ARG* 1.3 61.2 + - + +
460A ILE 3.9 0.4 - - - -
483A LYS* 3.0 52.5 + - - +
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Residues in contact with ARG 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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376A GLU* 6.1 0.2 - - - +
377A LYS* 3.2 31.7 + - - +
379A PRO* 3.5 30.5 - - + +
380A VAL 2.9 22.7 + - - -
456A ASP* 2.9 36.7 + - - +
458A GLU* 1.3 82.5 - - + +
460A ILE* 1.3 60.6 + - - +
483A LYS* 4.3 5.4 - - + -
604A LEU* 3.2 22.8 - - + +
605A LYS* 3.0 41.6 + - - +
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Residues in contact with ILE 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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380A VAL* 3.3 17.7 - - + +
382A VAL* 4.2 10.8 - - + -
445A ILE* 4.7 7.6 - - + -
449A LEU* 4.0 26.9 - - + -
456A ASP 3.7 5.8 - - - +
457A ARG* 3.4 31.0 - - + +
458A GLU 3.9 2.4 + - - -
459A ARG* 1.3 79.9 - - - +
461A GLY* 1.3 66.2 + - - +
481A LEU* 4.3 22.8 + - + +
482A PHE* 3.1 30.0 - - + +
483A LYS* 3.0 25.2 + - - +
604A LEU* 3.5 4.9 - - - +
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Residues in contact with GLY 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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380A VAL 2.7 14.2 + - - +
381A ILE* 4.3 2.5 - - - -
382A VAL* 2.7 30.6 + - - +
460A ILE* 1.3 74.7 - - - +
462A ILE* 1.3 63.0 + - - +
482A PHE* 4.1 1.3 - - - -
484A ALA 3.1 14.6 - - - -
600A PHE* 4.4 4.0 - - - -
604A LEU* 3.3 19.8 - - - +
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Residues in contact with ILE 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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382A VAL* 3.3 18.2 - - + +
384A VAL* 3.9 24.0 - - + -
438A PHE* 5.9 1.1 - - + -
441A ILE* 5.1 4.9 - - + -
461A GLY* 1.3 75.6 - - - +
463A THR* 1.3 65.4 + - - +
471A MET* 4.5 7.2 - - + +
472A THR* 3.7 18.7 - - + +
475A ALA* 3.8 22.7 - - + -
476A LEU* 4.2 11.9 - - + -
482A PHE* 3.6 39.9 - - + -
484A ALA 3.1 8.4 + - - +
485A GLY* 3.0 7.4 - - - -
486A ILE 3.0 22.0 + - - -
600A PHE* 4.1 3.0 - - - -
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Residues in contact with THR 463 (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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381A ILE* 3.8 14.1 - - + -
382A VAL 2.8 14.8 + - - +
383A PHE* 3.5 31.4 - - + +
384A VAL* 3.0 25.6 + - - +
462A ILE* 1.3 76.7 - - - +
464A GLY* 1.3 60.1 + - - +
472A THR* 3.3 6.9 + - - -
486A ILE* 2.9 20.7 + - - +
488A GLU* 4.1 4.2 + - - -
596A PHE* 3.4 20.7 - - + -
600A PHE* 4.0 11.7 - - - -
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Residues in contact with GLY 464 (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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383A PHE* 6.1 0.9 - - - -
384A VAL 3.6 10.1 - - - -
392A TYR* 5.8 0.9 - - - -
463A THR* 1.3 81.8 + - - +
465A ILE* 1.3 63.5 + - - -
468A GLY 3.3 14.4 - - - -
469A GLY* 3.3 11.2 - - - -
472A THR* 3.2 5.5 + - - -
486A ILE 3.3 1.4 + - - +
488A GLU* 3.0 28.3 + - - +
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Residues in contact with ILE 465 (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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384A VAL 4.2 2.4 + - - -
386A GLY* 3.7 9.9 + - - -
397A LYS* 4.2 21.3 - - - +
464A GLY* 1.3 77.6 - - - -
466A ALA* 1.3 76.2 + - + +
468A GLY* 2.9 15.6 + - - -
469A GLY 3.4 0.4 - - - -
488A GLU* 3.2 30.7 - - + +
489A ASN* 4.2 12.3 - - + +
578A HIS* 4.5 14.4 - - + +
579A GLY* 6.1 0.2 - - - -
581A SER* 3.6 28.5 - - - +
592A ARG* 4.4 6.5 - - - +
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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