Contacts of the helix formed by residues 453 - 467 (chain A) in PDB entry 3SXS
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 SER 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 MET* 1.3 80.6 - - - +
454A GLU* 1.3 59.8 + - - +
455A ASP* 3.2 16.1 + - - +
456A GLU* 3.2 29.3 + - - +
457A PHE* 3.1 27.0 + - - +
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Residues in contact with GLU 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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452A MET 3.8 1.0 + - - -
453A SER* 1.3 73.0 + - - +
455A ASP* 1.4 68.1 + - - +
457A PHE* 3.4 21.3 - - - +
458A PHE* 3.5 7.6 + - - +
480A SER* 5.3 3.6 - - - +
483A TYR* 2.8 28.8 + - - +
485A ILE* 3.7 17.8 - - - +
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Residues in contact with ASP 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 SER* 3.2 7.2 + - - +
454A GLU* 1.4 78.6 - - - +
456A GLU* 1.3 63.0 + - - +
457A PHE 3.3 0.4 - - - -
458A PHE* 3.7 9.1 + - - +
459A GLN* 3.5 28.0 + - - +
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Residues in contact with GLU 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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452A MET* 3.7 23.1 - - + +
453A SER* 3.2 36.2 + - - +
455A ASP* 1.3 75.2 - - - +
457A PHE* 1.4 64.1 + - - +
459A GLN* 3.4 8.2 + - + +
460A GLU* 3.1 31.5 + - + +
535A ARG* 5.6 4.3 + - - -
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Residues in contact with PHE 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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410A MET* 5.2 1.8 - - + -
447A ILE* 3.9 22.0 - - + -
452A MET* 3.5 19.9 - - + +
453A SER 3.1 14.6 + - - +
454A GLU* 3.4 14.1 - - - +
455A ASP 3.3 0.2 - - - -
456A GLU* 1.4 76.5 - - - +
458A PHE* 1.4 59.1 + - + +
460A GLU* 3.3 2.9 + - - +
461A ALA* 2.9 35.2 + - + +
478A VAL* 3.6 37.7 - - + -
480A SER* 4.4 6.7 - - - -
485A ILE* 3.4 38.8 - - + -
487A ILE* 3.7 25.4 - - + -
555A PHE* 4.3 7.0 - + - -
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Residues in contact with PHE 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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410A MET* 4.3 22.4 - - + +
454A GLU 3.5 9.3 + - - +
455A ASP* 4.0 9.6 - - - +
456A GLU 3.4 0.6 - - - -
457A PHE* 1.4 79.4 - - + +
459A GLN* 1.3 79.3 + - - +
461A ALA* 3.9 4.1 - - - +
462A GLN* 3.0 52.1 + - + +
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Residues in contact with GLN 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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455A ASP* 3.5 14.2 + - - +
456A GLU* 3.4 10.6 + - - +
458A PHE* 1.3 93.0 - - - +
460A GLU* 1.3 55.3 + - + +
462A GLN* 3.5 16.2 + - - +
463A THR* 2.6 40.4 + - - +
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Residues in contact with GLU 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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452A MET* 4.1 15.0 - - + -
456A GLU* 3.1 21.0 + - + +
457A PHE* 3.5 9.2 - - - +
459A GLN* 1.3 75.9 - - + +
461A ALA* 1.3 60.1 + - - +
463A THR* 3.3 8.3 + - - -
464A MET* 3.0 30.5 + - - +
535A ARG* 5.1 2.9 + - - -
554A ASP 4.4 1.7 - - - +
555A PHE* 3.6 23.4 - - + -
556A GLY* 2.6 40.6 + - - -
557A MET 4.3 0.7 + - - -
558A THR* 4.4 17.8 + - - +
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Residues in contact with ALA 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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410A MET* 3.7 29.8 - - + -
457A PHE* 2.9 25.1 + - + +
458A PHE 3.9 2.0 - - - +
460A GLU* 1.3 74.7 - - - +
462A GLN* 1.3 57.1 + - - +
464A MET* 3.4 5.7 + - - +
465A MET* 3.0 28.6 + - - +
475A PHE* 3.8 10.9 - - + -
478A VAL* 4.1 19.1 - - + -
487A ILE* 6.3 0.2 - - - -
555A PHE* 5.3 3.4 - - - -
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Residues in contact with GLN 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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410A MET* 4.0 10.2 - - - -
458A PHE* 3.0 40.5 + - + +
459A GLN* 3.7 21.8 + - - +
461A ALA* 1.3 74.3 - - - +
463A THR* 1.4 60.7 + - - +
465A MET* 3.3 15.1 + - + +
466A LYS* 3.0 31.3 + - + +
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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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459A GLN* 2.6 26.2 + - - +
460A GLU* 3.3 10.3 + - - +
462A GLN* 1.4 75.5 + - - +
464A MET* 1.3 62.3 + - - +
466A LYS* 3.3 9.0 + - + +
467A LEU* 3.1 49.5 + - + +
532A PHE* 3.8 29.6 - - + -
558A THR* 4.0 15.3 - - + +
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Residues in contact with MET 464 (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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1A PP2 4.2 10.8 - - + -
460A GLU 3.0 16.2 + - - +
461A ALA* 3.7 5.4 - - - +
462A GLN 3.3 0.2 - - - -
463A THR* 1.3 77.0 - - - +
465A MET* 1.3 61.4 + - - +
466A LYS 3.6 0.2 + - - -
467A LEU* 3.7 20.1 + - - +
468A SER* 4.5 1.7 + - - -
473A VAL* 4.1 23.9 - - + +
475A PHE* 3.9 36.8 + - + +
487A ILE* 4.5 2.0 - - - -
489A THR* 3.7 28.7 - - + -
553A SER* 5.9 0.4 - - - +
554A ASP* 3.5 26.9 - - - +
555A PHE* 3.9 32.3 - - + +
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Residues in contact with MET 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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409A HIS* 5.0 4.7 - - - -
410A MET* 3.8 47.8 - - + +
461A ALA 3.0 15.8 + - - +
462A GLN* 3.5 15.9 - - + +
463A THR 3.3 0.2 - - - -
464A MET* 1.3 76.6 - - - +
466A LYS* 1.3 63.9 + - - +
467A LEU 3.6 0.2 + - - -
468A SER* 3.6 15.1 + - - -
475A PHE* 3.6 22.4 - - + -
476A TYR 6.1 0.2 - - - +
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Residues in contact with LYS 466 (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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462A GLN* 3.0 18.9 + - + +
463A THR* 3.3 10.3 + - - +
465A MET* 1.3 77.2 - - - +
467A LEU* 1.3 58.6 + - + +
468A SER* 3.2 8.5 + - - -
526A PHE* 4.8 4.5 - - - -
530A HIS* 3.3 41.1 + - + +
532A PHE* 4.5 18.0 - - + -
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Residues in contact with LEU 467 (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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463A THR* 3.1 40.3 + - + +
464A MET 3.7 12.6 - - - +
465A MET 3.4 0.2 - - - -
466A LYS* 1.3 80.8 - - + +
468A SER* 1.3 58.1 + - - +
469A HIS 3.8 0.3 + - - -
472A LEU* 3.4 25.2 - - + +
473A VAL 5.4 1.7 - - - +
526A PHE* 3.7 23.8 - - + -
527A LEU* 3.8 23.3 - - + -
530A HIS* 3.8 29.8 - - + -
532A PHE* 4.1 18.2 - - + -
554A ASP* 4.4 10.3 - - - +
558A THR* 5.1 3.6 - - + -
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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