Contacts of the helix formed by residues 467 - 482 (chain A) in PDB entry 2XPH
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 ASN 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A LYS* 5.4 4.2 - - - +
456A ASP* 3.2 31.8 + - - +
459A THR* 3.3 22.6 + - + +
465A TRP 3.2 4.1 + - - +
466A LEU* 1.3 77.2 - - - +
468A ASP* 1.3 66.5 + - - +
469A GLU* 2.9 32.9 + - - +
470A ILE* 3.0 19.4 + - - +
471A ILE* 3.4 12.5 + - - +
534A TRP* 4.9 3.1 - - - -
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Residues in contact with ASP 468 (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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467A ASN* 1.3 76.7 - - - +
469A GLU* 1.3 62.6 + - - +
471A ILE* 3.3 3.5 + - - +
472A ASN* 2.7 46.2 + - - +
495A THR* 3.7 20.8 + - - +
496A PHE* 3.9 23.9 - - + -
529A HIS* 4.0 15.7 + - - -
534A TRP* 3.7 23.0 - - - -
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Residues in contact with GLU 469 (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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450A LEU* 4.2 18.3 - - + +
451A THR 4.9 5.2 - - - +
452A ILE* 3.8 11.5 - - + +
456A ASP* 3.6 31.2 - - - +
467A ASN* 2.9 23.2 + - - +
468A ASP* 1.3 77.7 + - - +
470A ILE* 1.3 68.5 + - - +
472A ASN* 3.8 1.1 - - - +
473A PHE* 2.9 25.5 + - - +
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Residues in contact with ILE 470 (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 ILE* 4.1 17.0 - - + -
456A ASP* 3.7 21.1 - - + +
457A ILE* 4.3 4.7 - - + -
459A THR* 3.5 23.1 - - - +
460A LEU* 3.8 22.0 - - + -
466A LEU* 3.5 29.4 - - + -
467A ASN* 3.0 17.1 + - - +
469A GLU* 1.3 76.1 - - - +
471A ILE* 1.3 59.1 + - - +
473A PHE* 3.2 2.8 + - - +
474A TYR* 2.8 27.4 + - - +
634A MET* 3.9 17.7 - - - -
638A ILE* 4.0 13.6 - - + +
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Residues in contact with ILE 471 (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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466A LEU* 3.9 22.4 - - + -
467A ASN 3.4 7.7 + - - +
468A ASP* 3.3 6.6 + - - +
469A GLU 3.3 0.4 - - - -
470A ILE* 1.3 80.2 - - - +
472A ASN* 1.3 64.0 + - - +
474A TYR* 3.3 6.8 + - - +
475A MET* 3.1 47.5 + - + +
495A THR* 3.8 22.7 - - + -
527A PRO* 4.4 8.7 - - + -
534A TRP* 3.4 48.2 - - + +
604A GLY* 3.9 14.8 - - - +
607A ALA* 5.9 3.1 - - + -
608A CYS* 4.2 6.7 - - - -
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Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 4.2 19.3 - - + +
468A ASP* 2.7 30.3 + - - +
469A GLU* 3.9 2.2 - - - +
471A ILE* 1.3 75.0 - - - +
473A PHE* 1.3 58.7 + - - +
475A MET* 3.3 4.5 + - - +
476A ASN* 2.8 37.1 + - - +
493A PHE 4.7 0.9 - - - +
494A ASN* 3.5 26.3 + - - +
495A THR* 2.8 50.2 + - - +
496A PHE* 4.6 4.4 - - - -
527A PRO* 4.9 1.0 - - - +
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Residues in contact with PHE 473 (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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445A SER* 3.7 18.8 - - - -
446A GLU 4.4 3.6 - - - -
447A ALA* 3.9 24.0 - - + -
448A PHE* 3.7 26.2 - + - -
450A LEU* 3.9 24.5 - - + +
452A ILE* 3.4 28.3 - - + -
469A GLU 2.9 18.0 + - - +
470A ILE* 3.4 4.0 - - - +
472A ASN* 1.3 77.3 - - - +
474A TYR* 1.3 62.6 + - - +
476A ASN* 3.4 4.9 + - - +
477A MET* 3.1 40.5 + - + +
638A ILE* 3.9 35.0 - - + -
641A ARG* 4.4 6.3 - - + -
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Residues in contact with TYR 474 (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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470A ILE 2.8 16.5 + - - +
471A ILE 3.3 4.9 + - - +
473A PHE* 1.3 78.5 - - - +
475A MET* 1.3 57.6 + - + +
477A MET* 3.3 24.6 + - + +
478A LEU* 3.1 48.8 + - + +
608A CYS* 3.6 42.0 - - + -
609A LYS* 3.5 12.7 + - + +
612A ASP* 3.3 27.0 + - - +
634A MET* 3.7 31.9 - - + -
637A GLU* 3.9 11.7 + - - -
638A ILE* 5.4 1.3 - - + +
643A LEU* 3.7 26.6 - - + +
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Residues in contact with MET 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ILE* 3.1 29.5 + - + +
472A ASN* 3.9 5.4 - - - +
473A PHE 3.3 0.2 - - - -
474A TYR* 1.3 74.6 - - + +
476A ASN* 1.3 62.8 + - - +
478A LEU* 3.1 10.5 + - - +
479A MET* 2.9 26.9 + - - +
492A ALA* 3.8 22.1 - - + +
493A PHE 5.6 1.3 - - - +
525A LEU* 3.9 29.2 - - - +
527A PRO* 4.6 15.5 - - + -
536A LEU* 4.4 11.2 - - + -
607A ALA* 4.0 7.0 - - + +
608A CYS* 3.9 37.7 - - - +
611A ALA* 3.9 13.2 - - + -
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Residues in contact with ASN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 3.7 41.0 - - + +
450A LEU* 3.8 12.1 - - - +
472A ASN* 2.8 32.1 + - - +
473A PHE 3.5 4.7 - - - +
475A MET* 1.3 76.2 - - - +
477A MET* 1.3 53.5 + - - +
479A MET* 3.0 21.9 + - - +
480A GLU* 2.7 35.5 + - - +
492A ALA* 5.5 4.4 + - - +
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Residues in contact with MET 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 4.1 10.2 - - + -
473A PHE* 3.1 28.1 + - + +
474A TYR* 3.3 35.0 + - + +
476A ASN* 1.3 73.9 - - - +
478A LEU* 1.3 57.2 + - - +
480A GLU* 3.7 11.1 - - - +
481A ARG* 2.9 28.6 + - - +
637A GLU* 3.7 25.4 - - + +
638A ILE* 3.7 23.8 - - + -
641A ARG* 3.9 20.6 - - + +
642A LYS 4.2 1.1 - - - -
643A LEU* 3.3 28.3 - - + +
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Residues in contact with LEU 478 (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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474A TYR* 3.1 40.4 + - + +
475A MET* 3.5 11.0 - - - +
476A ASN 3.1 0.6 - - - -
477A MET* 1.3 74.2 - - - +
479A MET* 1.3 66.1 + - - +
481A ARG* 3.4 32.3 + - - +
482A SER* 3.0 22.9 + - - -
490A VAL* 4.5 3.9 - - - +
525A LEU* 4.2 14.4 - - + -
611A ALA* 3.6 34.3 - - + +
612A ASP* 3.7 16.8 - - + +
615A THR* 4.0 9.4 + - + +
643A LEU* 3.8 15.9 - - + -
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Residues in contact with MET 479 (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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475A MET 2.9 12.2 + - - +
476A ASN* 3.2 23.6 - - - +
478A LEU* 1.3 74.2 - - - +
480A GLU* 1.3 65.7 + - - +
482A SER* 2.6 25.7 + - - -
483A LYS* 3.7 7.0 + - - +
490A VAL* 3.1 29.8 - - - +
491A HIS* 3.5 25.4 - - + +
492A ALA* 3.4 33.7 - - + +
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Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PHE* 3.8 21.5 - - + -
476A ASN 2.7 19.3 + - - +
477A MET* 3.7 8.3 - - - +
479A MET* 1.3 73.5 - - - +
481A ARG* 1.3 61.6 + - - +
483A LYS* 3.0 42.3 + - - +
484A GLU* 4.5 0.5 + - - +
641A ARG* 2.4 47.1 + - - +
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Residues in contact with ARG 481 (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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477A MET 2.9 19.4 + - - +
478A LEU* 3.5 16.4 + - - +
479A MET 3.2 0.2 - - - -
480A GLU* 1.3 77.6 - - - +
482A SER* 1.3 61.3 + - - +
483A LYS 3.1 1.7 + - - -
484A GLU* 3.3 38.4 + - - +
487A LEU* 3.5 18.3 - - + +
612A ASP* 2.5 36.7 + - - -
615A THR* 3.2 25.9 + - - -
616A LYS* 3.2 29.7 - - - +
643A LEU* 3.8 28.8 - - + +
644A LEU 4.5 6.3 + - - -
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Residues in contact with SER 482 (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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478A LEU 3.0 8.1 + - - -
479A MET 2.6 21.0 + - - -
481A ARG* 1.3 76.6 - - - +
483A LYS* 1.3 63.3 + - - +
484A GLU 3.3 2.3 + - - +
487A LEU* 3.9 23.6 - - - +
488A PRO 3.3 21.4 - - - +
489A SER* 3.9 8.5 - - - -
490A VAL* 3.2 37.7 + - - +
615A THR* 5.9 1.3 - - - -
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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