Contacts of the helix formed by residues 456 - 469 (chain A) in PDB entry 2XT6
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 GLU 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ILE* 3.3 10.1 - - - +
455A LEU* 1.3 86.5 + - - +
457A PRO* 1.4 68.4 - - + +
458A GLU* 3.4 3.1 - - + +
459A GLN* 3.2 42.1 + - + +
460A GLN* 3.4 9.4 + - - +
703A GLY* 5.7 0.5 - - - -
733A LYS* 3.3 24.8 + - - -
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Residues in contact with PRO 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 LEU 3.3 10.8 - - - +
456A GLU* 1.4 80.0 - - - +
458A GLU* 1.3 67.0 + - + +
460A GLN* 3.1 13.7 + - + +
461A ARG* 2.9 47.5 + - + +
380B ARG* 5.8 3.8 - - + +
402B ASP* 4.4 29.6 - - + +
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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 GLU* 5.1 2.9 - - + -
457A PRO* 1.3 79.7 - - + +
459A GLN* 1.3 58.0 + - + +
461A ARG* 3.3 26.9 + - - +
462A TRP* 3.0 29.0 + - + +
731A PHE* 4.2 21.3 - - + -
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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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454A ILE* 3.4 9.7 - - + +
456A GLU* 3.2 35.4 + - + +
457A PRO 3.2 0.4 - - - -
458A GLU* 1.3 72.6 - - + +
460A GLN* 1.3 64.2 + - - +
462A TRP* 3.5 2.4 - - - +
463A ILE* 3.2 30.5 + - - +
727A PHE* 3.4 16.7 - - + -
731A PHE* 3.5 51.0 + - + +
733A LYS* 2.6 38.7 + - - +
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Residues in contact with GLN 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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451A TYR* 3.3 42.1 - - + +
452A THR* 3.5 24.9 + - - +
454A ILE* 2.6 32.2 + - + +
455A LEU 5.2 0.2 - - - -
456A GLU 3.4 6.8 + - - +
457A PRO* 3.1 13.5 + - + +
459A GLN* 1.3 74.6 - - - +
461A ARG* 1.4 59.4 + - + +
463A ILE* 3.4 1.9 + - - -
464A GLN* 2.9 27.3 + - - +
380B ARG* 3.0 23.2 - - - +
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Residues in contact with ARG 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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457A PRO* 2.9 34.2 + - + +
458A GLU* 3.5 39.8 + - - +
460A GLN* 1.4 72.1 - - + +
462A TRP* 1.3 56.7 + - - +
464A GLN* 3.3 13.6 + - - +
465A GLU* 2.8 55.7 + - - +
401B PRO* 6.3 0.6 - - - +
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Residues in contact with TRP 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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458A GLU 3.0 17.5 + - - +
459A GLN 3.5 6.3 - - - +
461A ARG* 1.3 76.7 - - - +
463A ILE* 1.3 70.6 + - + +
465A GLU* 3.5 4.4 + - - -
466A ARG* 3.0 78.4 + - - +
707A PHE* 5.9 0.2 - + - -
723A LEU* 3.7 24.7 - - + -
726A ASP* 3.8 17.5 - - + -
727A PHE* 3.4 52.9 - + + -
730A ALA* 3.9 11.4 - - + +
731A PHE* 3.5 27.4 - + + -
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Residues in contact with ILE 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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449A VAL* 3.8 20.9 - - + -
451A TYR* 3.7 32.1 - - + -
454A ILE* 3.9 5.6 - - + -
459A GLN 3.2 12.3 + - - +
460A GLN 3.8 2.7 - - - +
462A TRP* 1.3 93.3 - - + +
464A GLN* 1.4 67.4 + - - +
466A ARG* 3.1 4.5 + - - +
467A VAL* 2.9 34.6 + - + +
705A PRO* 3.5 32.3 - - + -
707A PHE* 4.5 9.6 - - + -
723A LEU* 5.7 1.3 - - + -
727A PHE* 3.5 19.7 - - + -
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Residues in contact with GLN 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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378A ARG* 3.3 34.3 + - - +
423A GLY* 5.8 3.6 - - - -
443A TYR* 4.5 2.9 - - - -
451A TYR* 3.0 29.9 + - - +
452A THR* 6.0 0.4 - - - +
460A GLN* 2.9 18.6 + - - +
461A ARG* 3.4 12.9 - - - +
463A ILE* 1.4 75.8 - - - +
465A GLU* 1.3 60.2 + - + +
467A VAL* 4.8 1.1 - - - -
468A GLU* 3.0 55.8 + - + +
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Residues in contact with GLU 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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424A PHE* 4.0 25.0 + - + +
461A ARG* 2.8 42.5 + - - +
462A TRP* 3.8 8.1 + - - +
464A GLN* 1.3 74.8 - - + +
466A ARG* 1.3 69.6 + - - +
468A GLU* 4.1 1.4 - - - -
469A THR* 2.9 37.9 + - + +
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Residues in contact with ARG 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 TRP* 3.0 85.9 + - - +
463A ILE* 3.1 4.5 + - - +
465A GLU* 1.3 91.9 + - - +
467A VAL* 1.3 60.0 + - - +
468A GLU 3.5 0.2 - - - -
469A THR* 3.2 15.1 + - - -
471A HIS* 3.5 15.6 + - - +
719A TRP* 3.8 5.9 - - + -
723A LEU* 3.7 21.3 - - + -
726A ASP* 5.7 2.3 + - - +
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Residues in contact with VAL 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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442A ALA* 3.3 29.8 - - + +
443A TYR* 3.7 35.7 - - + +
449A VAL* 3.9 20.2 - - + -
463A ILE* 2.9 23.9 + - + +
464A GLN* 4.4 1.8 - - - +
466A ARG* 1.3 77.7 - - - +
468A GLU* 1.4 60.0 + - - +
469A THR 3.5 0.7 - - - +
471A HIS* 3.9 12.5 - - - -
707A PHE* 4.5 0.9 - - + -
719A TRP* 3.8 25.8 - - + -
723A LEU* 4.2 13.0 - - + -
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Residues in contact with GLU 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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378A ARG* 2.8 40.2 + - - -
438A VAL* 3.3 34.6 - - + +
439A LEU* 5.0 5.8 - - + -
442A ALA* 4.2 4.9 - - + -
443A TYR* 2.5 40.3 + - + +
464A GLN* 3.0 25.5 + - - +
465A GLU* 4.1 1.1 - - - +
467A VAL* 1.4 74.4 - - - +
469A THR* 1.3 63.8 + - - +
470A LYS 4.0 0.3 + - - -
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Residues in contact with THR 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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465A GLU* 2.9 26.1 + - + +
466A ARG* 3.2 14.6 + - - -
467A VAL 3.5 0.7 - - - +
468A GLU* 1.3 79.5 - - - +
470A LYS* 1.4 63.5 + - - +
471A HIS* 3.1 26.4 + - - +
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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