Contacts of the helix formed by residues 451 - 464 (chain A) in PDB entry 7EHI
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 ASP 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A MET* 4.4 0.9 - - - -
448A ALA* 3.0 22.1 + - - +
449A HIS* 3.1 2.8 - - + +
450A GLU* 1.3 73.2 - - - +
452A LYS* 1.3 63.6 + - - +
453A GLN* 3.1 13.2 + - - +
454A LEU* 3.0 33.3 + - + +
455A ALA* 3.1 18.0 + - - +
579A ASN* 4.2 11.7 + - - -
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Residues in contact with LYS 452 (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 MET* 4.3 16.2 - - + -
450A GLU 3.3 6.8 + - - +
451A ASP* 1.3 74.1 + - - +
453A GLN* 1.3 57.9 + - - +
455A ALA* 3.1 2.0 + - - +
456A LYS* 2.8 47.7 + - + +
499A ASP* 3.0 40.1 + - - +
501A ASP* 3.0 33.8 + - - +
502A LEU* 4.1 12.8 - - + -
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Residues in contact with GLN 453 (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 ASP* 3.1 9.5 + - - +
452A LYS* 1.3 80.9 - - - +
454A LEU* 1.3 60.3 + - - +
456A LYS* 3.3 14.8 + - - +
457A SER* 3.0 29.8 + - - -
569A THR* 3.2 43.4 + - - +
578A PRO 5.0 2.2 - - - +
579A ASN* 2.8 38.1 - - + +
580A ASP* 4.1 6.4 + - - +
581A PHE* 3.8 2.0 - - - -
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Residues in contact with LEU 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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404A PHE* 3.7 37.5 - - + +
405A LEU* 4.0 22.9 - - + -
448A ALA* 4.2 16.8 - - + +
451A ASP* 3.0 28.9 + - + +
453A GLN* 1.3 78.3 - - - +
455A ALA* 1.3 61.6 + - - +
457A SER* 3.1 5.4 + - - -
458A ILE* 3.0 36.3 + - + +
552A ASN* 4.9 0.4 - - - +
579A ASN* 4.0 27.5 - - + +
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Residues in contact with ALA 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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444A LEU* 3.9 29.5 - - + +
445A MET* 3.8 29.6 - - + -
448A ALA* 4.4 5.3 - - + +
451A ASP 3.1 10.5 + - - +
452A LYS* 3.1 8.2 + - + +
454A LEU* 1.3 77.9 - - - +
456A LYS* 1.3 62.7 + - + +
458A ILE* 3.3 2.6 + - - +
459A LEU* 3.0 31.1 + - + +
502A LEU* 5.6 2.5 - - + -
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Residues in contact with LYS 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 LYS* 2.8 35.7 + - + +
453A GLN* 3.6 22.8 - - - +
455A ALA* 1.3 77.5 - - - +
457A SER* 1.3 56.0 + - - +
459A LEU* 3.4 4.5 + - - +
460A THR* 2.9 34.7 + - - -
501A ASP* 2.7 34.0 + - - -
502A LEU* 3.9 11.7 - - + -
505A PHE* 3.8 55.6 - - + +
569A THR* 4.7 4.9 - - + +
581A PHE* 3.8 8.3 - - + -
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Residues in contact with SER 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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404A PHE* 3.8 23.5 - - - -
453A GLN 3.0 16.4 + - - -
454A LEU* 3.1 9.1 + - - -
456A LYS* 1.3 76.0 - - - +
458A ILE* 1.3 58.6 + - - +
460A THR* 3.4 0.9 + - - -
461A PHE* 2.9 32.9 + - - +
550A PHE* 4.0 5.6 - - - -
552A ASN* 4.4 4.6 + - - -
579A ASN* 3.0 23.1 + - - +
580A ASP 5.9 0.2 - - - -
581A PHE* 3.6 19.8 - - - -
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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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400A ILE* 4.5 7.4 - - + +
401A LEU* 3.9 24.7 - - + -
404A PHE* 3.5 40.4 - - + -
405A LEU* 3.9 22.7 - - + -
436A VAL* 4.1 15.7 - - + -
444A LEU* 3.8 26.0 - - + -
448A ALA* 5.1 1.1 - - + -
454A LEU* 3.0 25.5 + - + +
455A ALA* 3.7 4.0 - - - +
457A SER* 1.3 76.5 - - - +
459A LEU* 1.3 62.0 + - - +
461A PHE* 3.9 1.4 - - - +
462A THR* 2.9 32.2 + - - +
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Residues in contact with LEU 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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436A VAL* 4.2 18.8 - - + -
444A LEU* 3.6 25.8 - - + -
455A ALA* 3.0 24.0 + - + +
456A LYS* 3.9 6.1 - - - +
458A ILE* 1.3 76.7 - - - +
460A THR* 1.3 57.9 + - - +
462A THR* 3.3 3.1 + - - -
463A PHE* 2.9 52.0 + - + -
470A SER 5.7 3.4 - - - +
471A ILE* 5.7 3.4 - - + -
475A THR* 4.3 17.3 - - + -
502A LEU* 5.1 8.1 - - + -
505A PHE* 5.1 0.2 - - + -
506A MET* 3.7 26.2 - - + -
509A LEU* 3.9 14.1 - - + -
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Residues in contact with THR 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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456A LYS 2.9 18.9 + - - -
457A SER 3.9 2.0 - - - -
459A LEU* 1.3 75.7 - - - +
461A PHE* 1.3 64.1 + - - +
463A PHE* 3.2 2.4 + - - +
464A MET* 3.1 26.5 + - + +
505A PHE* 3.2 23.9 - - - -
509A LEU* 3.9 21.9 - - + +
550A PHE* 4.1 5.6 - - + -
567A LEU* 4.5 1.1 - - + -
581A PHE* 3.3 23.4 - - + -
583A ILE* 4.0 26.2 - - + -
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Residues in contact with PHE 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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400A ILE* 4.0 14.6 - - + -
404A PHE* 3.7 27.8 - + + -
413A LEU* 3.8 24.2 - - + -
417A MET* 3.8 22.7 - - + -
457A SER 2.9 19.0 + - - +
458A ILE 3.9 2.0 - - - +
460A THR* 1.3 75.6 - - - +
462A THR* 1.3 62.5 + - - +
464A MET* 3.3 11.2 + - - +
465A GLN* 3.0 35.1 + - - -
535A ILE* 4.0 20.9 - - + -
537A LEU* 3.6 32.8 - - + -
550A PHE* 3.7 30.4 - + + -
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Residues in contact with THR 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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397A THR* 4.1 8.2 - - + +
400A ILE* 3.8 20.7 - - + +
434A ASN* 3.9 35.1 + - + +
436A VAL* 3.6 27.8 - - + +
458A ILE 2.9 19.0 + - - -
459A LEU* 3.7 4.3 - - - -
461A PHE* 1.3 77.2 - - - +
463A PHE* 1.3 62.4 + - + +
465A GLN* 3.1 30.9 + - - +
467A GLY 5.2 0.5 - - - +
469A PRO* 5.2 3.8 - - + +
513A ARG* 4.8 1.0 + - - -
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Residues in contact with PHE 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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144A VAL* 4.1 11.7 - - + -
459A LEU* 2.9 42.5 + - + +
460A THR 3.2 4.9 + - - +
462A THR* 1.3 80.4 - - + +
464A MET* 1.3 57.7 + - + +
465A GLN 3.3 0.2 - - - -
469A PRO* 3.7 39.3 - - + -
470A SER 4.9 4.7 - - - -
471A ILE* 3.9 29.6 - - + -
506A MET* 4.3 4.9 - - + -
509A LEU* 3.8 33.7 - - + -
510A VAL* 4.1 15.9 - - + -
513A ARG* 2.9 47.4 + - + +
517A ILE* 3.8 5.8 - - + +
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Residues in contact with MET 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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460A THR* 3.1 16.3 + - + +
461A PHE 3.7 7.6 - - - +
462A THR 3.1 1.0 - - - -
463A PHE* 1.3 77.6 - - + +
465A GLN* 1.3 61.1 + - - +
509A LEU* 6.2 0.9 - - + -
512A VAL* 6.3 0.2 - - + -
517A ILE* 4.0 13.9 - - + -
525A ILE* 4.4 1.9 - - - +
537A LEU* 3.8 22.7 - - + +
539A ARG* 2.9 39.9 + - + +
546A ILE* 4.1 33.7 - - + +
547A VAL 4.3 0.2 - - - -
548A GLY* 3.9 20.4 - - - +
550A PHE* 4.0 17.3 - - - -
583A ILE* 3.7 28.5 - - + -
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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