Contacts of the helix formed by residues 456 - 464 (chain C) in PDB entry 6E7P
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 456 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C TRP* 3.6 9.9 - - - +
455C ARG* 1.3 79.4 - - - +
457C LEU* 1.3 64.3 + - - +
458C SER* 3.1 21.1 + - - -
459C MET* 3.2 19.2 + - - +
460C VAL* 3.1 23.6 + - - +
88D GLN* 4.8 9.6 - - - +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C CYS* 5.1 10.3 - - + +
441C PHE* 3.7 31.9 - - + -
444C TRP* 3.5 49.1 - - + -
456C SER* 1.3 75.3 - - - +
458C SER* 1.3 57.9 + - - +
460C VAL* 3.9 6.9 - - - +
461C SER* 2.9 33.8 + - - -
81D ILE* 5.8 4.0 - - + -
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Residues in contact with SER 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B GLN* 3.1 27.6 + - - -
484B GLN* 4.3 14.0 + - - -
491B TRP* 4.3 22.7 - - - -
495B GLN* 4.8 3.2 + - - +
456C SER* 3.1 15.8 + - - -
457C LEU* 1.3 78.6 - - - +
459C MET* 1.3 56.8 + - - +
461C SER* 4.3 5.1 - - - -
462C GLU* 3.2 21.3 + - - +
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Residues in contact with MET 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B PHE* 4.7 8.3 - - + -
481B GLN* 3.3 29.4 - - + +
452C VAL* 3.9 16.2 - - + +
453C LYS* 3.2 24.2 - - - +
455C ARG* 4.7 10.3 - - + -
456C SER* 3.2 20.7 + - - +
457C LEU 3.1 0.8 - - - -
458C SER* 1.3 79.6 + - - +
460C VAL* 1.3 52.8 + - - +
461C SER 3.3 0.4 - - - -
462C GLU* 3.0 7.0 + - - +
463C CYS* 2.6 38.0 + - + +
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Residues in contact with VAL 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C TYR 4.8 1.1 - - - +
440C CYS* 3.9 25.4 - - + +
443C GLY* 5.1 2.0 - - - -
444C TRP* 4.4 15.9 - - + +
454C PHE* 3.7 40.4 - - + +
456C SER 3.1 17.7 + - - +
457C LEU* 3.9 6.7 - - - +
459C MET* 1.3 75.1 - - - +
461C SER* 1.3 58.2 + - - +
463C CYS* 4.2 5.2 - - - +
464C LEU* 2.9 52.1 + - + +
497C TYR* 5.4 0.9 - - - +
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Residues in contact with SER 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B TYR* 2.7 29.9 + - - -
436C TYR* 2.8 32.1 + - - -
440C CYS* 4.3 11.8 - - - -
457C LEU 2.9 16.4 + - - -
458C SER* 4.8 4.5 - - - -
460C VAL* 1.3 77.4 - - - +
462C GLU* 1.3 54.5 + - - +
465C PHE* 3.3 8.2 - - - +
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Residues in contact with GLU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B PHE* 4.3 10.5 - - + -
477B PHE* 3.4 53.3 - - + +
478B ALA* 4.4 1.2 + - - -
481B GLN* 3.3 22.6 + - - -
495B GLN* 3.2 29.5 + - - +
499B TYR* 3.7 11.9 - - - +
458C SER 3.2 16.0 - - - +
459C MET* 3.0 10.7 + - - +
461C SER* 1.3 76.9 - - - +
463C CYS* 1.3 60.1 + - - +
464C LEU 3.2 1.8 - - - -
465C PHE* 4.6 1.6 - - - -
466C SER* 2.9 34.4 + - - -
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Residues in contact with CYS 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B PHE* 4.1 15.0 - - + -
453C LYS* 3.7 33.2 - - - +
454C PHE* 3.5 32.8 - - + -
459C MET 2.6 20.7 + - - +
460C VAL 4.3 0.4 - - - +
462C GLU* 1.3 73.0 - - - +
464C LEU* 1.3 58.6 + - - +
466C SER* 3.7 9.0 + - - -
467C LEU* 3.2 23.4 - - - +
472C ASP* 5.5 1.9 - - - +
476C THR* 4.0 15.5 - - - -
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Residues in contact with LEU 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C TYR* 4.2 8.5 - - + -
439C TYR* 4.2 10.5 - - + +
440C CYS* 3.8 16.8 - - - -
454C PHE* 4.6 13.7 - - + -
460C VAL* 2.9 38.1 + - + +
463C CYS* 1.3 80.8 - - - +
465C PHE* 1.3 63.9 + - - +
466C SER 3.3 0.2 - - - -
467C LEU* 3.1 19.5 + - + +
468C ILE* 3.3 18.9 + - - +
497C TYR* 3.9 30.5 - - + +
498C LEU* 5.1 2.9 - - + -
501C PHE* 3.7 32.4 - - + -
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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