Contacts of the helix formed by residues 456 - 464 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 4.8 10.8 - - - +
444D TRP* 3.6 8.7 - - - +
455D ARG* 1.3 79.5 - - - +
457D LEU* 1.3 64.0 + - - +
458D SER* 3.1 22.0 + - - -
459D MET* 3.2 19.8 + - - +
460D VAL* 3.1 23.2 + - - +
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Residues in contact with LEU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 5.7 4.3 - - + -
440D CYS* 5.1 10.8 - - + +
441D PHE* 3.7 31.9 - - + -
444D TRP* 3.5 50.0 - - + -
456D SER* 1.3 74.7 - - - +
458D SER* 1.3 57.6 + - - +
460D VAL* 3.9 6.5 - - - +
461D SER* 2.9 34.0 + - - -
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Residues in contact with SER 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C GLN* 3.1 27.6 + - - -
484C GLN* 4.3 14.1 + - - -
491C TRP* 4.3 22.0 - - - -
495C GLN* 4.8 3.2 + - - +
456D SER* 3.1 15.8 + - - -
457D LEU* 1.3 77.1 - - - +
459D MET* 1.3 56.5 + - - +
461D SER* 4.3 5.1 - - - -
462D GLU* 3.2 19.9 + - - +
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Residues in contact with MET 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C PHE* 4.8 7.9 - - + -
481C GLN* 3.3 29.2 - - + +
452D VAL* 3.9 15.7 - - + +
453D LYS* 3.2 25.4 - - - +
455D ARG* 4.7 10.1 - - + -
456D SER* 3.2 20.0 + - - +
457D LEU 3.1 0.4 - - - -
458D SER* 1.3 79.5 + - - +
460D VAL* 1.3 54.1 + - - +
461D SER 3.3 0.4 - - - -
462D GLU* 3.0 7.8 + - - +
463D CYS* 2.6 37.4 + - - +
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Residues in contact with VAL 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D TYR 4.8 1.3 - - - +
440D CYS* 3.9 25.4 - - + +
443D GLY* 5.1 2.5 - - - -
444D TRP* 4.4 15.0 - - + +
454D PHE* 3.7 40.6 - - + +
456D SER 3.1 18.2 + - - +
457D LEU* 3.2 6.5 + - - +
459D MET* 1.3 75.2 - - - +
461D SER* 1.3 57.8 + - - +
463D CYS* 4.2 5.4 - - - +
464D LEU* 2.9 53.2 + - + +
497D TYR* 5.4 0.4 - - - +
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Residues in contact with SER 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C TYR* 2.7 29.5 + - - -
436D TYR* 2.8 33.0 + - - -
440D CYS* 4.3 11.6 - - - -
457D LEU 2.9 17.7 + - - -
458D SER* 4.8 4.5 - - - -
460D VAL* 1.3 76.5 - - - +
462D GLU* 1.3 54.2 + - - +
465D PHE* 3.3 8.8 - - - +
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Residues in contact with GLU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C PHE* 4.4 10.5 - - + -
477C PHE* 3.4 52.5 - - + +
478C ALA* 4.4 1.0 + - - -
481C GLN* 3.2 23.0 + - - -
495C GLN* 3.2 29.2 + - - +
499C TYR* 3.7 12.3 - - - +
458D SER 3.2 16.2 - - - +
459D MET* 3.0 11.2 + - - +
461D SER* 1.3 76.8 - - - +
463D CYS* 1.3 59.5 + - - +
464D LEU 3.2 1.6 - - - -
465D PHE* 4.6 2.0 - - - -
466D SER* 2.9 34.6 + - - -
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Residues in contact with CYS 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C PHE* 4.1 14.8 - - + -
453D LYS* 3.7 33.7 - - - +
454D PHE* 3.5 32.3 - - + -
459D MET 2.6 19.8 + - - +
460D VAL 4.3 0.4 - - - +
462D GLU* 1.3 73.6 - - - +
464D LEU* 1.3 58.4 + - - +
466D SER* 3.7 7.4 + - - -
467D LEU* 3.2 23.8 - - - +
472D ASP* 5.5 2.4 - - - +
476D THR* 4.0 14.4 - - - -
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Residues in contact with LEU 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D TYR* 4.2 9.0 - - + -
439D TYR* 4.2 10.8 - - + +
440D CYS* 3.8 17.0 - - - -
454D PHE* 4.6 13.9 - - + -
460D VAL* 2.9 38.8 + - + +
463D CYS* 1.3 80.6 - - - +
465D PHE* 1.3 64.0 + - - +
466D SER 3.3 0.2 - - - -
467D LEU* 3.1 18.9 + - + +
468D ILE* 3.3 18.5 + - - +
497D TYR* 3.9 30.3 - - + +
498D LEU* 5.1 2.7 - - + -
501D PHE* 3.7 32.3 - - + -
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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