Contacts of the helix formed by residues 460 - 470 (chain D) in PDB entry 5MNJ
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 CYS 460 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437D CYS* 3.3 8.2 - - + +
443D ARG* 3.2 35.2 - - + +
444D PRO 3.3 18.1 + - - +
446D ASP* 3.3 9.4 - - - +
447D GLY 3.4 0.9 - - - -
459D THR* 1.3 81.0 + - - +
461D PHE* 1.3 66.1 + - - +
462D HIS* 3.7 3.4 - - + -
463D CYS* 3.3 19.6 + - - -
464D ALA* 3.1 19.6 + - - +
501D ZN 2.3 34.8 - - - -
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Residues in contact with PHE 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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454C LYS* 4.4 11.9 - - + -
446D ASP* 2.9 17.1 + - - +
447D GLY* 3.1 9.5 - - - +
460D CYS* 1.3 72.4 - - - +
462D HIS* 1.3 73.1 + + + +
464D ALA* 3.4 0.9 + - - +
465D ARG* 2.9 65.6 + - - +
484D VAL* 3.8 23.8 - - + -
485D ILE* 3.6 10.8 - - - -
486D LYS* 3.4 56.3 - - + +
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Residues in contact with HIS 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D ARG* 4.0 39.5 - - - +
460D CYS* 3.3 2.9 - - + -
461D PHE* 1.3 86.6 - + + +
463D CYS* 1.3 66.1 + - - +
465D ARG* 3.4 31.6 + - - +
466D ARG* 3.0 51.5 + - - +
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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
----------------------------------------------------------
437D CYS* 3.9 5.4 - - - -
439D LEU* 3.9 22.9 - - + -
440D CYS* 3.8 18.2 - - - -
443D ARG* 3.8 7.0 - - - -
459D THR* 4.2 2.2 - - - -
460D CYS* 3.3 6.0 - - - +
462D HIS* 1.3 77.5 - - - +
464D ALA* 1.3 58.5 + - - +
466D ARG* 3.0 13.4 + - - +
467D LEU* 2.9 34.5 + - - +
501D ZN 2.5 34.3 - - - -
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Residues in contact with ALA 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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447D GLY* 4.3 6.1 - - - -
449D ILE* 3.8 18.6 - - + -
459D THR* 3.4 19.4 + - - +
460D CYS 3.1 13.8 + - - +
461D PHE 3.8 0.4 - - - +
463D CYS* 1.3 76.5 - - - +
465D ARG* 1.3 62.9 + - - +
467D LEU* 3.4 10.6 + - - +
468D LYS 3.1 17.7 + - - -
481D ILE* 4.8 1.6 - - - +
484D VAL* 3.4 32.2 - - + +
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Residues in contact with ARG 465 (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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461D PHE* 2.9 50.3 + - - +
462D HIS* 3.7 30.9 + - - +
463D CYS 3.2 0.2 - - - -
464D ALA* 1.3 78.4 - - - +
466D ARG* 1.3 58.3 + - + +
468D LYS* 3.7 7.9 + - + +
469D LYS* 3.2 29.3 + - + +
484D VAL* 3.9 13.9 - - + +
117E ASP* 5.3 12.4 + - - -
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Residues in contact with ARG 466 (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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443D ARG* 4.1 20.0 - - - +
462D HIS* 3.0 42.8 + - - +
463D CYS* 3.0 11.7 + - - +
465D ARG* 1.3 78.5 - - + +
467D LEU* 1.3 64.9 + - - +
469D LYS* 3.4 10.9 + - + +
470D ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 467 (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 LEU* 4.1 22.9 - - + -
449D ILE* 4.3 11.9 - - + -
459D THR* 4.7 2.0 - - + -
463D CYS 2.9 19.1 + - - +
464D ALA* 3.7 6.3 - - - +
466D ARG* 1.3 74.0 - - - +
468D LYS* 1.3 66.9 + - - +
470D ALA* 3.2 7.9 + - + -
472D ALA* 3.1 44.4 + - + +
473D SER 5.0 0.4 - - - +
475D PRO* 3.9 35.2 - - + -
481D ILE* 4.2 10.1 - - + -
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Residues in contact with LYS 468 (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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464D ALA 3.1 14.6 + - - +
465D ARG* 3.7 10.1 - - + +
467D LEU* 1.3 79.3 - - - +
469D LYS* 1.3 58.4 + - - +
471D GLY* 2.9 21.5 + - - -
472D ALA 4.6 2.2 - - - -
481D ILE* 3.4 38.6 + - + +
482D GLN 3.3 25.2 + - - -
483D LEU* 5.2 2.0 - - - +
484D VAL* 4.0 17.5 - - + +
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Residues in contact with LYS 469 (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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465D ARG* 3.2 17.1 + - + +
466D ARG* 3.7 11.2 - - + +
467D LEU 3.2 0.4 - - - -
468D LYS* 1.3 80.6 - - + +
470D ALA* 1.3 59.9 + - - +
471D GLY 3.2 0.9 + - - -
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Residues in contact with ALA 470 (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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466D ARG 3.0 16.9 + - - +
467D LEU* 3.2 7.4 + - + +
469D LYS* 1.3 74.9 - - - +
471D GLY* 1.3 58.1 + - - +
472D ALA* 3.1 9.2 + - + +
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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