Contacts of the helix formed by residues 454 - 463 (chain D) in PDB entry 1KPS
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 LYS 454 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D LEU 5.3 1.8 - - - +
452D GLY 3.2 2.3 + - - -
453D PRO* 1.3 75.3 - - + +
455D VAL* 1.3 52.3 - - - +
456D SER 2.9 5.8 - - - -
457D VAL* 2.6 59.6 + - + +
458D LEU* 2.8 26.3 + - + +
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Residues in contact with VAL 455 (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 LEU* 4.1 10.1 - - + -
439D PHE* 5.5 0.4 - - + -
448D LEU* 3.6 30.3 - - + +
451D LEU* 3.5 32.9 + - + -
452D GLY 3.1 18.8 + - - +
453D PRO* 2.9 6.7 + - + +
454D LYS* 1.3 76.2 - - - +
456D SER* 1.3 69.6 + - - +
458D LEU* 3.8 13.1 - - - +
459D ILE* 3.5 29.5 + - + +
491D ALA* 5.5 8.3 - - + +
495D ALA* 5.1 7.6 - - + -
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Residues in contact with SER 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D PRO 3.4 12.1 + - - -
454D LYS 2.8 0.6 + - - -
455D VAL* 1.3 86.1 - - - +
457D VAL* 1.3 64.5 + - - +
459D ILE* 4.2 1.6 - - - +
460D VAL* 3.1 24.4 - - - +
491D ALA 5.1 0.3 + - - -
494D ASP* 4.2 20.9 - - - +
495D ALA* 4.3 8.2 + - - +
498D ALA* 3.4 22.1 - - - +
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Residues in contact with VAL 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D PRO 5.2 0.4 - - - +
454D LYS* 2.6 50.4 + - + +
456D SER* 1.3 79.0 - - - +
458D LEU* 1.3 65.5 + - + +
460D VAL* 3.6 8.7 + - + +
461D GLN* 3.6 31.1 + - + +
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Residues in contact with LEU 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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436D LEU* 3.7 26.5 - - + +
451D LEU* 4.8 14.1 - - + +
454D LYS* 2.8 24.0 + - + +
455D VAL* 3.8 23.8 - - + +
456D SER 3.5 0.4 - - - -
457D VAL* 1.3 74.0 - - + +
459D ILE* 1.3 54.3 + - - +
460D VAL 3.0 1.6 - - - -
461D GLN* 2.6 15.1 + - - +
462D GLN* 2.5 47.5 + - + +
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Residues in contact with ILE 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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436D LEU* 3.5 26.2 - - + +
439D PHE* 5.8 1.1 - - + -
440D LEU* 5.2 6.1 - - + -
455D VAL* 3.5 19.7 - - + +
456D SER 4.2 7.2 - - - +
458D LEU* 1.3 74.5 - - - +
460D VAL* 1.3 65.2 + - + +
461D GLN 3.0 1.1 + - - -
462D GLN* 3.8 9.4 - - - -
463D THR* 2.8 38.9 + - + +
474D ALA* 5.7 1.3 - - + -
478D VAL* 4.8 15.9 - - + -
495D ALA* 3.6 43.5 - - + +
499D LEU* 3.8 23.8 - - + +
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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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456D SER 3.1 22.4 - - - +
457D VAL* 3.6 12.5 + - + +
458D LEU 2.9 0.8 + - - -
459D ILE* 1.3 79.5 - - + +
461D GLN* 1.3 59.7 + - + +
463D THR 3.8 0.5 - - - +
465D THR* 2.8 24.4 + - - -
498D ALA* 3.8 29.8 - - + +
499D LEU* 3.9 9.0 - - - +
502D LYS* 3.1 43.2 + - + +
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Residues in contact with GLN 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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457D VAL* 3.7 24.5 - - + +
458D LEU* 2.6 14.2 + - - +
460D VAL* 1.3 79.0 - - + +
462D GLN* 1.3 53.9 + - + +
463D THR 2.7 23.9 + - - +
502D LYS* 4.7 8.7 - - - +
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Residues in contact with GLN 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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436D LEU* 3.2 54.2 - - + +
437D SER* 4.5 12.8 + - - +
440D LEU* 5.5 5.6 - - + +
458D LEU* 2.5 35.1 + - + +
459D ILE* 3.8 2.2 - - - -
461D GLN* 1.3 71.6 - - + +
463D THR* 1.3 61.1 + - + +
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Residues in contact with THR 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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440D LEU* 5.0 11.7 - - + -
459D ILE* 2.8 33.9 + - + +
460D VAL 3.8 0.7 - - - +
461D GLN* 2.7 15.4 + - - +
462D GLN* 1.3 81.7 - - + +
464D ASP* 1.3 60.7 + - - +
465D THR* 2.8 25.3 + - - -
470D LYS* 5.4 6.5 - - - -
471D VAL* 5.3 2.8 - - - +
474D ALA* 4.1 22.5 - - + +
499D LEU* 4.3 12.4 - - + +
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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