Contacts of the helix formed by residues 455 - 475 (chain A) in PDB entry 4KPF
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A ALA* 2.7 20.0 + - + +
452A ILE 3.7 3.8 - - - +
453A ILE 3.5 0.8 - - - -
454A GLY* 1.3 73.2 - - - +
456A GLU* 1.3 64.9 + - - +
457A ARG* 2.9 15.0 + - - +
458A THR* 2.4 43.4 + - - +
459A MET* 3.0 21.1 + - - +
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Residues in contact with GLU 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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354A ARG* 2.7 44.6 + - - -
358A LEU* 5.6 1.4 - - - +
453A ILE 5.4 3.8 + - - +
454A GLY 4.1 2.5 + - - -
455A ASP* 1.3 72.5 + - - +
457A ARG* 1.3 56.3 + - - +
459A MET* 3.6 9.8 - - - +
460A TYR* 3.0 53.1 + - + -
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 2.9 14.7 + - - +
456A GLU* 1.3 75.6 - - - +
458A THR* 1.3 55.4 + - - +
459A MET 3.0 1.3 - - - -
460A TYR* 3.2 5.6 + - + +
461A ASN* 2.7 57.5 + - - +
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Residues in contact with THR 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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448A MET 5.3 0.2 - - - +
451A ALA* 4.0 9.7 - - + +
452A ILE* 3.5 37.7 - - + +
455A ASP* 2.4 40.3 + - - +
457A ARG* 1.3 71.8 - - - +
459A MET* 1.3 64.8 + - - +
461A ASN* 3.2 12.9 + - - +
462A LEU* 3.1 21.1 + - - +
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Residues in contact with MET 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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354A ARG* 3.3 42.2 - - + +
357A ILE* 4.1 14.4 - - + +
358A LEU* 4.3 13.2 - - + -
452A ILE* 3.4 40.2 - - + +
455A ASP 3.0 11.0 + - - +
456A GLU* 3.6 11.7 - - - +
458A THR* 1.3 76.2 - - - +
460A TYR* 1.3 103.9 + - + +
462A LEU* 3.0 16.2 + - - +
463A MET* 3.0 15.6 + - - +
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Residues in contact with TYR 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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194A ILE* 3.7 31.2 - - + +
350A ILE* 3.6 32.5 - - + +
351A ALA* 5.5 1.6 - - - -
354A ARG* 4.0 13.7 - - + +
456A GLU* 3.0 42.7 + - + +
457A ARG* 3.8 5.8 - - + +
459A MET* 1.3 102.5 - - + +
461A ASN* 1.3 62.5 + - - +
463A MET* 3.2 15.3 + - - +
464A LYS* 3.0 28.4 + - + +
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Residues in contact with ASN 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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457A ARG* 2.7 43.1 + - - +
458A THR* 3.4 15.6 + - - +
459A MET 3.0 0.2 + - - -
460A TYR* 1.3 72.2 - - - +
462A LEU* 1.3 58.6 + - - +
464A LYS* 3.2 29.7 + - - +
465A LYS* 2.9 28.2 + - - +
468A ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 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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357A ILE* 4.0 14.8 - - + -
360A ARG* 4.0 21.8 - - - +
452A ILE* 3.2 32.3 - - + -
458A THR 3.1 8.7 + - - +
459A MET* 3.0 11.1 + - - +
461A ASN* 1.3 78.6 - - - +
463A MET* 1.3 62.9 - - - +
465A LYS* 3.1 26.2 + - - +
466A GLU* 2.9 45.5 + - + +
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Residues in contact with MET 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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194A ILE* 2.9 33.7 - - + -
349A TYR* 5.4 0.7 - - + -
350A ILE* 3.3 49.6 - - + +
353A ARG* 3.7 26.5 - - + +
354A ARG* 4.4 5.8 - - - -
357A ILE* 3.6 22.0 - - + +
459A MET* 3.0 8.0 + - - +
460A TYR* 3.5 21.8 - - + +
461A ASN 3.2 0.2 - - - -
462A LEU* 1.3 80.2 - - - +
464A LYS* 1.3 62.1 + - - +
466A GLU* 3.3 3.8 + - - +
467A LEU* 3.0 33.8 + - + +
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Residues in contact with LYS 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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191A VAL* 4.1 17.7 - - + -
194A ILE* 3.5 37.2 - - + -
195A ASP* 3.2 31.4 + - - +
460A TYR* 3.0 15.3 + - + +
461A ASN* 3.3 28.3 + - - +
463A MET* 1.3 73.4 - - - +
465A LYS* 1.3 65.4 + - - +
466A GLU 3.1 0.3 + - - -
467A LEU* 3.2 7.5 + - - +
468A ARG* 2.9 55.0 + - - +
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Residues in contact with LYS 465 (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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461A ASN 2.9 13.1 + - - +
462A LEU* 3.3 29.3 - - + +
464A LYS* 1.3 76.2 - - - +
466A GLU* 1.3 64.7 + - - +
468A ARG* 3.3 14.1 + - - +
469A GLU* 3.1 47.4 + - + +
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Residues in contact with GLU 466 (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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132A GLN* 4.4 7.7 - - - +
158A ALA 5.7 0.4 - - - -
353A ARG* 3.2 22.6 + - - +
357A ILE* 4.5 4.7 - - - +
360A ARG* 2.8 35.4 + - - -
462A LEU* 2.9 39.5 + - + +
463A MET* 3.8 4.5 - - - +
465A LYS* 1.3 75.3 + - + +
467A LEU* 1.3 67.7 + - - +
469A GLU* 3.0 29.5 + - - +
470A VAL* 3.1 18.1 + - + +
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Residues in contact with LEU 467 (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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158A ALA 4.0 11.0 + - - +
160A PRO* 4.5 1.6 - - + -
187A ILE* 3.5 41.7 - - + +
190A ALA* 4.6 9.4 - - + -
191A VAL* 4.2 12.8 - - + -
194A ILE* 3.9 24.5 - - + -
349A TYR* 3.7 38.1 - - + +
353A ARG* 5.5 5.4 - - + +
463A MET* 3.0 24.4 + - + +
464A LYS 3.5 7.0 - - - +
466A GLU* 1.3 75.6 - - - +
468A ARG* 1.3 61.6 + - - +
470A VAL* 3.2 7.4 + - - +
471A LYS 3.0 17.5 + - - -
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Residues in contact with ARG 468 (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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187A ILE* 4.8 1.8 - - + -
191A VAL* 3.6 37.0 - - + +
195A ASP* 4.9 3.0 + - - -
461A ASN 5.4 0.4 + - - -
464A LYS* 2.9 52.2 + - - +
465A LYS* 3.5 11.6 - - - +
466A GLU 3.1 0.2 - - - -
467A LEU* 1.3 71.3 - - - +
469A GLU* 1.3 61.7 + - - +
471A LYS* 3.0 12.4 + - + +
472A LYS* 2.8 29.8 + - - +
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Residues in contact with GLU 469 (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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129A TYR* 6.4 0.2 - - - -
465A LYS* 3.1 41.3 + - + +
466A GLU* 3.0 26.0 + - - +
468A ARG* 1.3 74.3 - - - +
470A VAL* 1.3 64.4 + - + +
472A LYS* 3.1 8.9 + - - +
473A LYS* 3.1 24.7 + - - +
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Residues in contact with VAL 470 (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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129A TYR* 4.0 28.9 - - + -
132A GLN* 6.0 0.2 - - - +
158A ALA* 3.8 19.3 - - + +
159A PHE* 3.8 21.8 - - + -
183A LEU* 4.3 4.9 - - + -
187A ILE* 3.7 17.9 - - + -
466A GLU* 3.1 14.8 + - + +
467A LEU 3.3 8.3 - - - +
469A GLU* 1.3 75.6 - - + +
471A LYS* 1.3 59.7 + - - +
473A LYS* 3.1 2.7 + - - -
474A PHE* 2.9 47.5 + - + +
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Residues in contact with LYS 471 (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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183A LEU* 4.0 11.9 - - + -
184A ALA* 3.9 24.0 - - + +
187A ILE* 4.0 16.4 - - + -
188A ASP* 2.8 38.0 + - - +
467A LEU 3.0 12.9 + - - +
468A ARG* 3.0 12.1 + - + +
470A VAL* 1.3 77.9 - - - +
472A LYS* 1.3 62.0 + - - +
475A ALA* 2.7 40.6 + - + +
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Residues in contact with LYS 472 (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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468A ARG 2.8 16.8 + - - +
469A GLU* 3.1 10.9 + - - +
471A LYS* 1.3 75.4 - - - +
473A LYS* 1.3 61.4 + - + +
475A ALA* 4.7 3.0 + - - +
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Residues in contact with LYS 473 (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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125A GLU* 2.8 34.6 + - - -
129A TYR* 3.4 29.7 + - - +
469A GLU 3.1 15.1 + - - +
470A VAL* 3.7 4.5 - - - +
471A LYS 3.0 0.6 - - - -
472A LYS* 1.3 81.9 - - + +
474A PHE* 1.3 81.0 + - + +
475A ALA 3.6 0.6 - - - +
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Residues in contact with PHE 474 (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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96A GLU* 4.4 9.3 - - - +
125A GLU* 4.2 13.2 - - + -
126A ILE* 3.8 49.6 - - + -
129A TYR* 3.3 50.5 - + - -
183A LEU* 4.2 11.8 - - + +
470A VAL* 2.9 33.2 + - + +
473A LYS* 1.3 102.6 - - + +
475A ALA* 1.3 68.3 + - - +
476A THR* 3.0 16.4 - - - +
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Residues in contact with ALA 475 (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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183A LEU* 4.4 8.5 - - - +
184A ALA* 4.0 22.4 - - + -
471A LYS* 2.7 28.0 + - + +
472A LYS* 4.5 3.4 + - - +
473A LYS 3.6 1.9 - - - +
474A PHE* 1.3 79.8 - - - +
476A THR* 1.3 61.6 + - - +
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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