Contacts of the helix formed by residues 438 - 451 (chain A) in PDB entry 1K2P
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A GLY* 3.6 10.2 + - - -
436A SER 4.1 0.4 + - - -
437A MET* 1.3 73.6 - - - +
439A GLU* 1.3 68.3 + - - +
440A ASP* 3.2 6.7 - - - -
441A GLU* 2.9 42.3 + - - +
442A PHE* 3.6 3.5 + - - +
470A ILE* 3.7 4.6 - - - +
596B MET* 4.9 5.7 - - - +
600B ARG 5.9 1.2 + - - -
601B PHE 5.6 1.4 + - - -
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Residues in contact with GLU 439 (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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397A ILE* 4.8 1.0 - - - +
438A SER* 1.3 71.5 - - - +
440A ASP* 1.3 70.6 + - - +
442A PHE* 3.7 2.6 + - - +
443A ILE* 3.0 36.1 + - + +
465A THR* 3.3 47.6 + - - +
466A LYS* 3.2 27.1 + - - -
467A GLN* 3.0 33.0 + - - +
470A ILE* 3.6 8.1 - - - +
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Residues in contact with ASP 440 (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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438A SER* 3.1 5.8 + - - -
439A GLU* 1.3 88.6 - - - +
441A GLU* 1.3 66.1 + - + +
443A ILE* 3.5 19.6 - - - +
444A GLU* 4.4 2.4 + - - +
600B ARG* 5.5 6.3 + - - -
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Residues in contact with GLU 441 (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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436A SER 4.2 4.9 - - - +
437A MET* 3.2 24.3 - - - +
438A SER* 2.9 43.0 + - - +
440A ASP* 1.3 77.8 - - + +
442A PHE* 1.3 59.2 + - - +
444A GLU* 3.0 32.3 - - - +
445A GLU* 5.0 1.6 - - - +
562B ARG* 5.5 3.3 + - - -
602B THR* 5.6 7.1 - - + +
603B ASN 5.9 0.9 + - - -
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Residues in contact with PHE 442 (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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413A PHE* 5.7 8.5 - + - -
432A ILE* 4.4 20.0 - - + -
437A MET* 6.1 3.4 - - + -
438A SER 3.6 6.0 + - - +
439A GLU 4.4 4.7 - - - +
441A GLU* 1.3 77.3 - - - +
443A ILE* 1.3 66.1 + - - +
444A GLU 3.3 0.2 - - - -
445A GLU* 3.1 19.4 + - + +
446A ALA* 2.8 33.8 + - + +
449A MET* 4.9 10.3 - - - -
460A LEU* 5.2 0.2 - - + -
463A VAL* 3.6 30.5 - - + -
465A THR* 4.2 7.2 - - + -
470A ILE* 4.0 25.1 - - + -
472A ILE* 3.4 31.9 - - + -
541A GLY 5.8 2.0 - - - -
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Residues in contact with ILE 443 (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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397A ILE* 5.6 2.0 - - + -
439A GLU* 3.0 31.6 + - + +
440A ASP* 3.5 14.1 - - - +
441A GLU 3.2 0.4 - - - -
442A PHE* 1.3 76.0 - - - +
444A GLU* 1.3 64.2 + - - +
446A ALA* 3.2 6.3 + - + +
447A LYS* 3.1 51.8 + - - +
463A VAL* 4.8 11.4 - - + -
465A THR* 4.1 20.6 - - + +
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Residues in contact with GLU 444 (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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440A ASP 4.4 2.4 + - - +
441A GLU* 3.0 19.9 - - - +
443A ILE* 1.3 79.8 - - - +
445A GLU* 1.3 83.0 + - + +
447A LYS* 3.0 13.6 + - - +
448A VAL* 2.9 34.0 + - + +
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Residues in contact with GLU 445 (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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441A GLU 5.0 1.8 - - - +
442A PHE* 3.1 23.4 + - + +
444A GLU* 1.3 96.4 - - + +
446A ALA* 1.3 56.8 + - - +
448A VAL* 3.6 11.5 - - + +
449A MET* 2.9 33.6 + - - +
541A GLY 3.7 20.4 - - - +
542A LEU* 4.0 9.6 - - - +
543A SER 4.0 5.2 - - - +
544A ARG* 3.0 32.6 + - - -
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Residues in contact with ALA 446 (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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442A PHE* 2.8 27.1 + - + +
443A ILE* 3.3 8.7 - - + +
444A GLU 3.1 0.2 - - - -
445A GLU* 1.3 74.8 - - - +
447A LYS* 1.3 65.5 + - + +
449A MET* 3.2 2.1 + - - +
450A MET* 3.0 38.7 + - + +
460A LEU* 4.1 5.8 - - - +
463A VAL* 3.5 34.5 - - + -
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Residues in contact with LYS 447 (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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443A ILE* 3.1 42.9 + - - +
444A GLU* 3.0 10.6 + - - +
446A ALA* 1.3 74.9 - - - +
448A VAL* 1.3 65.1 + - + +
450A MET* 3.5 11.3 + - + +
451A ASN* 3.2 28.3 + - - +
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Residues in contact with VAL 448 (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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444A GLU* 2.9 20.4 + - + +
445A GLU* 3.6 12.8 - - + +
447A LYS* 1.3 79.3 - - + +
449A MET* 1.3 62.7 + - + +
451A ASN* 3.4 18.1 + - - +
452A LEU* 3.7 10.7 + - - +
517A PHE* 4.3 24.0 - - + -
545A TYR* 4.3 23.7 - - + +
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Residues in contact with MET 449 (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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442A PHE* 4.9 14.1 - - - -
445A GLU 2.9 19.4 + - - +
446A ALA 3.9 3.4 - - - +
448A VAL* 1.3 73.9 - - + +
450A MET* 1.3 57.4 + - - +
451A ASN 3.0 5.2 - - - -
452A LEU* 2.8 34.8 + - - +
458A VAL 6.0 0.2 - - - +
460A LEU* 4.2 33.0 + - + +
472A ILE* 4.9 5.6 - - + -
474A THR* 5.8 4.3 - - + -
517A PHE* 4.8 7.6 - - + -
540A PHE* 4.0 30.7 - - + +
541A GLY* 3.1 46.4 - - - +
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Residues in contact with MET 450 (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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446A ALA* 3.0 35.0 + - + +
447A LYS* 4.1 9.2 - - + +
449A MET* 1.3 75.2 - - - +
451A ASN* 1.3 63.4 + - - +
452A LEU 3.1 8.4 - - - +
453A SER* 4.4 4.3 + - - -
460A LEU* 3.4 33.4 - - + +
461A TYR 3.4 27.4 - - - +
462A GLY* 4.1 10.3 - - - -
463A VAL* 4.7 9.2 - - + +
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Residues in contact with ASN 451 (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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447A LYS 3.2 14.7 + - - +
448A VAL* 3.5 13.7 - - - +
449A MET 3.0 0.8 - - - -
450A MET* 1.3 79.4 + - - +
452A LEU* 1.3 64.8 + - + +
453A SER* 3.7 4.2 + - - -
511A TYR* 3.9 7.6 + - - -
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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