Contacts of the helix formed by residues 429 - 445 (chain A) in PDB entry 1KEK
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 GLY 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ALA* 3.2 6.7 + - - +
428A ASP* 1.3 79.0 + - - +
430A THR* 1.3 64.3 + - - +
431A VAL 3.4 2.5 - - - -
432A GLY* 3.2 2.1 + - - -
433A ALA* 3.0 23.4 + - - +
560A ASN* 4.0 11.2 - - - +
1209B GLY 3.2 17.9 + - - +
1210B GLU* 4.4 0.6 - - - -
1211B ALA* 3.5 17.2 - - - +
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Residues in contact with THR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PHE* 4.0 12.1 - - + +
424A GLY* 4.0 13.3 - - - +
428A ASP* 2.5 29.7 + - - -
429A GLY* 1.3 78.4 - - - +
431A VAL* 1.3 64.9 + - + +
433A ALA* 3.3 5.9 + - - +
434A ASN* 2.9 42.1 + - - +
464A THR* 6.0 1.3 - - - -
466A SER* 4.5 3.6 - - - +
490A HIS* 2.9 41.8 + - + +
559A ILE* 5.2 0.5 - - - +
560A ASN* 5.4 2.2 - - - +
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY 3.4 0.6 - - - -
430A THR* 1.3 77.4 - - + +
432A GLY* 1.3 63.5 + - - +
434A ASN* 3.2 9.6 + - - +
435A LYS* 3.0 48.0 + - - +
453A PHE* 4.0 16.1 - - + -
455A TYR* 3.5 25.6 - - + +
464A THR* 3.4 38.4 - - + +
466A SER* 4.2 2.0 - - - +
1209B GLY* 3.9 14.1 + - - +
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Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY 3.7 1.6 - - - -
430A THR 3.2 0.4 - - - -
431A VAL* 1.3 77.0 - - - +
433A ALA* 1.3 55.9 + - - +
435A LYS* 3.4 5.6 + - - +
436A GLN* 3.0 33.7 + - - +
1208B SER 4.5 4.0 - - - -
1209B GLY* 3.0 33.0 + - - -
1210B GLU* 4.2 4.9 - - - -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY 3.0 15.8 + - - +
430A THR* 3.7 7.0 - - - +
431A VAL 3.3 0.2 - - - -
432A GLY* 1.3 73.0 - - - +
434A ASN* 1.3 63.5 + - - +
436A GLN* 3.2 2.8 + - - -
437A ALA* 2.8 27.4 + - - +
490A HIS* 6.3 1.8 - - + -
560A ASN* 4.5 13.0 - - + +
564A GLN* 3.0 41.4 + - + +
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Residues in contact with ASN 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PHE* 3.6 32.7 - - - -
430A THR* 2.9 28.5 + - - +
431A VAL 3.2 4.2 + - - +
433A ALA* 1.3 79.5 - - - +
435A LYS* 1.3 57.6 + - - +
437A ALA* 3.1 7.9 + - - +
438A ILE* 2.9 34.8 + - - +
453A PHE* 3.7 14.3 - - + -
466A SER* 2.7 37.1 + - - -
468A LEU* 4.1 10.7 - - + +
490A HIS* 5.4 0.5 - - - -
564A GLN* 5.7 0.5 - - - +
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 5.1 10.1 - - + -
431A VAL* 3.0 32.3 + - - +
432A GLY* 3.7 5.4 - - - +
434A ASN* 1.3 77.6 - - - +
436A GLN* 1.3 62.9 + - + +
438A ILE* 3.2 7.9 + - + +
439A LYS* 3.0 46.3 + - + +
453A PHE* 3.9 24.9 - - + -
455A TYR* 4.7 2.6 + - - -
1204B ALA* 5.8 0.4 - - - +
1205B ARG 2.8 26.0 + - - +
1206B PRO* 3.1 18.5 + - - +
1207B ASP* 5.1 1.1 - - - -
1208B SER* 2.6 33.7 + - - +
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Residues in contact with GLN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY 3.0 20.3 + - - +
433A ALA* 3.6 5.2 - - - +
435A LYS* 1.3 75.6 - - + +
437A ALA* 1.3 57.4 + - - +
439A LYS* 3.1 16.0 + - - +
440A ILE* 2.8 46.9 + - + +
564A GLN* 4.2 8.7 - - - +
586A SER* 4.7 3.5 + - - +
589A LYS* 4.0 21.6 + - - +
590A ALA* 5.4 8.3 - - - +
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ALA 2.8 17.5 + - - +
434A ASN* 3.4 8.5 - - - +
436A GLN* 1.3 78.0 - - - +
438A ILE* 1.3 62.0 + - - +
440A ILE* 4.6 0.2 - - - -
441A ILE* 3.1 33.8 + - - +
468A LEU* 5.1 3.8 - - + -
470A PHE* 4.7 0.4 - - - -
564A GLN* 3.7 12.1 - - - +
567A PHE* 3.7 29.2 - - + -
568A PHE* 3.9 13.7 - - + -
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Residues in contact with ILE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 4.2 13.8 - - - +
180A ILE* 4.0 27.8 - - + -
434A ASN 2.9 19.1 + - - +
435A LYS* 3.2 12.5 + - - +
437A ALA* 1.3 74.8 - - - +
439A LYS* 1.3 61.7 + - - +
441A ILE* 4.4 0.2 - - - +
442A GLY* 3.0 27.0 + - - -
449A ALA* 4.0 20.0 - - + +
450A GLN 4.8 2.7 - - - +
451A GLY* 3.7 33.0 - - - +
453A PHE* 4.8 5.2 - - + -
468A LEU* 3.9 21.3 - - + -
470A PHE* 4.0 15.3 - - + -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 2.9 37.4 + - - +
180A ILE* 4.1 21.2 - - - +
435A LYS* 3.0 42.2 + - + +
436A GLN* 3.1 25.1 + - - +
438A ILE* 1.3 79.4 - - - +
440A ILE* 1.3 58.2 + - + +
443A ASP* 2.9 47.2 + - - +
589A LYS* 5.2 7.0 - - - +
1206B PRO 5.6 2.0 + - - -
1207B ASP* 6.1 1.1 - - - +
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLN* 2.8 40.0 + - + +
437A ALA 3.9 3.6 - - - +
439A LYS* 1.3 72.9 - - - +
441A ILE* 1.3 63.5 + - - +
443A ASP* 4.7 0.7 - - - -
444A ASN* 2.7 36.4 + - - +
564A GLN* 5.3 2.0 - - - +
568A PHE* 4.0 27.6 - - + -
582A LEU* 3.6 36.1 - - + +
583A LEU* 4.9 7.2 - - + -
586A SER* 3.4 34.5 - - - +
589A LYS* 4.8 8.7 - - - +
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Residues in contact with ILE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ALA 3.1 18.0 + - - +
440A ILE* 1.3 74.5 - - + +
442A GLY* 1.3 64.4 + - - +
445A THR* 2.6 52.0 + - + +
447A LEU* 4.2 5.4 - - + -
470A PHE* 3.8 28.9 - - + -
567A PHE* 3.8 29.8 - - + -
568A PHE* 3.9 20.4 - - + -
573A VAL* 3.6 31.0 - - + -
574A LEU* 4.8 7.6 - - + -
582A LEU* 5.2 1.8 - - - -
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Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 4.5 8.1 - - - -
182A LYS* 2.9 42.1 + - - -
438A ILE 3.0 19.0 + - - -
439A LYS 3.9 0.2 - - - -
441A ILE* 1.3 78.8 - - - +
443A ASP* 1.3 64.6 + - - +
445A THR* 3.4 5.7 - - - +
447A LEU 4.6 3.4 - - - -
449A ALA* 4.9 6.3 - - - +
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Residues in contact with ASP 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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6A MET* 6.0 1.0 - - - -
7A THR* 4.7 11.1 + - - +
439A LYS* 2.9 31.0 + - - +
440A ILE* 4.7 0.4 - - - -
442A GLY* 1.3 79.3 - - - +
444A ASN* 1.3 72.0 + - - +
445A THR 3.6 0.7 - - - -
589A LYS* 5.4 5.2 + - - -
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Residues in contact with ASN 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ILE* 2.7 35.3 + - - +
442A GLY 3.3 0.2 - - - -
443A ASP* 1.3 90.1 - - - +
445A THR* 1.4 66.5 + - + +
578A LYS* 3.6 19.5 + - - +
582A LEU* 3.3 40.4 - - + +
585A LYS* 5.6 1.2 + - - -
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Residues in contact with THR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LYS* 3.1 18.7 + - - -
441A ILE* 2.6 26.5 + - + +
442A GLY 3.4 3.3 - - - +
443A ASP 3.6 0.7 - - - -
444A ASN* 1.4 87.0 - - + +
446A ASP* 1.3 66.0 + - - +
447A LEU* 3.1 29.6 + - - +
574A LEU* 3.5 37.5 - - + -
578A LYS* 4.6 4.0 - - - -
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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
------------------------------------------------------------
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