Contacts of the helix formed by residues 354 - 366 (chain A) in PDB entry 1KKQ
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 ILE 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A PRO 4.2 3.6 - - - +
351A PHE* 2.7 39.0 + - + +
352A CYS 3.6 0.2 - - - -
353A ASP* 1.3 75.5 - - - +
355A MET* 1.3 62.5 + - - +
356A GLU 3.4 0.2 - - - -
357A PRO* 3.0 13.7 - - - +
358A LYS* 3.1 24.0 + - - +
440A HIS* 3.7 30.7 - - + +
443A LEU* 4.0 17.0 - - + +
444A VAL* 5.1 7.6 - - + -
447A ILE* 4.3 14.8 - - + -
775A 471 3.6 50.0 - - + -
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Residues in contact with MET 355 (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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318A PHE* 5.1 1.3 - - + -
321A LEU* 3.5 32.3 - - + -
325A MET* 4.2 4.0 - - + -
330A MET* 3.9 16.8 - - + -
344A LEU* 3.8 36.8 - - + -
351A PHE 4.5 1.0 + - - -
352A CYS 5.0 1.0 + - - -
354A ILE* 1.3 84.8 - - + +
356A GLU* 1.3 63.2 + - - +
357A PRO* 3.4 0.4 - - - -
358A LYS* 3.6 15.5 + - + +
359A PHE* 3.2 42.8 + - + -
440A HIS* 6.3 0.4 - - - -
775A 471 4.3 44.6 - - + +
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Residues in contact with GLU 356 (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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341A ARG* 2.7 46.2 + - - +
345A LYS* 3.5 41.8 + - + +
352A CYS 4.0 19.5 + - - +
353A ASP* 4.6 3.8 - - + -
354A ILE 3.4 0.8 - - - +
355A MET* 1.3 73.8 - - - +
357A PRO* 1.3 72.6 - - + +
359A PHE* 3.6 0.6 + - - -
360A ASP* 3.3 22.9 + - + +
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Residues in contact with PRO 357 (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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353A ASP* 3.3 21.8 - - + +
354A ILE 3.0 18.6 - - - +
355A MET 3.4 0.4 - - - -
356A GLU* 1.3 95.5 - - + +
358A LYS* 1.3 66.7 + - + +
360A ASP* 3.6 7.3 - - + +
361A PHE* 3.2 22.7 + - - +
436A LEU* 4.1 20.3 - - + +
439A GLU* 5.8 1.1 - - - +
443A LEU* 5.2 3.1 - - + -
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Residues in contact with LYS 358 (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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318A PHE* 3.4 52.3 - - + -
321A LEU* 4.8 1.8 - - + -
325A MET* 4.3 6.9 - - + +
354A ILE* 3.1 31.6 + - - +
355A MET* 3.9 22.2 - - + +
356A GLU 3.3 0.4 - - - -
357A PRO* 1.3 84.9 - - + +
359A PHE* 1.3 65.0 + - - +
361A PHE* 3.3 4.9 + - - +
362A ALA* 2.9 24.5 + - - +
436A LEU* 4.3 21.7 + - + -
440A HIS* 2.6 41.8 + - - +
443A LEU* 5.9 2.0 - - - +
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Residues in contact with PHE 359 (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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325A MET* 3.4 37.5 - - + -
326A ASN 3.1 26.7 - - - -
329A GLY* 3.3 15.5 - - - -
330A MET* 3.2 30.7 - - + -
341A ARG* 3.6 47.1 - - + +
344A LEU* 4.6 6.5 - - + -
355A MET* 3.2 37.0 + - + +
356A GLU* 3.9 4.7 - - - +
357A PRO 3.5 0.2 - - - -
358A LYS* 1.3 78.1 - - - +
360A ASP* 1.3 58.1 + - - +
362A ALA* 3.3 1.7 + - - +
363A MET* 3.0 36.7 + - - +
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Residues in contact with ASP 360 (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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341A ARG* 3.9 11.8 - - - +
356A GLU* 3.3 16.0 + - + +
357A PRO* 3.6 8.2 - - + +
359A PHE* 1.3 77.2 - - - +
361A PHE* 1.3 68.2 + - - +
363A MET* 3.0 17.2 + - - +
364A LYS* 3.5 32.1 + - - +
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Residues in contact with PHE 361 (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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318A PHE* 4.3 5.8 - - + -
319A ALA* 4.9 0.9 - - - -
322A SER* 3.6 19.5 - - - -
357A PRO 3.2 14.0 + - - +
358A LYS 3.3 5.8 + - - +
360A ASP* 1.3 82.9 - - - +
362A ALA* 1.3 63.8 + - + +
364A LYS* 3.6 13.4 + - - +
365A PHE* 3.0 52.6 + + + +
429A LYS* 4.6 9.4 + - + -
432A ASP* 4.1 24.5 - - + -
433A LEU* 3.4 45.3 - - + -
436A LEU* 3.9 20.9 - - + -
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Residues in contact with ALA 362 (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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322A SER* 3.5 26.5 - - - +
325A MET* 3.7 25.4 - - + -
358A LYS 2.9 17.4 + - - +
359A PHE 3.6 5.4 - - - +
360A ASP 3.0 0.2 - - - -
361A PHE* 1.3 83.3 - - + +
363A MET* 1.3 62.1 + - + +
364A LYS 3.2 0.4 - - - -
365A PHE* 4.1 1.3 - - - -
366A ASN* 3.0 33.1 + - - +
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Residues in contact with MET 363 (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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226A ARG* 5.6 0.2 - - - +
325A MET 4.5 1.3 - - - -
326A ASN* 3.6 28.9 - - - +
327A LYS* 3.5 35.2 - - + +
341A ARG* 4.6 7.9 - - - +
359A PHE* 3.0 25.9 + - - +
360A ASP* 3.0 12.7 + - - +
362A ALA* 1.3 88.1 - - + +
364A LYS* 1.3 63.6 + - + +
366A ASN* 4.0 17.5 + - + +
367A ALA* 3.7 15.6 + - - +
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Residues in contact with LYS 364 (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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360A ASP* 3.5 32.4 + - - +
361A PHE* 4.1 10.5 - - - +
363A MET* 1.3 79.6 - - + +
365A PHE* 1.3 60.0 + - - +
366A ASN 3.1 1.8 - - - -
367A ALA* 2.9 28.0 + - - +
368A LEU* 3.5 8.1 + - - +
429A LYS* 4.6 21.8 + - - +
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Residues in contact with PHE 365 (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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222A LYS* 5.5 1.5 + - - -
319A ALA* 4.6 12.1 - - + -
322A SER* 4.3 14.4 - - - -
361A PHE* 3.0 48.4 + + + +
362A ALA* 4.0 4.3 - - - +
364A LYS* 1.3 78.7 - - - +
366A ASN* 1.3 62.7 + - - +
367A ALA 3.1 0.4 - - - -
368A LEU* 3.4 22.5 + - + +
369A GLU 4.3 0.9 + - - -
370A LEU* 3.8 30.4 + - + +
375A ILE* 5.3 12.3 - - + -
378A PHE* 3.8 33.2 - + - -
426A LEU* 4.0 5.4 - - + -
429A LYS* 3.8 33.8 - - + +
433A LEU* 5.1 0.4 - - + -
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Residues in contact with ASN 366 (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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222A LYS* 3.6 25.5 + - - +
226A ARG* 3.1 20.4 + - - +
322A SER* 2.9 38.9 + - - +
325A MET 3.9 3.8 - - - +
362A ALA 3.0 19.9 + - - +
363A MET* 4.0 14.9 - - + +
364A LYS 3.1 0.2 - - - -
365A PHE* 1.3 78.8 + - - +
367A ALA* 1.3 62.9 + - - +
368A LEU 3.2 0.9 - - - -
369A GLU* 3.3 17.2 + - - +
375A ILE* 6.2 0.2 - - - +
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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