Contacts of the helix formed by residues 371 - 382 (chain D) 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 ASP 371 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394B VAL* 3.9 28.2 + - + +
395B GLY* 4.4 7.4 + - - -
222D LYS* 4.5 3.6 - - - -
369D GLU 3.8 1.9 + - - +
370D LEU* 1.3 73.9 - - - +
372D ASP* 1.3 62.9 + - - +
373D SER* 2.8 27.4 + - - -
374D ASP* 2.9 34.7 + - - +
375D ILE* 3.1 16.1 + - - +
415D ASN* 4.7 3.1 - - - +
416D HIS* 4.6 5.9 + - - +
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Residues in contact with ASP 372 (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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211D TYR* 3.6 22.2 - - + +
214D TYR* 2.5 43.1 + - + -
215D LEU* 5.5 0.7 - - + -
221D ASN* 3.5 4.9 - - - +
222D LYS* 2.7 22.7 + - - +
223D VAL* 2.7 47.9 + - + +
371D ASP* 1.3 74.7 - - - +
373D SER* 1.3 59.3 + - - +
374D ASP 3.3 0.2 - - - -
375D ILE* 4.0 5.6 - - - +
376D SER* 3.4 18.4 + - - -
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Residues in contact with SER 373 (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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391B LEU 5.2 0.4 - - - -
392B LEU* 3.1 27.8 + - - +
211D TYR* 3.9 22.6 + - - +
371D ASP* 2.8 18.4 + - - -
372D ASP* 1.3 72.6 - - - +
374D ASP* 1.3 63.8 + - - +
376D SER* 3.5 11.4 + - - -
377D LEU* 3.6 14.9 - - - +
411D HIS* 2.5 40.8 + - - -
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Residues in contact with ASP 374 (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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370D LEU* 3.6 21.1 - - + -
371D ASP* 2.9 27.2 + - - +
373D SER* 1.3 77.1 - - - +
375D ILE* 1.3 66.7 + - - +
376D SER 3.1 0.8 + - - -
377D LEU* 3.2 4.7 + - - +
378D PHE* 3.0 24.4 + - - +
408D LEU* 4.4 7.3 - - + +
411D HIS* 2.9 34.9 + - - -
412D LEU* 3.6 14.2 - - + +
416D HIS* 2.8 35.1 + - - -
426D LEU* 5.7 1.3 - - + +
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Residues in contact with ILE 375 (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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214D TYR* 3.6 26.0 - - + +
222D LYS* 4.0 29.2 - - + +
319D ALA* 5.7 1.6 - - + +
320D MET* 4.2 21.3 - - + +
323D SER* 3.8 20.2 - - - +
365D PHE* 5.4 9.2 - - + -
370D LEU* 4.0 20.2 - - + +
371D ASP 3.1 18.6 - - - +
372D ASP 4.2 2.2 - - - +
374D ASP* 1.3 78.0 - - - +
376D SER* 1.3 56.5 + - - +
378D PHE* 3.6 9.5 - - + +
379D VAL* 3.0 30.1 + - + +
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Residues in contact with SER 376 (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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210D ILE* 3.4 11.4 - - - +
211D TYR* 3.5 23.1 + - - +
214D TYR* 3.4 42.6 - - - -
290D PHE* 3.5 5.4 - - - -
372D ASP 3.4 10.2 + - - -
373D SER 3.5 11.4 + - - -
374D ASP 3.1 0.4 - - - -
375D ILE* 1.3 77.9 - - - +
377D LEU* 1.3 66.7 + - - +
378D PHE 3.2 0.4 - - - -
379D VAL* 4.7 0.2 - - - -
380D ALA* 3.3 21.5 + - - +
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Residues in contact with LEU 377 (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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392B LEU* 6.1 0.7 - - + -
207D ALA* 3.9 32.3 - - + +
210D ILE* 3.6 39.3 - - + -
211D TYR* 6.0 0.2 - - + -
373D SER 3.6 16.4 - - - +
374D ASP 3.2 5.6 + - - +
376D SER* 1.3 78.6 + - - +
378D PHE* 1.3 60.5 + - - +
380D ALA* 3.8 3.4 - - - -
381D ALA* 3.1 28.2 + - - +
404D ILE* 3.5 8.7 - - + +
407D VAL* 4.0 16.2 - - + +
408D LEU* 4.1 30.3 - - + +
411D HIS* 4.3 14.1 - - + +
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Residues in contact with PHE 378 (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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319D ALA* 3.9 12.6 - - + -
365D PHE* 3.7 25.1 - + - -
370D LEU* 5.3 1.6 - - + -
374D ASP 3.0 17.3 + - - +
375D ILE* 3.6 11.4 - - + +
377D LEU* 1.3 75.9 - - - +
379D VAL* 1.3 60.3 + - + +
380D ALA 3.0 5.2 + - - -
381D ALA* 3.2 3.6 + - - +
382D ILE* 2.8 36.0 + - + +
408D LEU* 4.5 11.6 - - + +
426D LEU* 3.8 42.0 - - + -
429D LYS* 4.3 4.5 - - + -
430D MET* 3.6 46.2 - - + -
433D LEU* 3.9 25.6 - - + -
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Residues in contact with VAL 379 (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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214D TYR* 5.2 0.9 - - + -
218D PHE* 5.1 0.2 - - + -
287D LEU* 4.1 17.5 - - + -
290D PHE* 3.4 29.2 - - + -
316D ALA* 4.1 15.9 - - + +
319D ALA* 4.6 9.6 - - + -
320D MET* 3.4 36.6 - - + -
375D ILE* 3.0 20.3 + - + +
376D SER* 4.4 1.6 - - - +
378D PHE* 1.3 80.7 - - + +
380D ALA* 1.3 59.1 + - - +
382D ILE* 3.4 13.7 - - - +
383D ILE* 3.3 18.9 - - - +
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Residues in contact with ALA 380 (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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210D ILE* 4.2 12.8 - - + -
290D PHE* 4.3 3.4 - - + -
294D ILE* 3.9 25.1 - - + -
376D SER 3.3 19.4 + - - +
377D LEU 3.8 4.7 - - - +
378D PHE 3.0 0.4 - - - -
379D VAL* 1.3 76.5 - - - +
381D ALA* 1.3 58.4 + - - +
382D ILE 2.9 4.3 - - - -
383D ILE* 2.8 19.4 + - - +
384D CYS* 3.0 15.8 + - - -
404D ILE* 4.1 17.3 - - + -
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Residues in contact with ALA 381 (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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377D LEU 3.1 17.1 + - - +
378D PHE* 3.2 5.8 + - - +
380D ALA* 1.3 78.1 - - - +
382D ILE* 1.3 59.4 + - - +
384D CYS* 4.1 4.6 - - - +
385D CYS* 4.1 0.5 + - - +
401D GLN* 2.8 35.2 - - + +
404D ILE* 3.8 19.4 - - + +
405D VAL* 4.1 23.1 - - + -
408D LEU* 4.7 6.1 - - + -
430D MET* 3.9 9.7 - - + +
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Residues in contact with ILE 382 (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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312D GLY* 3.3 28.9 - - - +
315D GLU* 3.6 31.9 - - + +
316D ALA* 3.8 8.7 - - + +
378D PHE* 2.8 28.3 - - + +
379D VAL* 3.4 17.7 - - + +
380D ALA 2.9 1.4 - - - -
381D ALA* 1.3 78.4 - - - +
383D ILE* 1.3 64.6 + - - +
385D CYS* 3.7 5.3 - - - +
388D ARG* 3.0 21.5 + - - +
430D MET* 3.6 35.9 - - + -
433D LEU* 5.7 2.0 - - + -
434D ARG* 5.6 2.7 - - - +
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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