Contacts of the helix formed by residues 371 - 384 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TYR* 5.6 0.7 + - - -
222B LYS* 4.8 4.5 - - - -
223B VAL* 6.5 0.7 - - + -
369B GLU 4.0 0.8 + - - +
370B LEU* 1.3 74.8 - - - +
372B ASP* 1.3 64.7 + - - +
373B SER* 2.9 23.6 + - - -
374B ASP* 2.4 49.6 + - - +
375B ILE* 3.1 16.1 + - - +
411B HIS* 4.6 0.2 - - - -
415B ASN* 5.4 5.5 + - - +
416B HIS* 4.0 6.1 + - - +
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 4.0 17.0 - - + +
214B TYR* 2.9 33.4 + - + -
215B LEU* 4.6 3.2 - - + +
221B ASN* 3.5 11.5 - - - +
222B LYS* 3.0 25.4 + - - +
223B VAL* 3.0 42.1 + - + +
371B ASP* 1.3 75.1 - - - +
373B SER* 1.3 62.1 + - - +
375B ILE* 3.8 6.2 - - - +
376B SER* 3.0 25.5 + - - -
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.8 37.0 - - - +
371B ASP* 2.9 24.4 + - - -
372B ASP* 1.3 79.3 - - - +
374B ASP* 1.3 60.5 + - - +
376B SER* 3.2 15.8 - - - -
377B LEU* 3.5 15.6 + - - +
411B HIS* 2.8 34.8 + - - -
415B ASN* 5.2 1.2 + - - -
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Residues in contact with ASP 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.7 15.6 - - + -
371B ASP* 2.4 35.8 + - - +
373B SER* 1.3 74.1 - - - +
375B ILE* 1.3 59.8 + - - +
376B SER 3.1 1.8 - - - -
377B LEU* 3.4 5.2 + - - +
378B PHE* 2.8 31.3 + - - +
408B LEU* 4.6 2.4 - - - +
411B HIS* 2.9 35.5 + - - -
412B LEU* 3.5 24.9 - - + +
416B HIS* 2.8 29.2 + - - -
426B LEU* 5.6 0.4 - - + +
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Residues in contact with ILE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TYR* 3.9 22.7 - - + +
222B LYS* 4.9 8.5 - - + +
319B ALA* 5.2 2.5 - - + +
320B MET* 4.3 15.3 - - + -
323B SER* 4.9 13.2 - - - +
365B PHE* 4.3 16.2 - - + -
370B LEU* 4.0 31.2 - - + +
371B ASP 3.1 19.5 + - - +
372B ASP* 3.4 9.8 + - - +
374B ASP* 1.3 73.1 - - - +
376B SER* 1.3 66.2 + - - +
378B PHE* 4.2 7.2 - - + -
379B VAL* 2.8 40.7 + - + +
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 3.9 18.2 - - - -
211B TYR* 3.4 17.0 - - - -
214B TYR* 3.1 35.2 - - - +
290B PHE* 3.7 6.8 - - - -
372B ASP 3.0 16.0 + - - -
373B SER 3.2 12.8 - - - -
375B ILE* 1.3 80.8 - - - +
377B LEU* 1.3 65.6 + - - +
379B VAL* 3.4 0.3 + - - -
380B ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ALA* 4.0 26.7 - - + +
210B ILE* 3.5 35.2 - - + -
211B TYR* 5.4 0.4 - - + -
373B SER* 3.5 15.2 + - - +
374B ASP* 3.4 3.2 + - - +
375B ILE 3.4 0.2 - - - -
376B SER* 1.3 85.7 - - - +
378B PHE* 1.3 62.5 + - - +
380B ALA* 3.3 4.1 + - - +
381B ALA* 3.0 23.2 + - - +
404B ILE* 3.8 6.9 - - + +
407B VAL* 4.0 16.2 - - + +
408B LEU* 3.8 24.1 - - + +
411B HIS* 3.9 33.7 - - + +
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Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ALA* 4.0 8.3 - - + -
365B PHE* 3.9 26.5 - + - -
370B LEU* 5.5 2.0 - - + -
374B ASP 2.8 19.4 + - - +
375B ILE* 3.7 9.0 - - + +
377B LEU* 1.3 76.8 - - - +
379B VAL* 1.3 59.6 + - + +
381B ALA* 3.1 8.9 + - - +
382B ILE* 3.0 48.9 + - + +
408B LEU* 4.4 10.2 - - + +
426B LEU* 3.5 43.5 - - + -
429B LYS* 4.4 1.3 - - + -
430B MET* 3.1 49.6 - - + -
433B LEU* 3.9 13.2 - - + -
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TYR* 5.3 1.1 - - + -
218B PHE* 5.0 0.7 - - + -
287B LEU* 4.2 20.9 - - + -
290B PHE* 3.6 21.5 - - + -
316B ALA* 4.2 13.2 - - + +
319B ALA* 4.6 10.5 - - + -
320B MET* 3.7 34.8 - - + -
375B ILE* 2.8 30.2 + - + +
376B SER* 3.9 3.6 - - - +
378B PHE* 1.3 74.3 - - + +
380B ALA* 1.3 56.7 + - - +
382B ILE* 3.4 9.0 + - - +
383B ILE* 3.2 24.8 + - + +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 4.0 15.0 - - + -
290B PHE* 4.3 3.6 - - + -
294B ILE* 3.7 29.4 - - + -
376B SER 3.1 15.9 + - - +
377B LEU 3.7 4.5 - - - +
378B PHE 3.2 0.2 - - - -
379B VAL* 1.3 73.4 - - - +
381B ALA* 1.3 66.7 + - - +
382B ILE 3.0 1.6 - - - -
383B ILE* 4.4 1.1 - - - +
384B CYS* 3.0 30.5 + - - +
404B ILE* 3.8 16.7 - - + +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B LEU 3.0 13.5 + - - +
378B PHE* 3.3 13.0 - - - +
380B ALA* 1.3 76.6 - - - +
382B ILE* 1.3 61.7 + - - +
384B CYS 3.9 4.7 - - - +
385B CYS* 4.0 2.1 - - - +
401B GLN* 3.2 25.9 + - - +
404B ILE* 3.8 11.4 - - + +
405B VAL* 3.8 26.9 - - + -
408B LEU* 4.9 5.4 - - + -
430B MET* 4.4 16.1 - - - +
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B GLY 4.0 12.1 - - - +
315B GLU* 3.9 33.2 - - + +
316B ALA* 4.1 8.3 - - + +
319B ALA* 4.2 8.5 - - + -
378B PHE* 3.0 48.4 + - + +
379B VAL* 3.4 13.0 - - - +
380B ALA 3.0 0.4 - - - -
381B ALA* 1.3 79.0 - - - +
383B ILE* 1.3 64.6 + - - +
385B CYS* 4.2 5.2 - - - +
388B ARG* 3.0 25.5 + - - +
430B MET* 4.6 13.5 - - + -
433B LEU* 3.8 18.4 - - + -
434B ARG* 5.2 1.1 + - - +
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Residues in contact with ILE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LEU* 3.6 36.3 - - + +
290B PHE* 4.5 7.4 - - + -
291B ALA* 4.2 9.6 - - + -
294B ILE* 5.0 2.5 - - + -
297B PHE* 4.0 25.8 - - + -
308B LEU* 3.6 34.4 - - + +
309B LEU* 4.1 21.3 - - + -
312B GLY 4.6 13.2 - - - +
313B VAL* 5.8 0.4 - - - -
316B ALA* 4.8 1.3 - - + -
379B VAL* 3.2 18.6 + - + +
380B ALA* 3.4 3.3 + - - +
382B ILE* 1.3 81.0 - - + +
384B CYS* 1.3 63.1 + - - +
385B CYS 3.1 6.9 + - - +
388B ARG* 4.7 3.7 + - - +
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Residues in contact with CYS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ILE* 4.3 11.4 - - - -
297B PHE* 4.0 18.2 - - - -
308B LEU* 4.2 8.7 - - - -
380B ALA 3.0 18.1 + - - +
381B ALA 3.9 3.0 - - - +
383B ILE* 1.3 78.1 - - - +
385B CYS* 1.3 58.7 + - - +
397B ILE* 4.1 9.5 - - + +
400B MET* 3.6 32.3 - - + -
401B GLN* 2.7 27.4 - - + +
404B ILE* 3.8 19.1 - - + -
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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