Contacts of the helix formed by residues 365 - 379 (chain A) in PDB entry 1KMC
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 GLU 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A LEU* 1.3 74.0 - - - +
366A ILE* 1.3 88.6 + - - +
367A MET* 2.7 35.2 + - - +
368A GLN* 2.8 37.7 + - + +
369A ILE* 3.1 10.2 + - - +
394A LEU* 5.3 0.7 - - - +
396A LYS 4.7 1.0 - - - +
397A GLU* 3.6 22.3 - - + +
398A LEU 2.7 36.0 + - - +
399A TYR* 3.3 28.8 - - + +
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 5.3 4.0 - - + -
281A PHE* 5.0 8.7 - - + -
328A LEU* 4.9 7.9 - - + -
364A LEU 3.7 1.2 + - - -
365A GLU* 1.3 84.6 - - - +
367A MET* 1.3 71.6 + - + +
369A ILE* 3.5 11.9 + - + +
370A LEU* 3.1 49.6 + - + +
394A LEU* 4.0 17.9 - - + -
398A LEU* 2.7 44.5 + - + +
400A PHE* 4.1 22.7 - - + -
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Residues in contact with MET 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 4.3 12.8 - - - -
365A GLU* 2.7 24.6 + - - +
366A ILE* 1.3 82.8 - - + +
368A GLN* 1.3 53.8 + - + +
370A LEU* 3.9 3.3 - - + +
371A THR* 2.7 43.2 + - - +
389A VAL* 3.9 37.0 - - + -
392A SER* 4.4 6.1 - - - +
394A LEU* 5.7 1.8 - - + -
367B MET* 3.3 57.0 - - + -
371B THR* 5.2 4.7 - - - +
392B SER* 4.5 9.0 - - - -
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.4 27.5 - - + +
365A GLU* 2.8 42.4 + - + +
367A MET* 1.3 73.9 - - + +
369A ILE* 1.3 67.6 + - - +
371A THR* 3.2 6.2 + - - -
372A ARG* 2.9 33.4 + - - +
399A TYR* 4.1 6.2 + - - -
397B GLU* 2.9 40.2 + - + +
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Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 4.8 1.3 - - + -
356A ILE* 3.4 28.2 - - + +
357A LEU* 4.0 23.6 - - + -
360A HIS 4.2 1.8 - - - +
361A GLY* 4.0 26.5 - - - +
364A LEU* 3.5 34.5 - - + +
365A GLU 3.5 10.3 - - - +
366A ILE* 3.6 13.0 - - + +
368A GLN* 1.3 77.3 - - - +
370A LEU* 1.3 65.3 + - + +
372A ARG* 3.1 6.6 + - - +
373A VAL* 2.9 35.0 + - + +
400A PHE* 4.6 9.2 - - + -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.3 5.8 - - + -
328A LEU* 3.8 24.7 - - + -
330A ALA* 3.9 22.7 - - + -
349A PHE* 5.2 4.7 - - + -
353A LEU* 4.0 27.4 - - + -
366A ILE* 3.1 36.5 + - + +
367A MET* 4.1 6.5 - - - +
369A ILE* 1.3 82.3 - - + +
371A THR* 1.3 58.1 + - - +
373A VAL* 3.2 8.3 + - + +
374A ASN* 2.9 32.1 + - - +
389A VAL* 3.9 26.4 - - + +
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Residues in contact with THR 371 (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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367A MET* 2.7 34.1 + - - +
368A GLN* 3.6 7.1 - - - -
369A ILE 3.2 0.2 - - - -
370A LEU* 1.3 76.2 - - - +
372A ARG* 1.3 65.5 + - + +
374A ASN* 3.0 22.2 + - - +
375A ASP* 3.0 12.6 + - - +
150B THR* 5.8 1.6 - - + -
367B MET* 5.2 4.7 - - - +
392B SER* 5.0 5.2 + - - -
394B LEU* 3.7 10.4 + - + +
395B THR 3.6 3.1 - - - +
396B LYS* 3.5 43.1 - - - +
397B GLU* 4.5 4.6 - - + +
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Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.9 22.4 - - + +
360A HIS* 3.4 33.5 + - - -
364A LEU* 3.4 33.1 - - - +
368A GLN* 2.9 19.6 + - + +
369A ILE 3.5 7.2 - - - +
371A THR* 1.3 76.7 - - - +
373A VAL* 1.3 64.0 + - - +
375A ASP* 3.4 7.0 + - - +
376A ARG* 3.0 23.4 + - - +
149B PRO* 3.5 7.9 - - - +
150B THR* 2.8 68.9 + - + +
397B GLU* 5.0 8.5 + - - -
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 4.0 29.4 - - + -
352A ALA* 3.7 18.6 - - + -
353A LEU* 3.8 36.6 - - + +
356A ILE* 4.1 16.2 - - + -
369A ILE* 2.9 22.4 + - + +
370A LEU* 3.4 11.2 - - + +
371A THR 3.1 0.2 - - - -
372A ARG* 1.3 76.3 - - - +
374A ASN* 1.3 64.4 + - - +
376A ARG* 3.1 6.6 + - - +
377A VAL* 2.9 30.8 + - + +
387A PRO* 4.8 1.3 - - + -
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Residues in contact with ASN 374 (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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370A LEU 2.9 18.2 + - - +
371A THR* 3.1 12.4 + - - +
373A VAL* 1.3 77.5 - - - +
375A ASP* 1.3 63.8 + - - +
377A VAL 3.5 0.3 + - - -
378A ALA* 3.0 24.4 + - - +
386A ILE* 3.8 11.8 - - + +
387A PRO* 2.9 44.2 - - - +
388A CYS 4.2 0.3 + - - -
389A VAL* 4.1 11.5 - - - +
392B SER* 3.7 23.4 + - - -
393B MET 4.1 1.2 - - - -
394B LEU 3.0 24.9 + - - +
395B THR* 4.3 1.1 - - - -
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Residues in contact with ASP 375 (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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371A THR 3.0 3.7 + - - +
372A ARG* 3.8 9.4 - - - +
374A ASN* 1.3 78.1 - - - +
376A ARG* 1.3 55.4 + - - +
378A ALA* 3.1 1.3 + - - +
379A ARG* 2.5 76.7 + - - +
150B THR* 5.3 4.0 - - + +
395B THR* 3.2 43.6 - - - +
396B LYS* 3.5 13.5 + - - -
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ALA* 3.7 22.6 - - + +
355A SER* 3.1 29.2 + - - -
356A ILE* 3.2 26.4 - - + +
372A ARG 3.0 15.0 + - - +
373A VAL* 3.1 12.3 + - - +
375A ASP* 1.3 77.2 - - - +
377A VAL* 1.3 57.3 + - - +
379A HIS* 2.9 66.3 + - - +
380A PHE* 3.5 9.5 - - + -
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Residues in contact with VAL 377 (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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348A TRP* 4.7 9.7 - - + -
349A PHE* 4.4 7.6 - - - +
352A ALA* 3.7 18.6 - - + -
373A VAL* 2.9 21.7 + - + +
376A ARG* 1.3 75.7 - - - +
378A ALA* 1.3 63.3 + - - +
380A PHE* 3.4 36.6 - - + +
385A GLN* 3.2 40.7 + - + +
387A PRO* 3.4 31.4 - - + -
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Residues in contact with ALA 378 (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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374A ASN 3.0 20.6 + - - +
375A ASP* 3.1 8.7 + - - +
377A VAL* 1.3 79.9 - - - +
379A ARG* 1.3 62.2 + - + +
384A LYS* 2.8 29.1 + - - -
385A GLN 3.6 9.9 - - - -
386A ILE* 4.1 14.1 - - + -
320B LYS 3.6 3.3 - - - +
321B ILE* 4.4 1.7 - - + -
322B PRO* 3.6 18.1 - - + +
325B ALA* 5.1 0.4 - - + -
395B THR* 4.2 7.9 - - + -
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP* 2.5 50.1 + - - +
378A ALA* 1.3 76.2 - - + +
379A HIS* 1.3 75.2 + - - +
380A PHE 3.2 9.5 + - - -
384A LYS* 3.5 10.6 + - - +
153B TYR* 6.2 0.8 - - - -
275B GLU* 3.8 32.1 + - - +
319B TYR* 5.7 18.7 - - + +
320B LYS 4.8 4.2 + - - +
321B ILE* 4.1 21.1 - - + +
326B ASP* 5.8 0.6 + - - -
395B THR* 4.1 10.8 + - - +
396B LYS* 3.2 22.9 - - - +
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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
------------------------------------------------------------
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