Contacts of the helix formed by residues 374 - 389 (chain A) in PDB entry 1KWG
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 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PRO 6.0 0.7 - - - -
317A PRO* 5.9 0.3 - - - +
354A GLN* 4.9 3.8 - - - +
364A ALA* 4.4 13.2 - - - +
365A GLY 3.7 18.2 + - - +
366A LEU 2.8 19.9 + - - +
367A HIS* 4.2 1.6 - - - -
368A ARG* 4.0 28.6 + - + +
372A ALA 3.4 1.2 + - - -
373A PRO* 1.3 75.1 - - - +
375A GLN* 1.3 84.2 + - - +
376A GLY 3.2 3.8 - - - +
377A PHE* 3.0 16.8 + - - +
378A PHE* 3.5 8.7 - - - -
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Residues in contact with GLN 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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315A PRO 5.7 0.4 - - - +
326A SER* 4.8 4.4 + - - -
327A PRO* 3.9 15.6 + - - +
328A ALA 4.3 0.6 + - - -
329A PRO* 3.7 34.0 - - - +
332A VAL* 6.3 0.9 - - + +
374A ASP* 1.3 85.3 + - - +
376A GLY* 1.3 62.8 + - - +
377A PHE 3.3 0.5 + - - -
378A PHE* 3.4 12.0 + - - +
379A GLU* 3.3 35.5 + - + +
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Residues in contact with GLY 376 (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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315A PRO* 3.7 23.3 + - - -
332A VAL* 4.4 15.9 - - - +
365A GLY 5.2 0.4 + - - -
366A LEU* 3.7 15.2 - - - +
374A ASP* 3.2 4.2 - - - +
375A GLN* 1.3 79.0 - - - +
377A PHE* 1.3 57.0 + - - +
379A GLU* 3.3 2.7 + - - +
380A ALA* 2.9 31.2 + - - +
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Residues in contact with PHE 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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22A ARG* 4.7 7.0 - - + -
25A GLU* 5.9 0.7 - - + -
26A ALA* 3.7 31.4 - - + -
352A TRP* 4.5 6.5 - + - -
366A LEU* 3.3 35.9 + - + +
367A HIS* 3.6 30.1 - + - -
373A PRO* 3.6 22.7 - - + -
374A ASP 3.0 8.7 + - - +
376A GLY* 1.3 76.3 - - - +
378A PHE* 1.3 77.8 + + - +
380A ALA* 3.2 4.3 + - + +
381A LYS* 2.9 51.2 + - + +
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Residues in contact with PHE 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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373A PRO* 3.6 35.4 - - + -
374A ASP 3.5 19.3 - - - -
375A GLN* 3.4 9.3 + - - +
376A GLY 3.4 0.4 - - - -
377A PHE* 1.3 93.8 - + - +
379A GLU* 1.3 58.6 + - + +
381A LYS* 3.5 10.2 + - + +
382A ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 379 (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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328A ALA 4.3 0.7 - - - +
329A PRO* 4.1 0.3 - - - +
330A GLY* 2.9 32.8 + - - -
331A MET 4.2 0.7 + - - -
332A VAL* 2.8 42.1 + - + +
333A ARG* 2.9 22.0 + - + +
375A GLN* 3.3 33.2 + - + +
376A GLY 3.3 6.7 + - - +
377A PHE 3.2 0.4 - - - -
378A PHE* 1.3 75.5 - - + +
380A ALA* 1.3 66.1 + - - +
382A ARG* 3.3 7.2 + - - +
383A VAL* 3.1 27.9 + - - +
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Residues in contact with ALA 380 (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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2A LEU* 3.6 11.3 - - + +
26A ALA* 5.2 0.4 - - + -
28A LEU* 5.6 4.9 - - + -
332A VAL* 5.0 0.6 - - - +
349A TYR* 3.6 45.5 - - + -
366A LEU* 4.4 8.1 - - + -
376A GLY 2.9 18.3 + - - +
377A PHE* 3.6 4.9 - - + +
379A GLU* 1.3 73.2 - - - +
381A LYS* 1.3 64.7 + - - +
383A VAL* 3.2 3.1 + - - +
384A ALA* 3.0 18.6 + - - +
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Residues in contact with LYS 381 (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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25A GLU* 3.2 26.9 + - - +
26A ALA* 4.0 21.6 + - + +
377A PHE* 2.9 42.5 + - + +
378A PHE* 3.8 11.7 - - + +
380A ALA* 1.3 76.2 - - - +
382A ARG* 1.3 62.8 + - - +
384A ALA* 3.2 2.9 + - - +
385A GLU* 3.0 51.4 + - + +
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Residues in contact with ARG 382 (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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333A ARG* 4.1 13.8 - - - +
378A PHE 3.0 18.1 + - - +
379A GLU* 3.5 7.9 - - - +
381A LYS* 1.3 77.1 - - - +
383A VAL* 1.3 57.7 + - - +
385A GLU* 3.2 21.5 + - - +
386A GLU* 2.9 58.9 + - - +
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Residues in contact with VAL 383 (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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2A LEU* 4.2 9.9 - - + -
333A ARG* 3.6 36.6 - - + +
336A THR* 3.7 26.7 - - + -
337A TRP* 3.8 24.2 - - + +
340A LEU* 4.3 9.9 - - + -
379A GLU 3.1 16.1 + - - +
380A ALA* 3.6 8.1 - - - +
382A ARG* 1.3 75.7 - - - +
384A ALA* 1.3 57.8 + - - +
386A GLU* 3.7 6.7 - - - +
387A LEU* 2.8 31.2 + - + +
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Residues in contact with ALA 384 (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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2A LEU* 3.7 18.5 - - + +
26A ALA 3.5 21.8 - - - +
27A GLY* 4.2 15.0 - - - +
28A LEU* 6.1 0.2 - - + -
380A ALA 3.0 11.2 + - - +
381A LYS 3.2 9.4 + - - +
383A VAL* 1.3 75.3 - - - +
385A GLU* 1.3 64.2 + - + +
387A LEU* 4.1 4.8 - - - +
388A ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 385 (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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26A ALA 6.0 0.2 - - - +
381A LYS* 3.0 43.0 + - + +
382A ARG* 3.2 29.4 + - - +
384A ALA* 1.3 79.1 - - + +
386A GLU* 1.3 62.4 + - + +
388A ALA* 3.6 15.4 + - - +
389A ALA* 3.8 7.4 + - - +
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Residues in contact with GLU 386 (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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333A ARG* 2.9 45.2 + - - -
337A TRP* 2.9 26.7 + - + -
382A ARG* 2.9 39.3 + - - +
383A VAL* 3.7 5.6 - - - +
385A GLU* 1.3 75.6 - - + +
387A LEU* 1.3 64.8 + - - +
389A ALA* 3.2 6.5 + - - +
390A LEU* 3.2 26.5 + - + +
629A LEU* 3.5 23.8 - - + +
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Residues in contact with LEU 387 (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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1A MET* 3.4 33.4 - - - +
2A LEU* 5.0 9.0 - - + -
337A TRP* 3.7 31.9 - - + -
340A LEU* 4.0 18.6 - - + -
383A VAL* 2.8 22.8 + - + +
384A ALA* 4.1 3.8 - - - +
386A GLU* 1.3 71.1 - - - +
388A ALA* 1.3 61.1 + - - +
390A LEU 2.9 34.4 + - - +
391A ALA* 3.8 3.6 + - - -
392A LEU* 4.2 14.1 - - + +
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Residues in contact with ALA 388 (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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384A ALA 3.1 18.4 + - - +
385A GLU* 3.6 10.8 - - - +
387A LEU* 1.3 76.4 - - - +
389A ALA* 1.3 58.6 + - + +
391A ALA* 5.1 1.9 + - - +
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Residues in contact with ALA 389 (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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385A GLU 3.8 6.7 + - - +
386A GLU* 3.2 8.7 + - - +
387A LEU 3.1 0.6 - - - -
388A ALA* 1.3 77.7 - - + +
390A LEU* 1.3 70.9 + - + +
391A ALA 3.8 2.5 + - - -
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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