Contacts of the helix formed by residues 330 - 342 (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 GLY 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ALA 3.1 0.2 + - - -
329A PRO* 1.3 71.7 - - - +
331A MET* 1.3 56.4 + - - +
333A ARG* 3.3 10.8 + - - +
334A LEU 2.9 22.7 + - - -
379A GLU* 2.9 29.7 + - - -
637A TYR 3.5 18.6 - - - +
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Residues in contact with MET 331 (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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286A ARG 3.7 16.8 - - - +
287A THR* 3.4 19.1 - - - +
327A PRO* 4.1 9.4 - - + -
328A ALA* 3.0 31.5 + - + +
329A PRO 3.4 0.4 - - - -
330A GLY* 1.3 75.8 - - - +
332A VAL* 1.3 61.1 + - - +
334A LEU* 3.7 16.4 - - + +
335A TRP* 2.8 70.9 + - + +
611A ASN 5.1 0.4 - - - +
612A TYR* 3.8 16.4 - - + -
637A TYR* 3.8 31.4 - - + -
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Residues in contact with VAL 332 (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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313A GLN* 5.2 0.8 - - + +
314A GLN 4.1 11.0 - - - +
315A PRO* 3.5 35.4 - - + +
327A PRO* 4.4 9.0 - - + -
331A MET* 1.3 74.8 - - - +
333A ARG* 1.3 57.4 + - - +
335A TRP* 3.5 14.1 + - + +
336A THR* 2.7 33.5 + - - +
349A TYR* 3.7 29.2 - - + +
375A GLN* 6.3 1.1 - - + +
376A GLY* 4.4 16.8 - - - +
379A GLU* 2.8 24.9 + - + +
380A ALA 5.0 0.7 - - - +
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Residues in contact with ARG 333 (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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330A GLY* 3.5 11.5 + - - +
332A VAL* 1.3 77.6 - - - +
334A LEU* 1.3 61.8 + - - +
336A THR* 3.3 2.9 + - - -
337A TRP* 3.0 27.3 + - + +
379A GLU* 2.9 24.7 + - + +
382A ARG* 4.1 18.0 - - - +
383A VAL* 3.6 22.2 - - + -
386A GLU* 2.9 41.0 + - - -
629A LEU* 3.9 20.6 - - - +
630A GLY* 5.5 1.6 - - - +
637A TYR 5.3 1.6 + - - -
638A ASP* 2.9 30.1 + - - +
639A LEU* 3.8 19.1 + - + +
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Residues in contact with LEU 334 (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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330A GLY 2.9 17.8 + - - +
331A MET* 3.7 22.0 - - + +
332A VAL 3.3 0.2 - - - -
333A ARG* 1.3 78.4 - - - +
335A TRP* 1.3 67.6 + - - +
336A THR 3.2 0.2 + - - -
337A TRP* 3.3 1.7 + - - +
338A GLU* 2.9 23.0 + - + +
610A PHE* 4.0 20.0 - - + -
611A ASN 3.7 24.7 - - - +
612A TYR* 3.8 33.2 - - + +
637A TYR 3.8 11.9 - - - +
638A ASP 3.7 22.4 - - - +
639A LEU* 3.9 11.9 - - + -
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Residues in contact with TRP 335 (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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265A SER* 5.9 0.2 - - - +
267A PRO* 3.6 29.3 - - + +
268A LEU* 3.7 19.5 - - + -
287A THR* 3.1 30.0 + - - -
293A ALA* 5.0 3.1 - - + -
297A HIS* 4.6 2.1 + - - -
313A GLN* 3.5 35.8 - - - +
314A GLN* 3.6 26.7 - - + -
327A PRO* 3.6 38.6 - - + -
331A MET* 2.8 38.6 + - + +
332A VAL* 3.9 7.2 - - + +
334A LEU* 1.3 75.0 - - + +
336A THR* 1.3 55.9 + - - +
338A GLU* 3.6 10.5 - - - +
339A ALA* 3.0 29.6 + - - +
612A TYR* 3.7 20.2 + - - -
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Residues in contact with THR 336 (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* 3.8 15.9 - - + -
313A GLN* 4.5 2.4 + - - +
332A VAL 2.7 22.0 + - - -
333A ARG* 3.5 4.9 - - - -
334A LEU 3.2 0.2 - - - -
335A TRP* 1.3 74.3 - - - +
337A TRP* 1.3 64.9 + - - +
339A ALA* 3.2 4.9 + - - +
340A LEU* 3.1 23.8 + - + +
347A VAL* 4.0 19.5 - - + +
349A TYR* 2.7 36.6 + - - +
383A VAL* 3.7 25.8 - - + -
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Residues in contact with TRP 337 (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* 3.0 23.7 + - + +
336A THR* 1.3 76.6 - - - +
338A GLU* 1.3 58.3 + - - +
340A LEU* 3.3 22.2 + - + +
341A ALA* 2.8 29.6 + - - +
383A VAL* 3.8 18.9 - - + +
386A GLU* 2.9 33.1 + - + -
387A LEU* 3.7 46.4 - - + -
390A LEU* 4.1 15.9 - - + -
392A LEU* 4.0 22.9 - - + -
608A PHE* 3.7 22.4 - + + -
610A PHE* 3.9 6.6 - - + -
629A LEU* 3.7 15.6 - - + +
639A LEU* 3.8 29.4 - - + -
641A VAL* 5.8 0.2 - - + -
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Residues in contact with GLU 338 (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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290A PRO 4.0 1.2 - - - +
293A ALA* 3.6 19.1 - - - +
294A ALA* 4.4 11.0 - - - -
297A HIS* 4.3 4.2 + - + -
334A LEU* 2.9 19.3 + - + +
335A TRP* 3.6 9.5 - - - +
337A TRP* 1.3 74.7 - - - +
339A ALA* 1.3 66.2 + - - +
341A ALA* 3.2 0.9 + - - +
342A HIS* 3.0 46.0 + - + +
435A ARG* 3.8 21.0 + - - -
610A PHE* 3.4 29.2 - - + -
612A TYR* 2.9 35.0 + - - -
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Residues in contact with ALA 339 (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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297A HIS* 3.5 30.7 + - + -
308A PHE* 4.1 1.0 - - - -
310A VAL* 3.8 11.4 - - + -
313A GLN* 5.0 1.6 - - - +
335A TRP 3.0 14.2 + - - +
336A THR* 3.2 8.9 + - - +
338A GLU* 1.3 77.3 - - - +
340A LEU* 1.3 60.6 + - - +
342A HIS* 3.2 10.6 + - - +
343A GLY 3.3 0.5 + - - -
344A ALA* 3.0 22.1 + - - +
347A VAL* 3.7 20.6 - - + -
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Residues in contact with LEU 340 (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 4.7 12.3 - - - +
2A LEU* 4.8 1.8 - - + -
336A THR* 3.1 20.3 + - + +
337A TRP* 3.6 37.2 - - + +
339A ALA* 1.3 76.8 - - - +
341A ALA* 1.3 56.9 + - - +
343A GLY* 2.9 8.0 + - - -
344A ALA 3.5 21.8 - - - +
345A GLU 4.9 1.1 - - - +
347A VAL* 4.0 16.4 - - + -
383A VAL* 4.3 12.8 - - + -
387A LEU* 4.0 28.5 - - + -
392A LEU* 4.2 13.9 - - + -
603A ARG* 2.8 27.9 + - - -
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Residues in contact with ALA 341 (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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337A TRP 2.8 21.2 + - - +
338A GLU 3.2 5.4 + - - +
340A LEU* 1.3 72.6 - - - +
342A HIS* 1.3 58.7 + - - +
343A GLY 3.1 3.2 + - - -
395A VAL* 4.9 0.7 - - - +
601A ARG* 3.5 26.9 + - + +
602A ARG 3.6 8.0 - - - +
603A ARG* 3.9 10.5 - - - +
608A PHE* 3.6 41.9 - - + -
610A PHE* 3.8 9.4 - - + -
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Residues in contact with HIS 342 (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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294A ALA* 3.6 27.1 + - + +
297A HIS* 3.5 25.6 - + + -
298A ASP* 2.9 30.1 + - - -
301A ARG* 2.9 27.7 + - - +
308A PHE* 3.3 8.5 - - - -
338A GLU* 3.0 42.1 + - + +
339A ALA 3.2 5.1 + - - +
341A ALA* 1.3 75.1 - - + +
343A GLY* 1.3 57.4 + - - +
344A ALA 3.7 0.4 - - - -
395A VAL* 4.7 0.4 - - - -
435A ARG* 3.6 20.0 + - - -
601A ARG* 3.6 39.9 - - + +
610A PHE* 5.1 0.6 - - - -
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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