Contacts of the helix formed by residues 338 - 352 (chain A) in PDB entry 1KEK
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 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP* 3.3 29.9 - - + +
330A THR* 3.1 20.3 - - - +
331A LYS 3.8 0.3 - - - -
332A GLU* 3.1 35.6 + - - +
337A GLY* 1.3 76.9 - - - +
339A PRO* 1.3 69.5 - - + +
340A LEU 3.4 1.8 - - - -
341A TYR* 3.3 6.9 + - + +
342A LEU* 3.0 19.2 + - - +
360A ALA* 5.6 3.2 - - + +
361A GLY 5.4 0.9 - - - +
362A ARG* 2.8 33.2 + - - +
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Residues in contact with PRO 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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131A TYR* 3.6 17.3 - - + -
134A ARG* 3.5 26.5 - - - +
305A TYR* 3.3 19.1 - - - +
328A ASP* 3.6 7.2 - - - +
330A THR* 3.6 13.9 - - + -
332A GLU* 3.2 28.3 - - - +
338A ASP* 1.3 89.5 - - + +
340A LEU* 1.3 57.2 - - - +
342A LEU* 3.3 8.6 + - + +
343A ASP* 2.9 32.2 + - - +
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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
----------------------------------------------------------
131A TYR* 3.5 11.4 + - - +
274A VAL* 4.3 6.3 - - + -
275A SER* 4.5 3.6 - - - -
276A MET* 4.5 12.8 - - + -
302A VAL* 4.0 27.4 - - + -
305A TYR* 3.8 24.0 + - + -
308A PHE* 3.9 20.2 - - + -
326A VAL* 3.5 13.9 - - + -
327A LEU 3.7 20.0 - - - +
328A ASP* 2.8 23.0 + - - +
339A PRO* 1.3 73.7 - - - +
341A TYR* 1.3 59.5 + - - +
343A ASP* 3.0 5.8 + - - +
344A VAL* 2.8 38.5 + - + +
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 3.5 16.7 - - + +
328A ASP* 3.1 13.7 + - - +
336A PRO 4.2 1.3 - - - -
337A GLY* 3.7 22.7 - - - -
338A ASP 3.5 7.4 - - - +
340A LEU* 1.3 78.2 - - - +
342A LEU* 1.4 67.7 + - + +
344A VAL* 3.2 1.7 + - - +
345A CYS* 2.9 54.5 + - - -
358A ILE* 3.9 25.7 + - + -
359A LEU 4.1 3.1 - - - -
360A ALA* 3.5 34.8 - - + -
388A ASN* 4.3 3.1 + - - -
389A HIS* 3.9 18.0 - + - -
346B SER* 4.3 4.1 + - - -
349B VAL* 4.1 8.8 - - - +
350B GLU* 2.8 27.9 + - - +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 5.3 7.4 - - - +
332A GLU* 5.8 1.1 - - - +
335A ALA* 5.3 0.2 - - + -
336A PRO* 4.3 3.6 - - + -
337A GLY* 3.2 31.4 - - - +
338A ASP 3.0 11.7 + - - +
339A PRO* 3.6 11.0 - - + +
341A TYR* 1.4 91.4 - - + +
343A ASP* 1.4 62.7 + - - +
345A CYS* 3.4 4.9 + - - +
346A SER* 3.1 23.0 + - - -
306B ARG* 5.3 3.1 - - - +
342B LEU* 4.1 32.3 - - + +
343B ASP* 3.9 16.4 - - - +
345B CYS* 5.7 0.2 - - - +
346B SER* 3.5 32.8 - - - +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A TYR* 2.8 31.9 + - - -
306A ARG* 2.9 33.0 + - - -
308A PHE* 3.8 20.8 - - + -
339A PRO 2.9 19.3 + - - +
340A LEU 3.6 5.8 - - - +
342A LEU* 1.4 71.5 - - - +
344A VAL* 1.3 63.2 + - - +
346A SER* 2.6 26.8 + - - -
347A ALA* 3.1 8.0 + - - +
336B PRO* 3.3 19.0 - - + +
342B LEU* 3.8 10.6 - - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 4.4 9.6 - - + -
308A PHE* 4.3 11.7 - - + -
313A PHE* 3.9 24.7 - - + -
324A ILE* 3.6 30.1 - - + -
326A VAL* 3.9 16.2 - - + -
340A LEU* 2.8 21.0 + - + +
341A TYR 3.7 3.6 - - - +
343A ASP* 1.3 77.4 - - - +
345A CYS* 1.3 62.3 + - - +
347A ALA* 3.0 17.8 + - - +
348A PHE* 3.2 27.2 + - + -
358A ILE* 4.5 4.0 - - + -
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Residues in contact with CYS 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 2.9 55.0 + - - +
342A LEU* 3.4 5.8 + - - +
344A VAL* 1.3 72.6 - - - +
346A SER* 1.3 57.3 + - - +
348A PHE* 3.1 3.5 + - - +
349A VAL* 2.8 33.6 + - - +
358A ILE* 4.5 10.3 - - - -
342B LEU 5.7 0.2 - - - +
345B CYS* 4.7 1.1 - - + -
346B SER* 4.4 14.6 - - - +
349B VAL* 3.4 40.7 - - + +
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU 3.1 7.2 + - - -
343A ASP 2.6 20.4 + - - -
345A CYS* 1.3 78.1 - - - +
347A ALA* 1.3 58.2 + - - +
349A VAL* 4.4 1.3 - - - +
350A GLU* 2.9 35.5 + - - +
336B PRO* 3.6 21.7 - - - +
341B TYR* 4.4 10.9 + - - -
342B LEU* 3.4 29.8 - - - -
345B CYS* 4.3 13.4 - - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 4.7 3.6 - - + -
310A SER* 3.3 28.6 - - - +
313A PHE* 4.4 12.8 - - + -
314A PHE* 3.6 22.1 - - + -
343A ASP 3.1 6.4 + - - +
344A VAL* 3.0 13.0 + - - +
346A SER* 1.3 81.9 + - - +
348A PHE* 1.4 57.1 + - - +
350A GLU* 3.6 3.9 - - - +
351A ARG* 3.0 29.5 + - - +
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 3.8 13.5 - + - -
314A PHE* 3.5 20.9 - + - -
317A LEU* 3.7 22.9 - - + -
324A ILE* 4.2 10.1 - - + -
344A VAL* 3.2 39.7 + - + -
345A CYS 3.1 5.9 + - - +
347A ALA* 1.4 75.7 - - - +
349A VAL* 1.3 67.3 + - - +
351A ARG* 3.3 26.9 + - - +
352A GLY 3.2 16.8 + - - -
353A GLU 4.6 1.4 + - - -
354A ALA 3.9 1.2 - - - +
355A MET* 3.7 25.1 - - - +
356A PRO* 3.4 35.9 - - + -
358A ILE* 3.6 23.3 - - + -
349B VAL* 5.6 0.2 - - + -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A CYS 2.8 23.4 + - - +
346A SER 4.4 0.9 - - - +
348A PHE* 1.3 77.1 - - - +
350A GLU* 1.3 66.2 + - - +
352A GLY* 3.1 14.4 + - - -
355A MET* 3.7 13.5 - - + -
341B TYR* 4.3 6.7 - - - +
345B CYS* 3.5 39.0 - - + +
349B VAL* 3.5 24.7 - - + -
355B MET* 4.6 7.4 - - + -
357B LYS* 5.0 7.2 + - - +
358B ILE* 4.0 28.3 - - + +
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Residues in contact with GLU 350 (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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310A SER* 5.8 5.9 - - - +
346A SER* 2.9 19.1 + - - +
347A ALA* 3.6 5.8 - - - +
349A VAL* 1.3 82.7 - - - +
351A ARG* 1.3 63.4 + - - +
352A GLY* 3.2 1.6 + - - -
336B PRO 4.4 4.5 - - - +
341B TYR* 3.1 16.1 + - - -
357B LYS* 5.4 6.2 + - - +
358B ILE 6.1 0.7 - - - -
388B ASN* 4.1 12.3 - - - +
389B HIS* 2.9 38.9 + - - -
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Residues in contact with ARG 351 (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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314A PHE* 3.5 45.9 - - + -
317A LEU* 4.1 11.5 - - - +
347A ALA 3.0 19.3 + - - +
348A PHE* 3.5 17.4 - - - +
349A VAL 3.3 0.2 - - - -
350A GLU* 1.3 77.7 - - - +
352A GLY* 1.3 60.9 + - - +
353A GLU* 3.4 50.1 + - - +
354A ALA* 2.5 48.3 + - - +
356A PRO* 4.3 1.4 - - - +
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Residues in contact with GLY 352 (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 PHE 3.2 5.2 + - - -
349A VAL 3.1 13.1 + - - -
350A GLU 3.1 4.1 - - - -
351A ARG* 1.3 78.7 - - - +
353A GLU* 1.3 61.9 + - - +
355A MET* 5.7 2.7 - - - -
355B MET* 6.5 1.3 - - - -
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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