Contacts of the helix formed by residues 338 - 352 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASP* 3.2 30.0 - - + +
330B THR* 3.4 11.8 - - + +
331B LYS* 3.7 0.5 - - - -
332B GLU* 3.1 34.2 + - - +
337B GLY* 1.3 76.3 - - - +
339B PRO* 1.3 70.0 - - + +
340B LEU 3.4 2.0 - - - -
341B TYR* 3.4 7.9 + - + +
342B LEU* 3.0 19.2 + - - +
361B GLY 5.5 0.9 - - - +
362B ARG* 2.7 39.5 + - - +
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Residues in contact with PRO 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.6 17.5 - - + -
134B ARG* 3.5 26.9 - - - +
305B TYR* 3.4 18.6 - - - +
328B ASP* 3.4 7.4 - - - +
330B THR* 3.6 14.4 - - + -
332B GLU* 3.3 26.5 - - - +
338B ASP* 1.3 90.7 - - + +
340B LEU* 1.3 57.7 + - - +
342B LEU* 3.4 7.0 + - + +
343B ASP* 3.0 33.5 + - - +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.5 11.7 - - - +
274B VAL* 4.1 15.3 - - + +
275B SER* 4.4 7.4 - - - -
276B MET* 4.6 6.1 - - + -
302B VAL* 4.0 25.8 - - + -
305B TYR* 3.9 24.0 + - + -
308B PHE* 4.0 15.0 - - + -
326B VAL* 3.5 15.0 - - + -
327B LEU 3.7 20.0 - - - +
328B ASP* 2.8 20.8 + - - +
339B PRO* 1.3 70.1 - - - +
341B TYR* 1.3 66.4 - - - +
343B ASP* 3.2 6.1 + - - +
344B VAL* 2.9 32.0 + - + +
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A SER* 4.4 5.6 + - - -
349A VAL* 4.3 8.8 - - - +
350A GLU* 3.1 21.8 + - - +
326B VAL* 3.5 17.2 - - + +
328B ASP* 3.0 14.6 + - - +
336B PRO 4.3 1.8 - - - -
337B GLY* 3.9 13.0 - - - -
338B ASP* 3.6 6.7 - - + +
340B LEU* 1.3 78.2 - - - +
342B LEU* 1.3 80.3 + - + +
344B VAL* 3.4 1.2 + - - +
345B CYS* 2.8 51.5 + - - -
358B ILE* 3.8 26.8 + - + -
359B LEU 4.1 2.5 - - - -
360B ALA* 3.7 37.5 - - + -
388B ASN* 4.4 4.4 + - - -
389B HIS* 4.0 16.7 + + - -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 6.4 0.2 - - - +
306A ARG* 5.2 3.6 - - - +
342A LEU* 4.1 34.2 - - + +
343A ASP* 3.8 18.8 - - - +
346A SER* 3.4 29.8 - - - +
134B ARG* 5.5 8.3 - - - +
332B GLU* 6.0 0.4 - - - +
335B ALA* 5.4 0.4 - - + -
336B PRO* 4.5 2.5 - - + -
337B GLY* 3.5 32.3 - - - +
338B ASP 3.0 13.2 + - - +
339B PRO* 3.8 7.2 - - + +
341B TYR* 1.3 90.8 - - + +
343B ASP* 1.4 65.1 + - - +
345B CYS* 3.2 4.7 + - - +
346B SER* 3.0 22.3 + - - -
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 3.2 19.5 - - + +
342A LEU* 3.9 10.7 - - - +
305B TYR* 2.8 30.7 + - - -
306B ARG* 2.9 29.6 + - - -
308B PHE* 3.9 24.4 - - + -
339B PRO 3.0 14.3 + - - +
340B LEU 3.2 7.4 + - - +
342B LEU* 1.4 77.2 - - - +
344B VAL* 1.3 60.1 + - - +
346B SER* 2.8 24.2 + - - -
347B ALA* 3.1 9.4 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 4.3 6.3 - - + -
308B PHE* 4.2 12.6 - - + -
313B PHE* 3.9 28.7 - - + -
324B ILE* 4.0 3.1 - - + -
326B VAL* 3.8 32.5 - - + -
340B LEU* 2.9 21.2 + - + +
341B TYR 3.8 2.5 - - - +
343B ASP* 1.3 70.1 - - - +
345B CYS* 1.3 69.7 + - - +
347B ALA* 3.1 16.5 + - - +
348B PHE* 3.3 35.8 + - + -
358B ILE* 4.7 5.6 - - + -
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Residues in contact with CYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A CYS* 4.7 1.3 - - + -
346A SER* 4.3 15.7 - - - +
349A VAL* 3.5 40.3 - - + +
341B TYR* 2.8 55.8 + - - +
342B LEU* 3.7 6.5 - - - +
344B VAL* 1.3 74.7 - - - +
346B SER* 1.3 62.9 + - - +
348B PHE* 3.2 7.9 + - - +
349B VAL* 3.1 24.9 + - - +
358B ILE* 4.4 5.6 - - - -
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 3.5 25.3 + - - +
341A TYR* 4.3 14.6 - - - -
342A LEU* 3.5 26.5 - - - -
345A CYS* 4.4 13.6 - - - +
342B LEU 3.0 6.8 + - - -
343B ASP 2.8 18.1 + - - -
345B CYS* 1.3 74.3 - - - +
347B ALA* 1.3 61.5 + - - +
349B VAL* 4.0 1.3 - - - +
350B GLU* 3.0 32.3 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 4.6 3.4 - - + -
310B SER* 3.5 27.1 - - - +
313B PHE* 4.4 12.6 - - + -
314B PHE* 3.3 22.8 - - + -
343B ASP 3.1 10.8 + - - +
344B VAL* 3.1 14.5 + - - +
346B SER* 1.3 75.7 + - - +
348B PHE* 1.3 58.5 + - - +
350B GLU* 3.8 4.0 - - - +
351B ARG* 3.0 30.1 + - - +
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Residues in contact with PHE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE* 3.9 15.0 - + - -
314B PHE* 3.9 12.3 - + - -
317B LEU* 4.1 18.6 - - + -
324B ILE* 4.1 14.1 - - + -
344B VAL* 3.3 38.5 + - + -
345B CYS 3.2 7.6 + - - +
347B ALA* 1.3 78.2 - - - +
349B VAL* 1.3 65.5 + - - +
351B ARG* 3.5 25.6 + - - +
352B GLY 3.4 12.3 + - - -
353B GLU 4.6 0.5 + - - -
354B ALA 4.0 2.5 - - - -
355B MET* 3.2 29.9 - - + +
356B PRO* 3.3 41.5 - - + -
358B ILE* 3.8 20.0 - - + -
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 4.1 8.3 - - - +
345A CYS* 3.4 40.4 - - + +
349A VAL* 3.5 24.5 - - + -
355A MET* 4.6 13.0 - - + -
357A LYS* 4.7 7.1 + - - +
358A ILE* 4.2 25.4 - - + +
345B CYS 3.1 17.3 + - - +
346B SER 4.2 1.6 - - - +
348B PHE* 1.3 74.5 - - - +
350B GLU* 1.3 68.1 + - - +
352B GLY* 3.2 14.4 + - - -
355B MET* 4.2 6.2 - - - +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO 4.2 4.6 - - - +
341A TYR* 2.8 24.9 + - - +
357A LYS* 4.6 11.5 + - - +
358A ILE 6.1 0.2 - - - -
388A ASN* 3.8 17.3 + - - +
389A HIS* 2.9 36.4 + - - -
310B SER* 6.3 1.6 - - - -
346B SER* 3.0 18.9 + - - +
347B ALA* 3.8 4.9 - - - +
349B VAL* 1.3 82.6 - - - +
351B ARG* 1.3 62.1 + - - +
352B GLY* 3.2 1.7 + - - -
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Residues in contact with ARG 351 (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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314B PHE* 3.7 44.8 - - + +
317B LEU* 3.9 15.8 - - - +
347B ALA 3.0 19.3 + - - +
348B PHE* 3.5 17.8 - - - +
350B GLU* 1.3 76.3 - - - +
352B GLY* 1.3 62.6 + - - +
353B GLU* 3.3 47.4 + - - +
354B ALA* 2.8 41.1 + - - +
356B PRO* 4.5 2.0 - - - +
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Residues in contact with GLY 352 (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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357A LYS* 6.2 0.9 - - - -
348B PHE 3.4 3.7 + - - -
349B VAL* 3.2 14.1 + - - -
350B GLU 3.1 4.1 - - - -
351B ARG* 1.3 80.3 - - - +
353B GLU* 1.3 61.9 + - - +
355B MET* 5.5 1.6 - - - -
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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
------------------------------------------------------------
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