Contacts of the helix formed by residues 336 - 349 (chain A) in PDB entry 2KR0
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 PHE 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A ALA* 3.7 22.7 - - + -
292A LEU 3.4 26.7 - - - -
293A THR 3.7 0.4 - - - -
294A PRO* 3.4 47.6 - - + -
297A MET* 3.9 18.4 - - + -
301A LEU* 3.9 17.3 - - + -
327A ILE* 4.2 12.1 - - + -
331A LEU* 5.3 4.9 - - + -
333A SER* 3.1 11.5 + - - +
335A GLN* 1.3 90.1 - - - +
337A GLN* 1.3 60.4 + - + +
339A ALA* 3.3 4.8 + - + +
340A LEU* 2.8 42.4 + - + +
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Residues in contact with GLN 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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36A THR* 3.6 17.7 - - + +
37A THR* 2.7 44.6 + - - +
285A GLN* 3.5 21.3 - - - +
286A VAL* 3.1 40.3 + - + +
289A ALA* 3.8 19.1 - - + +
333A SER* 3.2 15.8 + - - +
334A PRO* 3.3 7.5 + - - +
336A PHE* 1.3 73.5 - - + +
338A GLN* 1.3 57.0 + - - +
340A LEU* 3.6 2.9 + - - -
341A GLY* 3.0 24.4 + - - -
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Residues in contact with GLN 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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36A THR* 4.0 20.1 + - + +
277A PRO 4.8 4.3 - - - +
278A ALA 5.5 4.9 - - - -
285A GLN* 5.9 1.0 + - - -
315A PRO* 4.8 20.1 - - - +
318A GLU* 3.9 30.0 - - + +
334A PRO* 2.9 21.5 + - + +
335A GLN 3.7 5.8 - - - +
337A GLN* 1.3 72.6 - - - +
339A ALA* 1.3 59.3 + - - +
341A GLY* 3.3 1.5 + - - -
342A MET* 3.0 48.2 + - + +
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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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301A LEU* 4.1 29.2 - - + -
310A LEU* 3.9 19.0 - - + +
320A LEU* 4.9 11.2 - - + +
321A PRO* 6.1 1.6 - - + -
335A GLN 3.1 18.6 + - - +
336A PHE* 3.3 8.0 + - + +
338A GLN* 1.3 75.8 - - - +
340A LEU* 1.3 56.2 + - - +
342A MET* 3.6 3.9 + - - +
343A PHE* 3.0 31.2 + - - +
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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
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285A GLN* 4.1 10.1 - - - +
288A LEU* 3.8 26.2 - - + +
289A ALA* 4.1 14.6 - - + +
292A LEU* 3.7 35.7 - - + +
297A MET* 4.0 17.3 - - + -
301A LEU* 5.2 3.6 - - + -
336A PHE* 2.8 37.7 + - + +
337A GLN* 3.8 6.5 - - - +
339A ALA* 1.3 71.6 - - - +
341A GLY* 1.3 57.2 + - - +
343A PHE* 3.5 12.2 - - + +
344A SER* 2.9 40.8 + - - +
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Residues in contact with GLY 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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285A GLN* 3.1 52.1 + - - -
337A GLN 3.0 11.6 + - - -
338A GLN* 3.8 1.6 - - - -
339A ALA 3.2 0.2 - - - -
340A LEU* 1.3 76.3 - - - +
342A MET* 1.3 59.3 + - - +
344A SER* 3.6 3.2 + - - -
345A ALA* 3.2 22.7 + - - +
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Residues in contact with MET 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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285A GLN* 5.1 0.7 - - - +
310A LEU* 3.5 43.6 - - + +
313A TYR* 4.6 17.2 - - + +
314A LEU* 3.7 31.4 - - + -
315A PRO* 4.9 3.6 - - + -
318A GLU* 4.9 2.7 - - + -
320A LEU* 3.9 26.7 - - + -
338A GLN* 3.0 43.1 + - + +
339A ALA* 4.0 5.2 - - - +
341A GLY* 1.3 71.9 - - - +
343A PHE* 1.3 63.4 + - - +
345A ALA* 3.5 7.6 + - - +
346A ALA* 3.3 22.3 + - - +
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Residues in contact with PHE 343 (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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292A LEU* 4.8 2.2 - - + -
297A MET* 4.7 15.9 - - + -
300A ILE* 3.6 29.4 - - + -
301A LEU* 4.2 9.4 - - + -
306A VAL* 3.9 19.3 - - + -
310A LEU* 3.8 9.3 - - + +
339A ALA 3.0 20.7 + - - +
340A LEU* 3.5 17.7 - - + +
342A MET* 1.3 75.0 - - - +
344A SER* 1.3 63.6 + - - +
346A ALA* 3.2 5.6 + - - +
347A LEU* 2.9 38.3 + - + +
352A LEU* 3.6 26.6 - - + +
356A MET* 4.0 15.3 - - + -
361A LEU* 6.1 0.4 - - + -
377A PHE* 4.0 29.4 - + - -
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Residues in contact with SER 344 (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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284A GLN* 5.2 3.1 - - - -
285A GLN* 5.5 5.3 - - - -
288A LEU* 3.5 25.9 - - - +
340A LEU* 2.9 27.3 + - - +
341A GLY* 3.6 8.0 + - - -
342A MET 3.5 0.2 - - - -
343A PHE* 1.3 74.9 - - - +
345A ALA* 1.3 56.4 + - - +
347A LEU* 3.7 9.2 - - - +
348A ALA* 2.8 32.7 + - - +
374A VAL* 3.8 16.0 - - - +
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Residues in contact with ALA 345 (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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285A GLN* 5.2 4.3 - - - +
313A TYR* 5.1 11.2 - - + -
341A GLY 3.2 14.5 + - - +
342A MET* 3.6 12.3 - - - +
343A PHE 3.3 0.4 - - - -
344A SER* 1.3 75.0 - - - +
346A ALA* 1.3 61.7 + - - +
348A ALA* 3.7 5.2 + - - +
349A SER* 2.9 28.2 + - - -
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Residues in contact with ALA 346 (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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309A ARG* 4.6 10.8 - - + +
310A LEU* 5.6 0.7 - - + -
313A TYR* 4.6 7.5 - - + -
342A MET 3.3 9.0 + - - +
343A PHE* 3.2 9.1 + - - +
345A ALA* 1.3 75.8 - - - +
347A LEU* 1.3 63.0 + - - +
349A SER* 3.6 1.4 + - - -
350A GLY 3.4 8.8 + - - -
351A GLN* 3.4 41.7 - - + +
352A LEU* 3.5 28.7 + - + -
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Residues in contact with LEU 347 (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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343A PHE* 2.9 27.9 + - + +
344A SER* 3.7 5.8 - - - +
346A ALA* 1.3 74.4 - - - +
348A ALA* 1.3 56.2 + - - +
350A GLY* 3.0 18.9 + - - -
352A LEU* 3.9 13.2 - - + +
356A MET* 3.9 20.4 - - + -
369A ALA* 3.6 41.4 - - + +
372A GLY* 3.4 13.7 - - - -
374A VAL* 3.9 24.7 - - + +
377A PHE* 3.5 37.9 - - + -
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Residues in contact with ALA 348 (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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344A SER 2.8 22.3 + - - +
345A ALA* 3.9 6.3 - - - +
346A ALA 3.5 0.2 - - - -
347A LEU* 1.3 71.8 - - - +
349A SER* 1.3 59.8 + - - +
350A GLY 3.7 0.3 + - - -
371A LYS 4.7 1.7 - - - +
372A GLY* 3.6 24.9 - - - +
374A VAL* 3.8 13.0 - - + +
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Residues in contact with SER 349 (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 TYR* 6.0 1.0 - - - -
345A ALA 2.9 20.6 + - - -
346A ALA* 3.7 8.0 - - - -
347A LEU 3.2 0.4 - - - -
348A ALA* 1.3 76.1 - - - +
350A GLY* 1.3 55.2 + - - +
351A GLN* 3.4 23.4 + - - +
371A LYS 5.3 0.9 - - - -
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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
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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