Contacts of the helix formed by residues 306 - 315 (chain A) in PDB entry 1K6O
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 THR 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A ALA 6.0 0.2 - - - -
305A ILE* 1.3 80.6 - - - +
307A LEU* 1.3 70.1 + - - +
308A TRP* 2.6 31.8 + - - +
309A GLN* 2.7 32.5 + - - +
310A PHE 2.9 10.0 + - - -
345A TRP* 3.7 4.5 - - - -
214E A 3.4 32.5 - - - +
215E C 3.3 16.4 - - - +
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Residues in contact with LEU 307 (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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306A THR* 1.3 66.9 - - - +
308A TRP* 1.3 57.9 + - - +
310A PHE* 2.8 5.5 + - + +
311A LEU* 2.7 70.8 + - + -
345A TRP* 3.0 42.3 - - + +
359A LEU* 3.8 27.8 - - + +
362A ALA* 3.6 30.1 - - + -
363A LEU* 3.9 11.2 - - + -
366A TYR* 3.3 17.9 - - + +
215E C 3.0 10.9 + - - +
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Residues in contact with TRP 308 (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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306A THR* 2.6 30.0 + - - +
307A LEU* 1.3 78.4 - - - +
309A GLN* 1.3 83.7 + - + +
311A LEU* 4.0 5.4 - - - -
312A LEU* 3.2 27.1 + - + +
366A TYR* 3.3 24.7 + + + -
371A ILE* 4.2 20.2 - - + +
372A ILE* 3.8 28.9 - - + -
384A PHE* 4.0 15.1 - + + -
390A ILE* 4.0 42.0 - - + -
215E C 4.4 1.1 + - - -
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Residues in contact with GLN 309 (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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304A ALA 4.1 7.6 + - - +
305A ILE* 3.9 15.8 - - + +
306A THR* 2.7 52.1 + - - +
308A TRP* 1.3 98.5 - - + +
310A PHE* 1.3 64.3 + - - +
312A LEU* 2.9 10.7 + - - +
313A GLN* 2.9 35.1 + - - +
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Residues in contact with PHE 310 (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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305A ILE* 3.6 15.1 - - + +
306A THR 2.9 0.6 + - - -
307A LEU 2.8 10.2 + - - +
309A GLN* 1.3 76.0 - - - +
311A LEU* 1.3 71.7 + - + +
313A GLN* 3.0 21.9 + - + +
314A LEU* 3.1 46.5 + - + +
341A VAL* 4.2 7.6 - - + -
344A LEU* 4.0 12.8 - - + -
345A TRP* 3.3 63.5 - + + -
348A ARG* 4.0 33.2 - - + -
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Residues in contact with LEU 311 (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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307A LEU* 2.7 48.5 + - + +
308A TRP* 4.1 4.9 - - - +
310A PHE* 1.3 77.3 - - + +
312A LEU* 1.3 63.4 + - - +
314A LEU* 2.9 20.0 + - + +
315A LEU* 3.1 15.4 + - + +
324A ILE* 3.9 12.3 - - + +
333A PHE* 4.0 26.2 - - + -
335A LEU* 5.2 5.4 - - + -
341A VAL* 3.9 28.5 - - + -
359A LEU* 5.1 3.4 - - + -
363A LEU* 4.0 22.0 - - + -
372A ILE* 4.9 6.5 - - + -
384A PHE* 4.7 7.2 - - + -
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Residues in contact with LEU 312 (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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308A TRP* 3.2 20.3 + - + +
309A GLN* 2.9 11.1 + - - +
311A LEU* 1.3 78.3 - - - +
313A GLN* 1.3 55.3 + - + +
315A LEU* 2.7 26.3 + - - +
316A GLN* 3.2 25.7 + - + +
326A TRP* 3.9 23.6 - - + -
384A PHE* 3.6 23.9 - - + -
387A TYR* 4.5 3.4 - - + -
390A ILE* 3.9 21.5 - - + -
391A LEU* 3.4 31.0 - - + -
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Residues in contact with GLN 313 (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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305A ILE* 3.3 34.2 - - - +
309A GLN* 2.9 27.7 + - - +
310A PHE* 3.0 18.2 + - + +
312A LEU* 1.3 75.1 - - - +
314A LEU* 1.3 60.4 + - + +
316A GLN* 3.9 13.2 + - - +
317A LYS* 3.1 36.4 + - - +
348A ARG* 4.7 3.6 + - - -
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Residues in contact with LEU 314 (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 PHE* 3.4 52.3 - - + +
311A LEU* 2.9 13.3 + - + +
313A GLN* 1.3 78.5 - - + +
315A LEU* 1.3 58.7 + - - +
316A GLN 3.1 8.1 + - - -
317A LYS* 3.4 18.6 + - + +
320A ASN* 3.7 31.2 + - - +
323A MET* 4.3 19.1 - - + -
324A ILE* 3.8 18.2 - - + -
341A VAL* 3.8 19.7 - - + -
344A LEU* 4.9 5.4 - - + -
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Residues in contact with LEU 315 (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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311A LEU* 3.1 7.1 + - + +
312A LEU* 2.7 9.9 + - - +
314A LEU* 1.3 78.0 - - - +
316A GLN* 1.3 58.8 + - - +
317A LYS 3.5 1.3 - - - -
320A ASN 5.3 0.2 - - - -
321A LYS* 5.7 3.1 + - - -
324A ILE* 3.5 36.1 - - + +
325A CYS* 3.6 30.7 - - - +
326A TRP* 3.1 68.9 + - + +
333A PHE* 3.6 18.8 - - + -
384A PHE* 4.0 8.1 - - + -
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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