Contacts of the helix formed by residues 284 - 296 (chain F) in PDB entry 3K6G
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 284 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396C PHE* 4.5 4.0 - - - -
282F THR* 3.6 8.9 + - - +
283F ILE* 1.3 76.4 - - - +
285F MSE 1.3 60.4 + - - -
286F MSE 3.2 3.4 - - - -
287F THR* 3.2 13.6 + - - -
288F LEU* 2.8 27.7 + - - +
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Residues in contact with MSE 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C LEU* 3.4 16.4 - - + -
393C ARG* 4.9 0.2 - - - +
396C PHE* 3.3 63.7 + - + +
397C ARG* 2.9 48.7 - - - +
284F GLY* 1.3 71.4 - - - -
286F MSE 1.3 73.6 + - + +
288F LEU* 3.5 6.5 + - - +
289F LYS* 3.0 22.0 + - - +
305F PHE* 4.0 7.2 - - + -
309F ASP* 3.3 17.0 - - - +
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Residues in contact with MSE 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C VAL* 3.8 22.2 - - + +
284F GLY* 3.2 0.8 - - - -
285F MSE 1.3 98.6 - - + +
287F THR* 1.3 60.8 + - - +
289F LYS* 3.1 42.0 + - + +
290F ALA* 3.0 26.9 + - - +
305F PHE* 4.7 3.4 - - + -
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Residues in contact with THR 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C VAL* 3.7 22.6 - - - +
310C GLU* 3.8 48.0 + - + +
311C VAL* 4.0 6.5 - - + +
314C ALA* 3.9 11.9 - - + -
283F ILE* 4.2 4.9 - - + -
284F GLY* 3.2 19.8 + - - +
286F MSE 1.3 77.9 - - - +
288F LEU* 1.3 59.3 + - - +
290F ALA* 3.3 2.8 + - - +
291F ALA* 2.9 28.3 + - - +
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Residues in contact with LEU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 3.8 26.6 - - + +
333C THR* 4.0 14.1 - - + +
336C PHE* 3.7 39.0 - - + -
337C LEU* 3.8 34.1 - - + +
341C GLY* 5.6 0.2 - - - -
396C PHE* 4.7 8.3 - - + -
283F ILE* 3.9 19.0 - - + +
284F GLY 2.8 16.0 + - - +
285F MSE 3.5 5.4 - - - +
286F MSE 3.2 0.2 - - - -
287F THR* 1.3 78.8 - - - +
289F LYS* 1.3 56.2 + - - +
291F ALA* 3.4 5.1 + - - +
292F PHE* 2.9 29.5 + - - +
305F PHE* 4.3 1.8 - - + -
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Residues in contact with LYS 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F MSE 3.0 16.6 + - - +
286F MSE 3.1 34.4 - - + +
287F THR 3.2 0.2 - - - -
288F LEU* 1.3 73.9 - - - +
290F ALA* 1.3 65.9 + - - +
292F PHE* 3.2 1.7 + - - +
293F LYS* 2.9 40.8 + - + +
302F GLU* 2.5 46.9 + - - +
305F PHE* 3.7 36.1 - - + -
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C VAL* 4.5 5.4 - - + -
311C VAL* 3.9 23.3 - - + -
286F MSE 3.0 14.3 + - - +
287F THR* 3.3 8.7 + - - +
289F LYS* 1.3 77.1 - - - +
291F ALA* 1.3 61.1 + - - +
293F LYS* 3.4 7.2 + - - +
294F THR* 2.9 29.9 + - - -
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Residues in contact with ALA 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C VAL* 3.8 10.0 - - + +
314C ALA* 3.9 16.4 - - + -
315C ILE* 4.0 15.0 - - + +
318C ILE* 3.8 22.0 - - + -
287F THR 2.9 18.3 + - - +
288F LEU 3.5 5.6 - - - +
290F ALA* 1.3 76.9 - - - +
292F PHE* 1.3 62.4 + - - +
294F THR* 3.1 13.6 + - - -
295F LEU* 3.1 19.9 + - + +
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Residues in contact with PHE 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 5.0 1.9 - - + +
329C LEU* 3.7 30.9 - - + +
330C SER* 4.3 11.0 - - - -
333C THR* 3.5 26.7 - - + +
288F LEU 2.9 17.4 + - - +
289F LYS 3.6 2.7 - - - +
291F ALA* 1.3 76.7 - - - +
293F LYS* 1.3 58.0 + - + +
295F LEU 3.2 0.9 + - - -
296F SER* 2.7 60.4 + - - -
301F SER 3.5 22.4 - - - -
304F ALA* 4.0 14.4 - - + -
305F PHE* 3.8 31.6 - + + -
308F LEU* 3.7 20.6 - - + -
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Residues in contact with LYS 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B GLN* 6.0 3.0 - - - +
289F LYS* 2.9 37.5 + - + +
290F ALA* 4.0 6.7 - - - +
292F PHE* 1.3 80.8 - - + +
294F THR* 1.3 62.0 + - - +
295F LEU 3.6 0.2 + - - -
296F SER* 3.9 10.2 + - - +
301F SER* 3.4 37.5 + - - +
302F GLU* 3.0 38.3 + - - +
305F PHE* 5.4 0.4 - - + -
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Residues in contact with THR 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C VAL* 4.5 5.2 - - - +
315C ILE* 3.8 25.8 - - + +
290F ALA* 2.9 18.2 + - - +
291F ALA 3.3 9.9 - - - -
292F PHE 3.1 0.2 - - - -
293F LYS* 1.3 80.2 - - - +
295F LEU* 1.3 65.3 - - + +
296F SER 4.6 2.4 - - - +
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Residues in contact with LEU 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ILE* 3.9 35.9 - - + -
318C ILE* 4.5 6.3 - - + -
319C ARG* 4.2 19.1 - - + +
322C MSE 4.0 26.7 - - + -
329C LEU* 3.7 23.7 - - + +
291F ALA 3.1 17.4 + - - +
294F THR* 1.3 85.3 - - + +
296F SER* 1.3 62.7 + - - +
297F GLY 3.7 1.0 + - - -
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Residues in contact with SER 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 3.6 8.9 - - - +
292F PHE* 2.7 48.1 + - - -
293F LYS* 3.9 7.9 + - - +
294F THR 3.6 2.7 - - - +
295F LEU* 1.3 75.3 - - - +
297F GLY* 1.3 61.9 + - - +
298F ALA* 3.0 28.1 + - - +
301F SER* 4.0 10.9 - - - -
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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