Contacts of the helix formed by residues 298 - 308 (chain G) in PDB entry 2QJK
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 298 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G PHE* 4.6 0.4 - + - -
140G MET* 3.7 43.5 - - + -
143G ALA* 4.6 2.0 - - + -
144G PHE* 4.5 10.3 - - + -
162G ILE* 5.3 0.9 - - + -
294G PRO* 4.3 11.0 - - + -
295G GLU* 2.4 54.0 + - - +
297G TYR* 1.3 99.7 - + - +
299G LEU* 1.3 64.6 + - - +
300G PRO* 3.3 4.7 - - - -
301G PHE* 3.0 19.8 + + - +
302G TYR* 3.1 9.8 + - - -
503G SMA 3.2 67.3 - - + +
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Residues in contact with LEU 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293G VAL* 3.7 28.0 - - + -
294G PRO* 3.8 19.1 - - + +
296G TRP* 3.1 30.6 + - + +
298G PHE* 1.3 75.5 - - - +
300G PRO* 1.3 70.6 - - + +
302G TYR* 2.8 9.0 + - + +
303G ALA* 2.7 22.5 + - - +
377G LEU 4.5 0.9 - - - -
378G THR* 3.6 33.9 - - + +
381G GLY* 4.0 14.5 - - - -
382G ALA* 4.2 14.4 - - + -
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Residues in contact with PRO 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 5.1 0.7 - - + +
296G TRP 3.7 7.0 - - - +
297G TYR* 4.5 4.3 - - - +
298G PHE* 3.3 4.9 - - - +
299G LEU* 1.3 91.9 - - + +
301G PHE* 1.3 78.4 + - + +
303G ALA* 3.0 13.2 + - - +
304G ILE* 3.1 13.9 + - - +
374G PHE* 4.0 30.3 - - + +
377G LEU* 3.6 25.4 - - + +
378G THR* 3.4 33.2 - - - +
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Residues in contact with PHE 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 4.0 8.5 - + - -
136G TYR* 3.1 32.8 - + - -
140G MET* 4.8 5.2 - - - -
297G TYR 5.0 2.0 - - - -
298G PHE 3.0 8.5 + - - +
300G PRO* 1.3 86.8 - - + +
302G TYR* 1.3 60.7 + - - +
304G ILE* 3.8 7.7 + - + +
305G LEU 3.2 15.2 + - - -
336G MET* 3.3 26.3 - - + +
339G ALA* 4.5 17.3 - - + -
340G ILE* 3.2 42.8 - - + -
343G MET* 4.7 9.4 - - + -
374G PHE* 4.7 12.8 - + - -
400G TRP* 5.0 10.3 - + - -
503G SMA 3.8 24.9 - - + -
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Residues in contact with TYR 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G ILE 4.8 4.9 + - - -
293G VAL* 5.4 0.4 - - + -
294G PRO* 3.7 26.8 - - + +
298G PHE 3.1 10.3 + - - +
299G LEU* 2.8 12.5 + - + +
301G PHE* 1.3 75.8 - - - +
303G ALA* 1.3 70.2 + - - +
305G LEU* 3.1 5.2 + - - +
306G ARG* 3.0 48.6 + - - +
381G GLY* 3.1 33.4 - - - -
503G SMA 3.4 61.1 - + + +
150L PRO 4.7 3.1 + - - -
151L CYS 2.9 17.3 + - - -
152L HIS* 3.6 14.1 - + - -
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Residues in contact with ALA 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G LEU 2.7 12.0 + - - +
300G PRO 3.2 9.9 - - - +
302G TYR* 1.3 74.9 - - - +
304G ILE* 1.3 65.1 + - - +
306G ARG* 2.9 25.2 + - - +
307G ALA* 3.0 14.2 + - - +
377G LEU* 3.4 36.3 - - + +
380G VAL* 4.1 9.6 - - + -
381G GLY* 4.2 7.2 - - - +
393G SER* 4.7 7.4 - - - -
397G SER* 5.0 0.2 - - - -
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Residues in contact with ILE 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G PRO 3.1 5.1 + - - +
301G PHE* 3.8 13.9 - - + +
303G ALA* 1.3 77.8 - - - +
305G LEU* 1.3 66.8 + - - +
307G ALA* 3.1 16.8 + - - +
308G PHE* 3.4 14.6 - - + -
335G ALA* 3.9 34.5 - - + +
336G MET* 4.1 4.0 - - - +
339G ALA* 3.8 23.3 - - + -
377G LEU* 3.5 32.9 - - + +
397G SER* 3.6 23.3 - - - +
400G TRP* 4.5 13.9 - - + -
401G PHE* 4.6 4.3 - - + -
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Residues in contact with LEU 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LEU* 4.0 22.0 - - + -
301G PHE 3.2 9.8 + - - +
302G TYR 3.1 9.8 + - - +
304G ILE* 1.3 81.8 - - - +
306G ARG* 1.3 62.9 + - - +
307G ALA 3.5 0.3 + - - -
308G PHE 3.8 10.7 + - - +
329G LYS 5.3 0.4 - - - +
332G GLY* 3.5 45.5 - - - +
333G VAL* 3.8 11.9 - - + +
336G MET* 4.0 17.3 - - + -
503G SMA 4.4 6.7 - - + -
131L HIS* 4.0 17.4 - - + +
132L LEU* 4.2 3.4 - - + -
152L HIS* 3.7 31.0 - - + +
166L PRO* 6.0 1.0 - - - +
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Residues in contact with ARG 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G TYR* 3.0 45.6 + - - +
303G ALA* 2.9 19.7 + - - +
305G LEU* 1.3 72.3 - - - +
307G ALA* 1.3 67.1 + - - +
308G PHE* 3.2 4.0 - - - -
309G THR* 3.8 15.1 - - - +
380G VAL* 2.8 24.2 + - - +
381G GLY* 3.6 11.7 + - - -
383G GLN 2.4 32.3 + - - -
384G GLN* 3.6 16.4 + - - +
385G THR* 4.4 24.2 + - + +
389G TYR* 5.6 1.0 - - - +
393G SER* 5.9 4.5 - - - +
131L HIS* 6.1 0.2 - - - -
152L HIS* 4.2 30.2 - - + +
166L PRO* 6.2 3.8 - - - +
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Residues in contact with ALA 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G ALA 3.0 9.0 + - - +
304G ILE 3.1 11.8 + - - +
306G ARG* 1.3 79.7 - - - +
308G PHE* 1.3 61.9 + - + +
309G THR* 3.1 12.8 + - - +
312G VAL* 3.7 10.6 - - - +
390G ASP* 5.2 3.4 - - - +
393G SER* 3.6 25.8 - - - +
394G LEU* 4.2 21.9 - - + +
397G SER* 3.8 18.6 - - - +
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Residues in contact with PHE 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G ILE* 3.4 24.9 - - + -
305G LEU 3.8 10.1 + - - +
306G ARG 3.2 2.4 - - - +
307G ALA* 1.3 72.7 - - + +
309G THR* 1.3 62.8 + - - +
312G VAL* 4.0 17.5 - - + -
314G VAL* 5.3 3.1 - - + -
315G VAL* 3.9 4.7 - - + -
328G ALA* 4.1 13.9 - - - +
331G PHE* 3.3 38.4 - + + -
332G GLY* 4.5 5.9 - - - -
335G ALA* 3.4 33.2 - - + -
394G LEU* 3.7 23.8 - - + -
397G SER* 4.1 20.9 - - - -
398G ALA* 5.6 1.1 - - - -
401G PHE* 5.3 7.0 - + - -
166L PRO* 4.3 8.5 - - - +
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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