Contacts of the helix formed by residues 298 - 308 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140P MET* 3.7 45.3 - - + -
143P ALA* 4.6 2.2 - - + -
144P PHE* 4.5 10.3 - - + -
162P ILE* 4.9 0.7 - - + -
294P PRO* 4.2 10.8 - - + -
295P GLU* 2.4 42.7 + - - +
297P TYR* 1.3 102.8 - + - +
299P LEU* 1.3 64.9 + - - +
300P PRO* 3.4 4.9 - - - -
301P PHE* 3.0 20.0 + + - +
302P TYR* 3.1 9.8 + - - +
503P SMA 3.5 73.0 - - + +
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Residues in contact with LEU 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293P VAL* 3.7 19.5 - - + -
294P PRO* 3.7 28.7 - - + +
295P GLU 3.3 0.6 + - - -
296P TRP* 3.1 30.4 + - + +
298P PHE* 1.3 75.8 - - - +
300P PRO* 1.3 70.3 - - + +
302P TYR* 2.7 9.1 + - + +
303P ALA* 2.7 22.7 + - - +
377P LEU 4.5 1.1 - - - -
378P THR* 3.7 33.2 - - + +
381P GLY* 4.0 14.1 - - - -
382P ALA* 4.2 14.8 - - + -
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Residues in contact with PRO 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P TYR* 5.1 1.1 - - + +
296P TRP 3.7 7.0 - - - +
297P TYR 4.5 4.3 - - - +
298P PHE* 3.4 3.6 - - - +
299P LEU* 1.3 91.4 - - + +
301P PHE* 1.3 80.2 + - + +
303P ALA* 2.9 10.7 + - - +
304P ILE* 3.1 12.3 + - - +
374P PHE* 4.0 31.2 - - + +
377P LEU* 3.8 33.9 - - + +
378P THR* 3.3 27.5 - - + +
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Residues in contact with PHE 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P TYR* 4.0 7.9 - + - -
136P TYR* 3.0 33.4 - + - -
140P MET* 4.8 4.5 - - - -
297P TYR 5.0 2.0 - - - -
298P PHE 3.0 11.9 + - - +
300P PRO* 1.3 85.8 - - + +
302P TYR* 1.3 60.4 + - - +
304P ILE* 3.8 8.8 + - + +
305P LEU 3.3 15.8 + - - -
336P MET* 3.4 30.2 - - + +
339P ALA* 4.5 17.0 - - + -
340P ILE* 3.2 42.8 - - + -
343P MET* 4.7 9.4 - - + -
374P PHE* 4.7 12.6 - + - -
400P TRP* 5.1 10.1 - + - -
503P SMA 4.1 17.7 - - + -
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Residues in contact with TYR 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O PRO 4.8 2.4 + - - -
151O CYS 2.9 19.3 + - - -
152O HIS* 3.5 19.5 - + - -
292P ILE 4.8 5.5 + - - -
293P VAL* 5.4 0.2 - - + -
294P PRO* 3.7 27.8 - - + +
298P PHE 3.1 10.9 + - - +
299P LEU* 2.7 13.5 + - + +
301P PHE* 1.3 76.0 - - - +
303P ALA* 1.3 69.5 + - - +
305P LEU* 3.0 5.5 + - - +
306P ARG* 3.0 47.8 + - - +
381P GLY* 3.1 34.5 - - - -
503P SMA 3.2 54.1 - + + +
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Residues in contact with ALA 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299P LEU 2.7 10.3 + - - +
300P PRO 3.2 9.2 - - - +
302P TYR* 1.3 77.4 - - - +
304P ILE* 1.3 65.6 + - - +
306P ARG* 2.8 22.5 + - - +
307P ALA* 3.0 12.3 + - - +
377P LEU* 3.3 36.8 - - + +
380P VAL* 4.1 10.1 - - + -
381P GLY* 4.1 7.0 - - - +
393P SER* 4.8 7.9 - - - -
397P SER* 5.0 0.2 - - - -
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Residues in contact with ILE 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P PRO 3.1 5.9 + - - +
301P PHE* 3.8 15.0 - - + +
303P ALA* 1.3 79.5 - - - +
305P LEU* 1.3 66.5 + - - +
307P ALA* 3.0 14.8 + - - +
308P PHE* 3.5 14.5 - - + -
335P ALA* 3.9 35.2 - - + +
336P MET* 4.2 4.0 - - - +
339P ALA* 3.8 22.4 - - + -
377P LEU* 3.4 33.4 - - + +
397P SER* 3.6 22.9 - - - +
400P TRP* 4.5 13.5 - - + -
401P PHE* 4.7 4.3 - - + -
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Residues in contact with LEU 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O HIS* 3.9 19.7 - - + +
132O LEU* 4.2 3.6 - - + -
152O HIS* 3.9 28.5 - - + +
166O PRO* 5.9 1.0 - - - +
165P LEU* 4.0 18.8 - - + -
301P PHE 3.3 10.6 + - - +
302P TYR 3.0 9.8 + - - +
304P ILE* 1.3 81.6 - - - +
306P ARG* 1.3 62.8 + - - +
307P ALA 3.4 0.3 + - - -
308P PHE 3.7 10.4 + - - +
329P LYS 5.4 0.9 - - - +
332P GLY* 3.6 46.9 - - - +
333P VAL* 3.8 12.1 - - + +
336P MET* 3.9 20.8 - - + +
503P SMA 4.3 6.1 - - + -
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Residues in contact with ARG 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O HIS* 6.0 0.9 - - - -
150O PRO 5.8 1.4 + - - -
151O CYS 5.1 1.0 + - - -
152O HIS* 4.2 31.3 - - + +
166O PRO* 6.0 5.5 - - + +
302P TYR* 3.0 48.9 + - - +
303P ALA* 2.8 18.3 + - - +
305P LEU* 1.3 74.0 - - - +
307P ALA* 1.3 67.0 + - - +
308P PHE* 3.2 6.2 - - - -
309P THR* 4.5 6.6 + - - +
380P VAL 2.9 21.2 + - - -
381P GLY* 3.1 11.9 + - - -
383P GLN 2.5 31.5 + - - -
384P GLN* 4.2 7.4 + - - +
385P THR* 4.3 34.3 + - + +
389P TYR* 6.2 0.2 - - - +
393P SER* 6.1 1.3 - - - +
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Residues in contact with ALA 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303P ALA 3.0 6.3 + - - +
304P ILE 3.0 11.9 + - - +
306P ARG* 1.3 81.1 - - - +
308P PHE* 1.3 62.2 + - + +
309P THR* 3.1 18.0 + - - +
312P VAL* 3.7 8.3 - - - +
390P ASP* 5.2 3.4 - - - +
393P SER* 3.5 25.1 - - - +
394P LEU* 4.1 21.1 - - + +
397P SER* 3.8 19.3 - - - +
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Residues in contact with PHE 308 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O PRO* 4.3 9.2 - - - +
304P ILE* 3.5 25.1 - - + -
305P LEU 3.7 11.7 + - - +
306P ARG 3.2 3.2 - - - +
307P ALA* 1.3 72.8 - - + +
309P THR* 1.3 60.5 + - - +
312P VAL* 4.0 17.7 - - + -
314P VAL* 5.7 3.6 - - + -
315P VAL* 4.0 4.5 - - + -
328P ALA* 4.2 13.3 - - - +
331P PHE* 3.3 37.9 - + + -
332P GLY* 4.5 4.7 - - - +
335P ALA* 3.4 33.4 - - + -
394P LEU* 3.6 24.2 - - + -
397P SER* 4.1 20.4 - - - -
398P ALA* 6.2 0.7 - - - -
401P PHE* 5.3 6.5 - + - -
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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