Contacts of the helix formed by residues 298 - 308 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D SMA 3.6 57.6 - - + +
105D PHE* 4.7 0.7 - + - -
140D MET* 3.7 50.9 - - + -
143D ALA* 4.7 0.2 - - + -
144D PHE* 4.5 11.0 - - + -
162D ILE* 4.9 1.3 - - + -
294D PRO* 4.3 10.3 - - + -
295D GLU* 2.4 52.3 + - - +
297D TYR* 1.3 103.0 - + - +
299D LEU* 1.3 63.9 + - - +
300D PRO* 3.3 4.5 - - - -
301D PHE* 3.0 12.2 + + - +
302D TYR* 3.0 17.6 + - - -
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Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL* 3.7 27.8 - - + -
294D PRO* 3.8 20.2 - - + +
295D GLU 3.3 0.4 + - - -
296D TRP* 3.1 30.4 + - + +
298D PHE* 1.3 76.7 - - - +
300D PRO* 1.3 64.6 - - + +
302D TYR* 2.8 8.6 + - + +
303D ALA* 2.6 29.5 + - - +
377D LEU 4.5 0.7 - - - -
378D THR* 3.6 34.5 - - + +
381D GLY* 3.9 14.3 - - - -
382D ALA* 4.2 14.8 - - + -
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Residues in contact with PRO 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR* 5.4 0.4 - - + -
296D TRP 3.7 7.4 - - - +
297D TYR 4.5 3.8 - - - +
298D PHE* 3.3 4.3 - - - +
299D LEU* 1.3 93.3 - - + +
301D PHE* 1.3 76.6 + - + +
303D ALA* 3.0 13.3 + - - +
304D ILE* 3.1 14.6 + - + +
374D PHE* 4.0 31.6 - - + +
377D LEU* 3.6 33.6 - - + +
378D THR* 3.4 23.3 - - - +
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Residues in contact with PHE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SMA 4.0 17.9 - - + -
109D TYR* 3.9 9.2 - + - -
136D TYR* 3.1 33.0 - + - -
140D MET* 4.8 4.3 - - - -
297D TYR 5.0 2.5 - - - -
298D PHE 3.0 8.9 + - - +
300D PRO* 1.3 88.4 - - + +
302D TYR* 1.3 61.3 + - - +
304D ILE* 3.7 8.3 + - + +
305D LEU 3.2 15.9 + - - -
336D MET* 3.4 30.0 - - + +
339D ALA* 4.5 17.5 - - + -
340D ILE* 3.2 43.7 - - + -
343D MET* 4.8 9.4 - - + -
374D PHE* 4.7 13.0 - + - -
400D TRP* 5.1 9.4 - + - -
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Residues in contact with TYR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C PRO 4.7 3.1 + - - -
151C CYS 3.0 18.7 + - - -
152C HIS* 3.6 26.7 - + - -
2D SMA 3.5 41.2 - + + +
292D ILE 4.8 5.9 + - - -
293D VAL* 5.4 0.4 - - + -
294D PRO* 3.7 32.0 - - + +
298D PHE 3.0 10.5 + - - +
299D LEU* 2.8 12.0 + - + +
301D PHE* 1.3 75.5 - - - +
303D ALA* 1.3 70.8 + - - +
305D LEU* 3.1 5.3 + - + +
306D ARG* 3.0 49.3 + - - +
381D GLY* 3.1 35.2 - - - -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D LEU 2.6 11.2 + - - +
300D PRO 3.2 9.6 - - - +
302D TYR* 1.3 79.6 - - - +
304D ILE* 1.3 63.9 + - - +
306D ARG* 2.9 19.7 + - - +
307D ALA* 3.0 13.0 + - - +
377D LEU* 3.4 36.3 - - + +
380D VAL* 4.1 10.1 - - + -
381D GLY* 4.2 7.0 - - - +
393D SER* 4.8 7.8 - - - -
397D SER* 5.0 0.4 - - - -
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Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D PRO 3.1 5.6 + - - +
301D PHE* 3.8 14.1 - - + +
303D ALA* 1.3 77.8 - - - +
305D LEU* 1.3 66.4 + - - +
307D ALA* 3.0 12.5 + - - +
308D PHE* 3.4 19.5 - - + -
335D ALA* 4.0 35.2 - - + +
336D MET* 4.1 3.8 - - - +
339D ALA* 3.8 24.0 - - + -
377D LEU* 3.5 32.5 - - + +
397D SER* 3.6 23.3 - - - +
400D TRP* 4.5 13.2 - - + -
401D PHE* 4.6 3.1 - - + -
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 4.0 16.6 - - + +
132C LEU* 4.3 3.6 - - + -
152C HIS* 3.7 31.4 - - + +
166C PRO* 6.0 0.7 - - - +
2D SMA 4.5 4.5 - - + -
165D LEU* 4.1 20.6 - - + -
301D PHE 3.2 10.2 + - - +
302D TYR* 3.1 11.0 + - - +
304D ILE* 1.3 80.8 - - - +
306D ARG* 1.3 64.0 + - - +
307D ALA 3.5 0.2 + - - -
308D PHE 3.8 8.8 + - - +
329D LYS 5.3 0.4 - - - +
332D GLY* 3.5 48.2 - - - +
333D VAL* 3.7 12.3 - - + +
336D MET* 4.1 16.8 - - + -
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Residues in contact with ARG 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 6.1 0.4 - - - -
150C PRO 5.6 1.8 + - - -
151C CYS 4.9 1.8 + - - -
152C HIS* 4.1 32.5 - - + +
166C PRO* 6.1 4.1 - - - +
302D TYR* 3.0 46.8 + - + +
303D ALA* 2.9 19.2 + - - +
305D LEU* 1.3 72.5 - - - +
307D ALA* 1.3 66.9 + - - +
308D PHE* 3.1 3.9 + - - -
309D THR* 3.6 14.2 - - - +
380D VAL 3.1 19.2 + - - -
381D GLY* 3.3 10.3 + - - -
383D GLN 2.4 31.7 + - - -
384D GLN* 4.0 7.7 + - - +
385D THR* 4.1 33.7 + - + +
393D SER* 6.2 1.1 - - - -
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Residues in contact with ALA 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA 3.0 7.2 + - - +
304D ILE 3.0 12.3 + - - +
306D ARG* 1.3 79.6 - - - +
308D PHE* 1.3 63.9 + - + +
309D THR* 3.1 15.2 + - - +
312D VAL* 3.7 9.5 - - - +
390D ASP* 5.2 2.9 - - - +
393D SER* 3.6 26.0 - - - +
394D LEU* 4.2 21.3 - - + +
397D SER* 3.8 18.4 - - - +
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Residues in contact with PHE 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PRO* 4.3 8.8 - - - +
304D ILE* 3.4 24.2 - - + -
305D LEU 3.8 10.0 + - - +
306D ARG 3.1 2.5 - - - +
307D ALA* 1.3 73.7 - - + +
309D THR* 1.3 61.8 + - - +
312D VAL* 4.0 17.7 - - + -
314D VAL* 5.8 1.8 - - + -
315D VAL* 3.8 4.7 - - + -
328D ALA* 4.1 13.9 - - - +
331D PHE* 3.3 37.9 - + + -
332D GLY* 4.4 6.5 - - - +
335D ALA* 3.4 34.1 - - + -
394D LEU* 3.7 24.0 - - + -
397D SER* 4.1 19.7 - - - -
398D ALA* 5.6 0.9 - - - -
401D PHE* 5.3 6.3 - + - -
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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