Contacts of the helix formed by residues 298 - 308 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105M PHE* 4.6 1.1 - + - -
140M MET* 3.7 47.6 - - + -
143M ALA* 4.6 1.6 - - + -
144M PHE* 4.5 11.2 - + + -
162M ILE* 6.0 0.2 - - + -
294M PRO* 4.2 10.8 - - + -
295M GLU* 2.4 44.5 + - + +
297M TYR* 1.3 103.0 - + - +
299M LEU* 1.3 64.7 + - - +
300M PRO* 3.3 5.3 - - - +
301M PHE* 3.0 20.6 + + - +
302M TYR* 3.1 8.7 + - - -
503M SMA 3.3 70.1 - - + +
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Residues in contact with LEU 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293M VAL* 3.7 20.0 - - + -
294M PRO* 3.7 29.1 - - + +
295M GLU 3.3 2.0 + - - -
296M TRP* 3.1 31.3 + - + +
298M PHE* 1.3 74.2 - - - +
300M PRO* 1.3 71.2 - - + +
302M TYR* 2.8 8.9 + - + +
303M ALA* 2.7 22.5 + - - +
377M LEU 4.5 1.3 - - - -
378M THR* 3.7 33.7 - - + +
379M TRP* 5.7 0.2 - - - -
381M GLY* 4.0 13.9 - - - -
382M ALA* 4.2 14.8 - - + -
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Residues in contact with PRO 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M TYR* 5.1 0.7 - - + +
296M TRP 3.7 7.4 - - - +
297M TYR 4.6 3.8 - - - +
298M PHE* 3.4 3.6 - - - +
299M LEU* 1.3 89.2 - - + +
301M PHE* 1.3 80.0 + - + +
303M ALA* 3.0 13.7 + - - +
304M ILE* 3.1 13.8 + - - +
374M PHE* 4.0 31.2 - - + +
377M LEU* 3.7 24.5 - - + +
378M THR* 3.3 34.9 - - - +
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Residues in contact with PHE 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M TYR* 4.0 9.9 - + - -
136M TYR* 3.0 34.1 - + - -
140M MET* 4.8 9.6 - - - -
297M TYR 5.0 2.5 - - - -
298M PHE 3.0 11.4 + - - +
300M PRO* 1.3 85.8 - - + +
302M TYR* 1.3 60.7 + - - +
304M ILE* 3.8 8.6 + - + +
305M LEU 3.3 14.9 + - - -
336M MET* 3.3 35.4 - - + +
339M ALA* 4.5 12.3 - - + -
340M ILE* 3.2 43.1 - - + -
343M MET* 4.7 10.1 - - + -
374M PHE* 4.7 11.2 - + - -
400M TRP* 5.1 9.4 - + - -
503M SMA 4.4 13.7 - - + -
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Residues in contact with TYR 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M ILE 4.7 4.7 + - - -
293M VAL* 5.4 0.2 - - + -
294M PRO* 3.7 29.5 - - + +
298M PHE 3.1 10.7 + - - +
299M LEU* 2.8 14.0 + - + +
301M PHE* 1.3 75.4 - - - +
303M ALA* 1.3 69.7 + - - +
305M LEU* 3.1 5.9 + - - +
306M ARG* 3.0 43.9 + - - +
381M GLY* 3.1 35.7 - - - -
503M SMA 3.5 47.3 - + + +
150R PRO 4.4 4.3 + - - -
151R CYS 2.8 29.1 + - - -
152R HIS* 3.7 14.1 - + - -
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Residues in contact with ALA 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299M LEU 2.7 11.3 + - - +
300M PRO 3.2 9.4 - - - +
302M TYR* 1.3 74.2 - - - +
304M ILE* 1.3 64.0 + - - +
306M ARG* 2.9 25.3 + - - +
307M ALA* 3.0 13.6 + - - +
377M LEU* 3.3 36.8 - - + +
380M VAL* 4.1 10.3 - - + -
381M GLY* 4.1 7.0 - - - +
393M SER* 4.7 6.7 - - - -
397M SER* 5.0 0.4 - - - -
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Residues in contact with ILE 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300M PRO 3.1 5.1 + - - +
301M PHE* 3.8 15.3 - - + +
303M ALA* 1.3 77.8 - - - +
305M LEU* 1.3 65.5 + - - +
307M ALA* 3.0 17.5 + - - +
308M PHE* 3.4 14.7 - - + -
335M ALA* 3.9 34.8 - - + +
336M MET* 4.1 4.0 - - - +
339M ALA* 3.8 23.8 - - + -
377M LEU* 3.4 34.3 - - + +
397M SER* 3.7 22.2 - - - +
400M TRP* 4.4 13.2 - - + -
401M PHE* 4.6 3.8 - - + -
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Residues in contact with LEU 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M LEU* 4.0 18.6 - - + -
301M PHE 3.3 11.0 + - - +
302M TYR* 3.1 10.8 + - - +
304M ILE* 1.3 79.8 - - - +
306M ARG* 1.3 60.2 + - - +
307M ALA 3.4 0.3 + - - -
308M PHE 3.7 10.9 + - - +
329M LYS 5.3 0.4 - - - +
332M GLY* 3.5 45.4 - - - +
333M VAL* 3.8 12.8 - - + +
336M MET* 4.0 20.2 - - - -
503M SMA 4.5 4.5 - - + -
131R HIS* 4.0 17.0 - - + +
132R LEU* 4.3 2.2 - - + -
152R HIS* 3.6 34.1 - - + +
166R PRO* 6.0 0.9 - - - +
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Residues in contact with ARG 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302M TYR* 3.0 46.0 + - - +
303M ALA* 2.9 20.8 + - - +
305M LEU* 1.3 72.6 - - - +
307M ALA* 1.3 67.1 + - - +
308M PHE* 3.2 3.4 - - - -
309M THR* 3.8 15.9 - - - +
380M VAL* 2.7 25.2 + - - +
381M GLY* 3.5 11.6 + - - -
383M GLN* 2.4 33.5 + - - +
384M GLN* 3.6 15.9 + - - +
385M THR* 4.4 22.1 - - + +
389M TYR* 5.4 1.6 - - - +
393M SER* 5.8 5.5 - - - +
131R HIS* 6.1 0.4 - - - -
152R HIS* 4.1 30.9 - - + +
166R PRO* 6.1 2.9 - - - -
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Residues in contact with ALA 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303M ALA 3.0 8.4 + - - +
304M ILE 3.0 11.8 + - - +
306M ARG* 1.3 79.5 - - - +
308M PHE* 1.3 63.2 + - + +
309M THR* 3.1 12.3 + - - +
312M VAL* 3.7 11.0 - - - +
390M ASP* 5.2 2.8 - - - +
393M SER* 3.6 24.9 - - - +
394M LEU* 4.1 22.2 - - + +
397M SER* 3.8 18.6 - - - +
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Residues in contact with PHE 308 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304M ILE* 3.4 25.6 - - + -
305M LEU 3.7 13.1 + - - +
306M ARG 3.2 1.4 - - - +
307M ALA* 1.3 75.2 - - + +
309M THR* 1.3 61.7 + - - +
312M VAL* 4.0 17.9 - - + -
314M VAL* 5.5 5.6 - - + -
315M VAL* 3.8 5.2 - - + -
328M ALA* 4.2 13.7 - - - +
331M PHE* 3.3 36.8 - + + -
332M GLY* 4.5 3.9 - - - +
335M ALA* 3.4 33.9 - - + -
394M LEU* 3.7 24.2 - - + -
397M SER* 4.1 20.6 - - - -
398M ALA* 5.6 0.9 - - - -
401M PHE* 5.3 6.7 - + - -
166R PRO* 4.2 7.6 - - - +
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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