Contacts of the helix formed by residues 295 - 314 (chain B) in PDB entry 3QKJ
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 LEU 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.7 11.2 - - + -
291B THR* 2.8 38.6 + - + +
292B PHE 3.8 1.0 - - - +
293B ASN 3.7 0.4 - - - -
294B LYS* 1.3 97.0 - - + +
296B VAL* 1.4 63.0 + - - +
297B SER* 3.8 20.6 - - - +
298B TYR* 3.2 14.7 + - + +
299B ARG* 3.2 20.2 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS 4.1 1.0 + - - -
295B LEU* 1.4 71.0 - - - +
297B SER* 1.4 60.2 + - - +
299B ARG* 3.2 37.9 + - + +
300B LYS* 2.9 32.1 + - + +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.8 19.4 - - - -
265B GLY* 5.3 1.6 - - - -
295B LEU* 3.8 17.0 - - - +
296B VAL* 1.4 83.1 - - - +
298B TYR* 1.4 58.5 + - - +
300B LYS* 3.5 9.7 + - - +
301B ALA* 3.0 27.9 + - - +
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Residues in contact with TYR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TRP* 3.6 16.5 - - - -
237B SER* 4.6 3.4 - - - -
238B TRP 3.6 20.7 + - - -
239B TRP* 3.7 31.4 - + + -
240B PRO* 5.0 0.2 - - + -
287B PHE* 3.7 7.6 - + - -
288B ASN* 3.0 40.4 + - - +
291B THR* 3.7 27.1 - - + +
292B PHE* 3.5 27.8 - + + -
295B LEU* 3.2 14.4 + - + +
297B SER* 1.4 76.9 + - - +
299B ARG* 1.3 61.8 + - - +
301B ALA* 3.3 3.0 + - - +
302B MET* 3.0 53.0 + - + +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 3.2 64.1 + - + +
293B ASN* 4.4 11.7 + - - +
294B LYS 4.9 2.8 + - - -
295B LEU 3.2 5.1 + - - +
296B VAL* 3.2 52.4 + - + +
298B TYR* 1.3 76.4 - - - +
300B LYS* 1.3 60.4 + - - +
302B MET* 3.3 4.9 - - - +
303B TYR* 3.2 18.7 + - - +
326B GLU* 6.1 6.4 - - - +
329B LEU* 3.4 15.6 - - + +
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SO4 2.8 40.7 + - - -
265B GLY* 4.0 22.0 - - - +
296B VAL* 2.9 17.3 + - + +
297B SER* 3.8 8.1 - - - +
299B ARG* 1.3 73.7 - - - +
301B ALA* 1.3 64.6 + - - +
303B TYR* 3.2 8.0 + - - +
304B HIS* 3.1 49.9 + - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.5 20.9 - - + +
240B PRO* 4.0 12.8 - - + -
264B PHE* 3.5 35.0 - - - +
265B GLY* 4.0 2.0 - - - -
297B SER 3.0 17.3 + - - +
298B TYR* 3.3 5.6 + - - +
300B LYS* 1.3 75.9 - - - +
302B MET* 1.4 56.7 + - + +
304B HIS 3.4 0.3 + - - -
305B ALA* 3.0 30.8 + - - +
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TRP* 3.6 18.6 - - + -
240B PRO* 3.6 38.8 - - + -
283B PHE* 3.9 31.0 - - - -
287B PHE* 4.1 9.2 - - + -
292B PHE* 4.1 13.7 - - + -
298B TYR* 3.0 39.6 + - + +
299B ARG* 3.3 10.8 - - - +
300B LYS 3.3 0.2 - - - -
301B ALA* 1.4 72.9 - - - +
303B TYR* 1.3 59.3 + - - +
305B ALA* 4.6 2.7 - - - -
306B LEU* 2.9 38.4 + - - +
329B LEU* 4.1 14.8 - - + -
333B LEU* 4.5 3.8 - - + -
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG 3.2 10.3 + - - +
300B LYS* 3.2 10.5 + - - +
302B MET* 1.3 79.1 - - - +
304B HIS* 1.3 85.7 + + - +
306B LEU* 3.8 0.5 - - - +
307B GLU* 2.9 56.0 + - + +
325B LEU* 5.1 5.2 - - + +
328B GLN* 3.4 40.0 + - + -
329B LEU* 3.8 16.1 - - + +
332B MET* 3.3 37.7 - - + +
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SO4 4.0 21.7 + - - -
264B PHE* 3.6 26.5 - - + -
265B GLY* 4.2 11.2 - - - +
300B LYS* 3.1 60.0 + - + +
301B ALA 4.0 2.2 - - - +
303B TYR* 1.3 98.7 - + - +
305B ALA* 1.3 63.3 + - - +
307B GLU* 3.8 4.8 - - - +
308B LYS* 3.2 17.8 + - - +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.5 1.7 - - - +
240B PRO* 3.6 28.3 - - + -
264B PHE* 3.6 22.3 - - + -
280B LEU* 4.4 14.8 - - + +
301B ALA 3.0 18.0 + - - +
302B MET* 4.0 4.7 - - + +
304B HIS* 1.3 77.2 - - - +
306B LEU* 1.4 60.0 + - + +
308B LYS* 3.3 5.7 + - - +
309B ALA* 3.1 24.9 + - - +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.6 6.3 - - + -
283B PHE* 3.9 17.0 - - + -
302B MET* 2.9 26.6 + - + +
303B TYR* 4.3 2.0 - - - +
305B ALA* 1.4 76.0 - - + +
307B GLU* 1.3 53.3 + - - +
309B ALA* 3.5 6.9 - - + +
310B ARG* 2.8 35.0 + - - +
329B LEU* 4.6 2.7 - - + -
332B MET* 3.8 38.3 - - + +
333B LEU* 3.8 28.3 - - + +
335B TRP* 4.0 4.8 - - + -
336B ALA* 3.7 23.3 - - + -
340B PHE* 4.0 15.0 - - + -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 2.9 42.9 + - + +
304B HIS* 3.8 7.0 - - - +
306B LEU* 1.3 72.6 - - - +
308B LYS* 1.3 64.7 + - - +
310B ARG* 2.9 49.1 + - - +
311B VAL* 3.1 29.3 + - + +
328B GLN* 5.5 0.9 - - - +
332B MET* 4.0 12.3 - - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.9 21.1 - - + -
242B MET* 3.8 25.3 - - + +
264B PHE* 4.0 10.1 - - + -
304B HIS 3.2 12.8 + - - +
305B ALA 3.5 9.2 - - - +
307B GLU* 1.3 75.9 - - - +
309B ALA* 1.4 61.9 + - - +
311B VAL* 3.5 6.0 + - + +
312B ARG* 3.1 51.9 + - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.9 16.5 - - + +
280B LEU* 4.6 1.8 - - + -
305B ALA 3.1 13.0 + - - +
306B LEU* 3.5 14.4 - - + +
308B LYS* 1.4 75.2 - - - +
310B ARG* 1.4 56.9 + - - +
312B ARG* 3.4 5.1 + - - +
313B ALA* 2.9 31.5 + - - +
335B TRP* 3.7 11.4 - - + -
340B PHE* 4.5 6.7 - - + -
348B LEU* 3.7 24.7 - - + +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU 2.8 20.8 + - - +
307B GLU* 2.9 42.7 + - - +
308B LYS 3.3 0.2 - - - -
309B ALA* 1.4 70.3 - - - +
311B VAL* 1.3 85.5 + - - +
313B ALA 3.5 0.3 + - - -
314B GLY 3.2 3.3 + - - -
315B LYS* 2.9 67.1 + - + +
316B THR* 4.1 14.6 - - - +
317B PHE* 3.6 37.2 - - + +
332B MET* 5.2 3.1 - - - -
335B TRP* 3.7 15.0 - - + -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 3.1 22.8 + - + +
308B LYS* 4.0 7.4 - - + +
309B ALA 3.4 0.2 - - - -
310B ARG* 1.3 100.2 - - - +
312B ARG* 1.3 65.5 + - + +
314B GLY* 3.2 14.0 + - - -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLY* 2.7 37.2 + - - -
228B LEU* 3.6 19.6 - - - +
242B MET* 3.9 8.5 - - - -
308B LYS* 3.1 47.1 + - - +
309B ALA 3.6 4.0 - - - +
311B VAL* 1.3 77.7 - - + +
313B ALA* 1.3 60.2 + - - +
314B GLY* 3.2 1.4 + - - -
347B GLY* 3.1 15.4 - - - +
348B LEU* 3.0 27.5 + - - -
349B LYS 3.8 10.7 - - - +
350B PRO* 3.6 24.6 - - + +
351B ASN 5.3 1.5 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 2.9 17.9 + - - +
310B ARG 4.0 2.9 - - - +
311B VAL 3.4 0.2 - - - -
312B ARG* 1.3 73.6 - - - +
314B GLY* 1.3 61.5 + - - +
315B LYS* 4.3 3.4 - - + +
335B TRP* 3.8 24.7 - - + -
343B THR* 3.4 35.2 - - + +
347B GLY* 3.1 18.9 + - - +
348B LEU* 4.6 1.3 - - + -
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG 3.2 0.4 + - - -
311B VAL 3.2 16.2 + - - -
312B ARG 3.2 1.8 + - - -
313B ALA* 1.3 79.2 - - - +
315B LYS* 1.3 59.8 + - - +
316B THR* 4.2 4.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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