Contacts of the helix formed by residues 295 - 314 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TRP* 4.7 10.3 - - + -
291A THR* 2.8 38.6 + - + +
292A PHE 3.8 1.0 - - - +
293A ASN 3.7 0.8 - - - -
294A LYS* 1.3 94.9 - - + +
296A VAL* 1.3 64.4 + - - +
297A SER* 3.8 21.1 - - - +
298A TYR* 3.2 13.9 + - + +
299A ARG* 3.2 18.9 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS 4.2 1.0 + - - -
295A LEU* 1.3 71.2 - - - +
297A SER* 1.4 58.7 + - - +
299A ARG* 3.1 38.7 + - + +
300A LYS* 2.9 31.5 + - + +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.8 18.6 - - - -
265A GLY* 5.2 2.1 - - - -
295A LEU* 3.8 17.8 - - - +
296A VAL* 1.4 81.8 - - - +
298A TYR* 1.3 57.0 + - - +
300A LYS* 3.5 7.7 + - - +
301A ALA* 3.0 27.4 + - - +
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TRP* 3.6 16.8 - - - -
237A SER* 4.6 3.1 - - - -
238A TRP 3.6 21.7 + - - -
239A TRP* 3.7 30.9 - + + -
240A PRO* 5.0 0.4 - - + -
287A PHE* 3.7 7.4 - + - -
288A ASN* 3.0 40.0 + - + +
291A THR* 3.6 29.6 - - + +
292A PHE* 3.5 27.1 - + + -
295A LEU* 3.2 15.1 + - + +
297A SER* 1.3 77.1 + - - +
299A ARG* 1.4 61.5 + - - +
301A ALA* 3.3 2.8 + - - +
302A MET* 3.0 57.9 + - + +
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.1 61.6 + - + +
293A ASN* 4.0 15.9 + - - +
294A LYS 4.5 4.0 + - - -
295A LEU 3.2 4.7 + - - +
296A VAL* 3.1 54.5 + - + +
298A TYR* 1.4 76.3 - - - +
300A LYS* 1.3 59.9 + - - +
302A MET* 3.4 5.1 + - - +
303A TYR* 3.2 18.4 + - - +
326A GLU* 6.3 3.8 - - - +
329A LEU* 3.5 15.2 - - + +
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLY* 4.7 5.6 - - - +
296A VAL* 2.9 18.5 + - + +
297A SER* 3.8 8.1 - - - +
299A ARG* 1.3 72.9 - - - +
301A ALA* 1.4 63.4 + - - +
303A TYR* 3.2 7.7 + - - +
304A HIS* 3.1 39.3 + - + +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.5 21.5 - - + +
240A PRO* 4.0 11.7 - - + -
264A PHE* 3.4 36.0 - - - +
265A GLY* 4.0 2.2 - - - -
297A SER 3.0 17.9 + - - +
298A TYR 3.3 5.8 + - - +
300A LYS* 1.4 74.0 - - - +
302A MET* 1.4 57.0 + - - +
304A HIS 3.5 0.3 + - - -
305A ALA* 3.0 30.7 + - - +
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TRP* 3.7 23.3 - - + -
240A PRO* 3.5 39.5 - - + -
280A LEU* 6.0 0.2 - - + -
283A PHE* 4.0 14.6 - - - -
287A PHE* 4.0 21.1 - - + -
292A PHE* 4.1 12.8 - - + -
298A TYR* 3.0 40.5 + - + +
299A ARG* 3.4 10.5 - - - +
301A ALA* 1.4 71.5 - - - +
303A TYR* 1.3 60.6 + - - +
305A ALA* 4.6 2.7 - - - -
306A LEU* 2.9 37.4 + - - +
329A LEU* 4.1 14.6 - - + -
333A LEU* 4.6 3.6 - - + -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG 3.2 10.1 + - - +
300A LYS* 3.2 10.9 + - - +
302A MET* 1.3 79.9 - - - +
304A HIS* 1.3 85.3 + + - +
306A LEU* 3.8 0.7 - - - +
307A GLU* 2.9 55.5 + - + +
328A GLN* 3.6 40.3 + - + -
329A LEU* 3.8 17.2 - - + +
332A MET* 3.3 36.3 - - + +
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Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 3.6 28.2 - - + -
265A GLY* 4.2 14.8 - - - +
300A LYS* 3.1 33.3 + - + +
301A ALA 4.1 2.5 - - - +
303A TYR* 1.3 97.4 - + - +
305A ALA* 1.3 62.0 + - - +
307A GLU* 3.6 5.2 + - - +
308A LYS* 3.2 17.3 + - - +
2D SO4 3.9 18.8 + - - -
252D ARG* 3.4 33.3 + - - -
255D MET* 6.1 1.8 - - + -
271D GLU* 4.5 7.4 + - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.5 1.9 - - - +
240A PRO* 3.6 28.9 - - + -
264A PHE* 3.6 22.3 - - + -
280A LEU* 4.4 14.5 - - + +
301A ALA 3.0 18.1 + - - +
302A MET* 4.0 4.3 - - + +
304A HIS* 1.3 76.8 - - - +
306A LEU* 1.4 61.4 + - + +
308A LYS* 3.3 5.7 + - - +
309A ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 4.6 6.7 - - + -
283A PHE* 3.9 17.3 - - + -
302A MET* 2.9 25.2 + - + +
303A TYR* 4.2 1.3 - - - +
305A ALA* 1.4 74.5 - - + +
307A GLU* 1.3 54.1 + - - +
309A ALA* 3.4 6.5 - - + +
310A ARG* 2.8 34.7 + - - +
329A LEU* 4.5 3.8 - - + -
332A MET* 3.8 41.4 - - + +
333A LEU* 3.8 27.8 - - + +
335A TRP* 4.0 5.3 - - + -
336A ALA* 3.7 23.6 - - + -
340A PHE* 4.0 14.8 - - + -
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 2.9 43.3 + - + +
304A HIS* 3.8 7.9 - - - +
305A ALA 3.3 0.2 - - - -
306A LEU* 1.3 73.5 - - - +
308A LYS* 1.3 63.9 + - - +
310A ARG* 2.9 49.2 + - - +
311A VAL* 3.1 30.4 + - + +
328A GLN* 5.5 2.3 + - - -
332A MET* 4.1 12.2 - - - +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SO4 2.8 29.4 + - - -
228A LEU* 3.9 20.6 - - + -
242A MET* 3.8 18.5 - - + +
264A PHE* 4.0 11.2 - - + -
304A HIS 3.2 12.7 + - - +
305A ALA 3.3 9.2 + - - +
307A GLU* 1.3 76.2 - - - +
309A ALA* 1.4 61.8 + - - +
311A VAL* 3.5 5.9 + - + +
312A ARG* 3.1 44.8 + - - +
255D MET* 6.4 0.7 - - + -
256D SER 4.3 15.6 + - - -
258D MET* 5.1 12.3 - - - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.9 17.4 - - + +
280A LEU* 4.6 2.0 - - + -
305A ALA 3.1 13.6 + - - +
306A LEU* 3.4 14.8 - - + +
308A LYS* 1.4 75.6 - - - +
310A ARG* 1.4 55.9 + - - +
312A ARG* 3.4 4.7 + - - +
313A ALA* 3.0 31.9 + - - +
335A TRP* 3.7 11.8 - - + -
340A PHE* 4.4 6.7 - - + -
348A LEU* 3.6 24.3 - - + +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SO4 3.2 45.8 + - - -
306A LEU 2.8 21.3 + - - +
307A GLU* 2.9 44.0 + - - +
309A ALA* 1.4 70.4 - - - +
311A VAL* 1.3 80.2 + - - +
313A ALA 3.5 0.2 + - - -
314A GLY 3.2 3.3 + - - -
315A LYS* 2.9 65.3 + - + +
316A THR* 4.1 5.1 - - - +
317A PHE* 3.6 36.8 - - + +
332A MET* 5.2 2.2 - - - -
335A TRP* 3.7 14.8 - - + -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SO4 4.8 5.4 - - - +
307A GLU* 3.1 23.9 + - + +
308A LYS* 3.5 7.2 + - + +
310A ARG* 1.3 100.9 - - - +
312A ARG* 1.3 65.4 + - + +
314A GLY* 3.2 13.6 + - - -
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SO4 3.4 39.6 + - - +
226A GLY* 2.7 35.9 + - - -
228A LEU* 3.6 20.1 - - - +
242A MET* 3.9 9.9 - - - -
308A LYS* 3.1 37.9 + - - +
309A ALA 3.6 4.0 - - - +
310A ARG 3.4 0.2 - - - -
311A VAL* 1.3 78.2 - - + +
313A ALA* 1.3 60.0 + - - +
314A GLY 3.2 1.4 + - - -
347A GLY* 3.1 15.4 - - - +
348A LEU* 3.0 26.9 + - - -
349A LYS 3.8 10.3 - - - +
350A PRO* 3.5 16.9 - - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA 3.0 18.5 + - - +
310A ARG 4.0 2.5 - - - +
312A ARG* 1.3 74.6 - - - +
314A GLY* 1.3 61.2 + - - +
315A LYS* 4.3 3.7 - - + +
335A TRP* 3.8 24.7 - - + -
343A THR* 3.4 34.0 - - + +
347A GLY* 3.1 19.2 + - - +
348A LEU* 4.6 1.6 - - + -
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ARG 3.9 0.2 - - - -
311A VAL* 3.2 17.1 + - - -
312A ARG 3.2 1.2 + - - -
313A ALA* 1.3 79.7 - - - +
315A LYS* 1.3 59.4 + - - +
316A THR* 4.2 5.3 + - - +
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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
------------------------------------------------------------
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