Contacts of the helix formed by residues 284 - 302 (chain A) in PDB entry 6CNB
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 ASP 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.1 9.5 - - - +
283A ASP* 1.3 70.7 - - - +
285A LEU* 1.3 66.3 + - + +
287A VAL* 2.5 36.6 + - - +
288A LYS* 3.3 14.1 + - + +
349A PRO 5.4 2.5 - - - +
350A ILE 4.9 6.1 - - - +
351A ARG 4.0 3.8 - - - +
352A GLY* 3.0 32.1 - - - +
356A ARG* 6.2 0.7 - - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO* 4.2 19.3 - - + -
268A ILE* 4.9 2.7 - - + -
269A ARG* 3.2 36.9 + - + -
283A ASP* 2.9 2.4 + - - -
284A ASP* 1.3 84.8 - - + +
286A THR* 1.3 57.4 + - - +
287A VAL 3.2 0.8 + - - -
288A LYS* 4.1 8.3 - - + +
289A LEU* 3.2 20.6 + - - +
326A TYR* 3.6 33.2 - - + +
352A GLY* 4.5 8.7 - - - +
353A PHE* 3.8 34.5 - - + -
356A ARG* 3.7 26.0 - - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.6 16.9 - - + -
53A ALA* 4.4 1.0 - - + +
54A LEU* 3.1 33.2 - - + +
269A ARG* 3.5 33.6 + - - +
271A SER* 5.4 2.7 + - - -
282A GLU* 5.2 4.5 - - + -
283A ASP* 2.9 25.7 + - - +
284A ASP 2.5 5.9 + - - -
285A LEU* 1.3 74.5 - - - +
287A VAL* 1.3 59.0 + - + -
290A THR* 3.0 25.4 - - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 5.9 2.0 - - + -
282A GLU* 3.5 39.5 - - + -
284A ASP* 2.5 19.1 + - - +
286A THR* 1.3 76.0 - - + +
288A LYS* 1.3 76.1 + - + +
290A THR* 3.1 8.7 - - + +
291A GLU* 2.9 22.3 + - + +
341A SER* 4.9 20.9 - - - +
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 3.3 15.7 + - + +
285A LEU* 4.0 5.3 + - + +
287A VAL* 1.3 82.2 - - + +
289A LEU* 1.3 59.1 + - - +
291A GLU* 2.8 28.4 + - - +
292A ILE* 2.9 13.1 + - + +
322A THR* 4.4 20.7 - - - +
325A MET* 4.2 20.8 - - - +
326A TYR* 3.9 30.7 - - + +
350A ILE* 3.7 35.3 - - + +
352A GLY* 6.2 1.6 - - - +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.7 7.2 - - + -
53A ALA* 3.9 16.4 - - + -
84A LEU* 4.1 20.1 - - + +
261A LEU* 5.3 4.5 - - + -
262A PRO 5.4 0.2 - - - +
263A ALA* 4.4 11.7 - - + -
264A PRO* 3.6 24.5 - - + -
269A ARG* 3.2 28.7 - - - +
285A LEU 3.2 17.9 + - - +
288A LYS* 1.3 78.6 - - - +
290A THR* 1.3 56.5 + - - +
292A ILE* 2.6 33.9 + - + +
293A VAL* 2.7 18.5 + - - +
326A TYR* 3.8 19.2 - - + +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 2.9 49.2 - - + +
40A PHE* 3.4 20.1 - - + -
53A ALA* 3.6 12.5 - - - +
286A THR 3.0 26.4 + - - +
287A VAL* 3.1 20.8 + - + +
289A LEU* 1.3 85.4 - - - +
291A GLU* 1.3 58.1 + - + +
293A VAL* 4.1 7.1 - - - +
294A TRP 3.8 8.0 + - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 5.1 1.3 - - - -
287A VAL* 2.9 14.1 + - + +
288A LYS* 2.8 12.5 + - - +
290A THR* 1.3 76.8 - - + +
292A ILE* 1.3 68.6 + - - +
293A VAL 3.2 1.8 - - - -
294A TRP* 2.7 30.7 + - + +
295A THR* 2.9 21.2 + - - +
318A TYR* 3.0 42.4 + - - +
322A THR* 3.4 22.3 - - - +
340A SER* 4.6 24.0 - - - +
341A SER* 6.1 2.0 - - - -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.9 26.0 - - + -
86A LEU* 4.5 7.0 - - + -
261A LEU* 4.3 7.9 - - + -
288A LYS 2.9 9.6 + - - +
289A LEU* 2.6 25.2 + - + +
291A GLU* 1.3 74.4 + - - +
293A VAL* 1.3 62.6 + - - +
295A THR* 3.2 5.4 - - - +
296A SER* 2.8 22.9 + - - -
319A LEU* 4.1 17.5 - - + -
322A THR* 3.5 24.7 - - + -
323A VAL* 3.8 39.3 - - + -
326A TYR* 4.4 9.4 - - + -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 18.6 - - + -
35A SER* 3.0 31.4 - - - +
36A THR 3.4 14.8 - - - +
37A ARG* 3.7 16.4 - - - -
38A ASP 4.7 0.2 - - - +
84A LEU* 3.5 28.7 - - + -
289A LEU* 2.7 17.7 + - + +
290A THR* 4.1 9.0 - - - +
292A ILE* 1.3 73.5 - - - +
294A TRP* 1.3 64.2 + - - +
296A SER* 3.3 6.0 - - - -
297A SER* 2.9 25.2 + - - +
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Residues in contact with TRP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.3 46.2 - - + -
38A ASP* 4.6 9.0 - - - +
290A THR 3.8 4.4 + - - +
291A GLU* 2.7 28.1 + - + +
293A VAL* 1.3 78.3 - - - +
295A THR* 1.3 64.1 + - - +
297A SER* 3.3 5.7 + - - -
298A LEU* 2.8 44.0 + - + +
340A SER* 4.0 20.4 + - - +
72R ALA* 4.3 20.4 - - + -
73R LEU* 4.0 36.6 - - + -
74R GLU* 6.0 0.7 - - - -
38Y A 5.5 1.7 - - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 2.9 27.4 + - - +
292A ILE* 3.2 24.7 - - + +
294A TRP* 1.3 79.6 - - - +
296A SER* 1.3 68.5 + - - +
298A LEU* 3.1 15.6 - - - +
299A ILE* 3.0 32.2 + - - +
315A HIS* 4.5 6.1 + - - +
318A TYR* 4.0 18.6 - - + -
319A LEU* 3.7 21.8 - - + +
322A THR* 5.5 0.7 - - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.0 1.6 - - - -
85A LYS 3.6 20.3 + - - -
86A LEU* 4.8 8.3 - - - -
87A ALA* 3.7 20.7 + - - +
292A ILE* 2.8 20.1 + - - -
293A VAL* 3.3 7.4 - - - -
295A THR* 1.3 74.9 - - - +
297A SER* 1.3 57.5 + - - +
299A ILE* 2.5 34.0 + - - +
300A LYS* 2.8 10.8 + - - +
319A LEU* 5.4 4.9 - - - -
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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
----------------------------------------------------------
35A SER 5.2 0.9 - - - -
36A THR 3.1 25.0 + - - -
37A ARG* 5.1 14.6 - - - -
293A VAL* 2.9 19.0 + - - +
294A TRP* 4.0 5.6 - - - -
296A SER* 1.3 73.6 + - - +
298A LEU* 1.3 56.8 + - - +
300A LYS* 3.6 10.6 - - - +
301A ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 2.8 31.8 + - + +
295A THR* 3.1 19.1 - - - +
296A SER 2.8 0.2 + - - -
297A SER* 1.3 77.2 - - - +
299A ILE* 1.3 53.0 + - - +
300A LYS 3.0 0.5 + - - -
301A ALA* 3.6 3.0 - - + -
302A GLY* 2.4 40.0 + - - +
307A ILE* 6.1 3.6 - - + -
315A HIS* 3.4 46.7 - - + +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 4.6 10.8 - - + +
88A LEU* 4.0 30.5 - - + +
295A THR* 3.0 18.3 + - - +
296A SER* 2.5 13.5 + - - +
298A LEU* 1.3 72.9 - - + +
300A LYS* 1.3 52.2 + - - +
302A GLY* 2.5 25.7 - - - +
303A LEU* 3.5 14.9 - - + +
307A ILE* 6.0 2.5 - - + -
312A MET* 5.3 8.3 - - + +
315A HIS* 3.9 20.2 - - + +
316A TRP* 3.6 38.4 - - + +
319A LEU* 4.6 15.3 - - + -
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 5.7 8.1 - - - +
87A ALA* 4.4 15.8 - - + +
296A SER* 2.8 11.8 + - - +
297A SER* 3.7 14.4 - - - +
299A ILE* 1.3 74.7 - - - +
301A ALA* 1.3 55.3 + - - +
302A GLY 2.6 16.8 - - - +
303A LEU* 5.4 1.6 - - - +
304A ASP* 3.2 14.2 + - - +
542O ARG* 4.4 25.5 + - - +
36Q PHE* 5.3 11.5 - - - -
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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
----------------------------------------------------------
297A SER 2.9 17.6 + - - +
298A LEU* 3.8 4.0 - - + +
300A LYS* 1.3 71.6 - - - +
302A GLY* 1.3 65.8 + - - +
304A ASP* 3.1 19.5 + - - +
305A LYS* 3.7 19.8 + - - +
306A GLY 4.6 0.3 + - - -
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 2.4 29.2 + - - +
299A ILE* 2.5 23.0 - - - +
300A LYS 2.6 11.3 - - - +
301A ALA* 1.3 63.3 - - - +
303A LEU* 1.3 56.8 + - - +
304A ASP 2.5 17.6 + - - -
305A LYS 5.2 0.2 - - - -
306A GLY* 5.3 2.0 - - - -
307A ILE* 4.0 25.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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