Contacts of the helix formed by residues 261 - 279 (chain A) in PDB entry 6A5T
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 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL 4.6 0.6 - - - +
248A ARG* 3.0 51.3 - - + +
249A PRO* 3.6 16.3 - - - +
250A SER* 3.9 4.6 - - - +
251A ILE* 5.3 6.1 - - - +
259A GLY 3.5 2.6 + - - -
260A GLN* 1.3 76.1 + - - +
262A ASP* 1.3 58.2 + - - +
263A LEU* 3.1 3.3 + - - +
264A THR* 2.7 33.1 + - - +
265A HIS 3.4 2.6 + - - -
329A ARG* 3.2 26.6 + - - -
1114B LEU* 5.6 4.3 - - - +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN 3.5 8.1 + - - +
261A ASP* 1.3 75.5 - - - +
263A LEU* 1.3 59.2 + - - +
265A HIS* 3.3 8.3 + - - +
266A LYS* 2.9 28.8 + - - +
317A GLN* 2.7 36.6 + - - +
321A ARG* 3.7 24.1 + - - -
323A VAL* 4.5 8.1 - - + +
324A LYS* 4.3 27.7 - - + +
329A ARG* 5.0 4.0 - - - +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 5.0 6.5 - - + -
247A VAL* 3.8 20.6 - - + -
248A ARG* 3.7 25.8 - - + -
261A ASP* 3.1 5.8 - - - +
262A ASP* 1.3 76.5 - - - +
264A THR* 1.3 66.1 + - - +
266A LYS* 3.3 4.6 + - + +
267A LEU* 2.9 30.7 + - + +
304A TYR* 4.0 26.2 - - + -
324A LYS 4.4 15.3 - - - +
325A ALA 4.5 2.2 - - - +
326A ILE* 4.3 21.3 - - + -
329A ARG* 3.4 31.2 - - - +
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.1 20.6 - - + -
53A LEU* 4.0 13.2 - - + +
54A ASN* 5.1 6.9 + - - +
248A ARG* 3.2 34.2 + - - +
260A GLN* 3.3 34.4 + - + +
261A ASP 2.7 17.4 + - - -
263A LEU* 1.3 75.0 - - - +
265A HIS* 1.3 57.6 + - + +
267A LEU* 3.3 4.8 + - - +
268A SER* 2.9 25.6 + - - -
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Residues in contact with HIS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 5.4 5.3 - - + +
260A GLN* 4.2 31.8 + - + +
261A ASP 3.4 2.4 + - - -
262A ASP* 3.3 14.0 + - - +
263A LEU 3.2 0.6 - - - -
264A THR* 1.3 78.8 - - + +
266A LYS* 1.3 66.5 + - - +
268A SER* 3.1 11.0 + - - -
269A ASP* 3.0 31.1 + - - +
317A GLN* 4.4 21.7 + - - +
318A LYS* 4.2 27.1 + - - +
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP 2.9 16.9 + - - +
263A LEU* 3.3 4.9 + - + +
265A HIS* 1.3 76.9 - - - +
267A LEU* 1.3 57.9 + - - +
269A ASP* 3.3 9.1 + - + +
270A ILE* 3.0 26.8 + - + +
300A HIS* 4.1 26.3 + - + +
303A THR* 3.5 29.8 + - - +
304A TYR* 3.5 38.4 - - + -
315A ALA* 4.2 16.2 - - - +
316A LEU 5.4 2.0 + - - -
323A VAL* 4.3 26.1 - - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.0 20.6 - - + +
84A MET* 4.5 4.3 - - + +
240A LEU* 4.6 16.8 - - + -
241A PRO 5.5 0.2 - - - +
242A VAL* 3.6 36.3 - - + -
243A PRO* 4.1 13.2 - - + -
248A ARG* 4.5 14.1 - - - +
263A LEU* 2.9 21.2 + - + +
264A THR 3.7 4.0 - - - +
266A LYS* 1.3 77.0 - - - +
268A SER* 1.3 59.1 + - - +
270A ILE* 3.3 12.2 + - + +
271A LEU* 2.8 30.3 + - - +
304A TYR* 4.4 24.5 - - + +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 3.9 17.8 + - - +
40A ILE* 5.2 7.8 - - - +
53A LEU* 3.8 12.7 - - - +
264A THR 2.9 14.8 + - - -
265A HIS* 3.1 16.1 + - - -
267A LEU* 1.3 77.3 - - - +
269A ASP* 1.3 60.9 + - - +
271A LEU* 3.2 4.4 + - - +
272A LYS* 2.9 42.8 + - - +
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Residues in contact with ASP 269 (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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265A HIS* 3.0 23.1 + - - +
266A LYS* 3.8 12.7 + - + +
267A LEU 3.3 0.2 - - - -
268A SER* 1.3 78.5 + - - +
270A ILE* 1.3 62.8 + - - +
272A LYS* 3.5 13.7 + - - +
273A ALA* 3.0 25.8 + - - +
300A HIS* 3.4 34.0 + - + +
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Residues in contact with ILE 270 (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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84A MET* 3.6 21.5 - - + -
86A LEU* 5.1 5.4 - - + -
240A LEU* 4.1 21.5 - - + -
266A LYS 3.0 17.3 + - - +
267A LEU* 3.6 9.2 - - + +
268A SER 3.3 0.2 - - - -
269A ASP* 1.3 78.6 - - - +
271A LEU* 1.3 59.0 + - - +
274A ASN* 2.8 28.4 + - + +
297A LEU* 3.7 13.3 - - + +
300A HIS* 3.4 27.8 - - + +
301A VAL* 3.6 38.8 - - + +
304A TYR* 4.2 13.2 - - + -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.4 8.3 - - + +
36A GLU 3.8 13.9 - - - +
37A TYR 3.2 39.5 - - - +
38A PRO* 3.3 14.8 - - + -
53A LEU* 4.9 6.5 - - + -
84A MET* 3.4 42.4 - - + -
267A LEU 2.8 19.9 + - - +
268A SER* 3.2 4.0 + - - +
270A ILE* 1.3 74.2 - - - +
272A LYS* 1.3 63.7 + - - +
274A ASN* 3.2 13.1 + - - +
275A ILE* 3.0 26.4 + - + +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 3.6 25.8 - - + +
268A SER* 2.9 27.0 + - - +
269A ASP* 3.8 14.0 + - - +
271A LEU* 1.3 76.5 - - - +
273A ALA* 1.3 63.5 + - - +
275A ILE* 3.1 4.9 + - - +
276A ASN* 2.9 36.8 + - - +
-46N T 5.0 0.2 - - - -
-45N G 2.5 43.4 + - - +
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Residues in contact with ALA 273 (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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269A ASP 3.0 17.0 + - - +
270A ILE 4.1 2.0 - - - +
272A LYS* 1.3 76.0 - - - +
274A ASN* 1.3 57.3 + - - +
276A ASN* 3.6 7.7 - - - +
277A VAL* 2.9 33.6 + - - +
293A VAL* 4.2 2.5 - - + +
296A LEU* 3.8 33.7 - - + -
297A LEU* 4.1 18.8 - - + +
300A HIS* 4.2 4.7 - - + +
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Residues in contact with ASN 274 (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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84A MET* 4.1 14.6 - - - +
85A GLU* 2.2 34.8 + - - +
86A LEU* 4.4 5.4 - - - +
87A ALA* 3.5 19.9 + - - +
270A ILE* 2.8 16.0 + - + +
271A LEU* 3.3 19.0 - - - +
272A LYS 3.1 0.2 - - - -
273A ALA* 1.3 75.0 - - - +
275A ILE* 1.3 68.1 + - - +
277A VAL* 3.0 15.3 + - - +
278A GLN* 3.0 19.1 + - - +
297A LEU* 3.7 12.1 - - + +
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Residues in contact with ILE 275 (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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36A GLU 3.4 25.6 - - - +
37A TYR* 5.9 1.8 - - + -
38A PRO* 3.6 24.5 - - + -
271A LEU* 3.0 15.9 + - + +
272A LYS* 3.9 3.4 - - - +
274A ASN* 1.3 82.3 - - + +
276A ASN* 1.3 64.1 + - - +
278A GLN* 3.0 17.4 + - - +
279A LYS* 3.0 56.9 + - + +
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Residues in contact with ASN 276 (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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272A LYS* 2.9 33.8 + - - +
273A ALA* 4.1 5.2 - - - +
275A ILE* 1.3 83.9 - - - +
277A VAL* 1.3 58.9 + - - +
279A LYS* 4.4 9.2 - - - +
280A LEU* 3.9 15.9 + - - +
293A VAL* 3.1 21.6 - - + +
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Residues in contact with VAL 277 (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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87A ALA* 3.9 19.5 - - + -
88A LYS* 4.8 9.4 - - + -
273A ALA 2.9 13.2 + - - +
274A ASN* 3.0 8.5 + - - +
276A ASN* 1.3 76.8 - - - +
278A GLN* 1.3 69.4 + - - +
279A LYS 3.3 0.2 - - - -
280A LEU* 3.2 16.4 + - - +
281A GLU* 3.9 6.7 + - - +
290A ILE* 6.4 0.4 - - + -
293A VAL* 3.3 42.0 - - + +
294A GLU* 3.8 19.5 - - + +
297A LEU* 4.3 12.8 - - + -
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Residues in contact with GLN 278 (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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34A LYS* 5.9 2.8 - - - +
85A GLU* 5.3 7.7 + - - +
86A LEU 5.5 1.2 + - - -
87A ALA* 3.7 25.4 - - + +
274A ASN* 3.0 20.6 + - - +
275A ILE* 3.0 18.8 + - - +
277A VAL* 1.3 79.9 - - - +
279A LYS* 1.3 71.2 + - + +
280A LEU 2.8 2.4 + - - -
281A GLU* 3.0 25.5 + - - +
282A MET* 3.8 7.4 + - - +
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Residues in contact with LYS 279 (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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275A ILE* 3.0 36.0 + - + +
276A ASN* 4.9 8.1 - - - +
277A VAL 3.3 0.4 - - - -
278A GLN* 1.3 81.9 - - + +
280A LEU* 1.3 62.5 + - + +
282A MET* 3.3 15.8 + - + +
283A ASP* 2.8 23.7 + - - +
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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
------------------------------------------------------------
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