Contacts of the helix formed by residues 288 - 306 (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 HIS 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 2.5 43.1 + - + +
287A GLN* 1.3 76.2 - - - +
289A ILE* 1.3 99.3 + - + +
290A ILE 3.2 0.7 - - - -
291A ASN* 3.3 8.9 + - - +
292A GLU* 2.9 28.3 + - - +
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Residues in contact with ILE 289 (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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280A LEU* 4.2 11.7 - - + -
285A SER* 5.5 0.7 - - - -
286A PRO* 4.4 17.3 - - + -
287A GLN 4.4 0.6 - - - +
288A HIS* 1.3 107.8 + - + +
290A ILE* 1.3 66.8 + - - +
292A GLU* 3.1 21.4 + - + +
293A VAL* 2.8 41.3 + - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 6.4 0.7 - - + -
280A LEU* 3.6 22.6 - - + +
281A GLU* 6.1 3.6 - - + +
285A SER* 3.0 36.6 - - - +
287A GLN* 3.3 50.5 - - - +
288A HIS 3.2 0.2 - - - -
289A ILE* 1.3 78.4 - - - +
291A ASN* 1.3 64.4 + - - +
293A VAL* 3.1 2.3 + - - +
294A GLU* 2.9 48.2 + - + +
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN* 2.7 35.2 + - - +
288A HIS* 3.3 10.6 + - - +
290A ILE* 1.3 75.7 - - - +
292A GLU* 1.3 57.1 + - - +
294A GLU* 3.1 22.2 - - - +
295A GLN* 2.9 35.1 + - - +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A HIS* 2.9 15.6 + - + +
289A ILE* 3.1 28.6 + - + +
291A ASN* 1.3 79.1 - - - +
293A VAL* 1.3 61.4 + - + +
295A GLN* 3.3 7.7 + - + +
296A LEU* 2.8 29.0 + - + +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA 4.2 4.2 - - - +
276A ASN* 3.1 35.4 - - + +
277A VAL* 3.3 19.0 - - + +
280A LEU* 4.0 16.8 - - + -
289A ILE* 2.8 26.3 + - + +
290A ILE 3.9 2.5 - - - +
292A GLU* 1.3 78.2 - - + +
294A GLU* 1.3 64.4 + - - +
296A LEU* 3.2 15.8 + - + +
297A LEU 3.0 17.8 + - - -
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 3.6 45.2 + - + +
90A VAL* 5.9 0.3 - - - +
277A VAL* 3.9 19.0 - - + +
290A ILE* 2.9 39.6 + - + +
291A ASN* 3.1 24.8 - - - +
293A VAL* 1.3 75.8 - - - +
295A GLN* 1.3 63.8 + - - +
297A LEU* 3.0 7.3 + - - +
298A GLN* 2.9 21.1 + - - +
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Residues in contact with GLN 295 (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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180A MET* 4.4 15.8 - - + +
181A LYS* 4.1 34.0 + - + +
291A ASN* 2.9 23.0 + - - +
292A GLU* 3.8 7.1 - - + +
294A GLU* 1.3 73.1 - - - +
296A LEU* 1.3 56.7 + - - +
298A GLN* 3.3 9.7 + - + +
299A PHE* 2.9 27.9 + - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.8 20.2 - - + -
292A GLU* 2.8 16.3 + - + +
293A VAL* 3.3 17.5 - - + +
295A GLN* 1.3 74.9 - - - +
297A LEU* 1.3 67.9 + - - +
299A PHE* 2.9 24.6 + - + -
300A HIS* 3.0 36.6 + - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.6 31.9 - - + -
87A ALA 4.9 6.7 - - - +
88A LYS* 4.3 11.2 - - + +
90A VAL* 4.0 15.9 - - + -
270A ILE* 3.7 33.0 - - + +
273A ALA* 4.1 9.4 - - + +
274A ASN* 3.7 20.0 - - + +
277A VAL* 4.3 14.1 - - + -
293A VAL 3.0 11.1 + - - +
294A GLU* 3.0 10.8 + - - +
296A LEU* 1.3 76.9 - - - +
298A GLN* 1.3 63.8 + - - +
300A HIS* 3.2 1.8 + - - +
301A VAL* 3.0 24.4 + - + +
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 4.5 11.4 + - - +
90A VAL* 3.0 34.4 - - + +
91A PHE* 3.2 47.3 + - + +
180A MET* 3.5 26.7 - - + +
205A PRO* 4.9 2.6 - - - +
294A GLU 2.9 11.5 + - - +
295A GLN* 3.3 15.3 - - + +
297A LEU* 1.3 77.1 - - - +
299A PHE* 1.3 57.0 + - - +
301A VAL* 3.2 4.7 + - - +
302A ALA* 2.8 31.3 + - - +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 3.9 19.7 - - + -
295A GLN* 2.9 14.3 + - + +
296A LEU* 2.9 24.2 + - + +
298A GLN* 1.3 75.9 - - - +
300A HIS* 1.3 69.4 + + - +
302A ALA* 3.3 1.1 + - + +
303A THR* 2.9 48.3 + - + +
312A GLN* 3.1 37.2 - - + -
313A PRO* 4.5 12.6 - - + -
315A ALA* 4.2 17.7 - - + -
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Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS* 4.1 18.0 + - + +
269A ASP* 3.4 38.3 + - + +
270A ILE* 3.4 22.7 - - + +
273A ALA* 4.2 11.4 - - + -
296A LEU* 3.0 54.4 + - + +
297A LEU* 3.8 4.7 - - - +
299A PHE* 1.3 82.4 - + - +
301A VAL* 1.3 66.8 + - - +
303A THR* 3.2 5.5 + - - -
304A TYR* 2.9 24.9 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.4 18.6 - - + -
90A VAL* 3.9 22.4 - - + -
91A PHE 4.3 3.1 - - - +
92A HIS* 6.0 0.2 - - - -
93A ILE* 5.4 0.8 - - - +
237A ILE* 3.8 29.4 - - + -
240A LEU* 4.8 10.3 - - + -
270A ILE* 3.6 24.5 - - + -
297A LEU* 3.0 19.2 + - + +
298A GLN* 3.8 4.9 - - - +
300A HIS* 1.3 75.6 - - - +
302A ALA* 1.3 65.6 + - - +
304A TYR* 3.6 2.6 - - + +
305A MET* 3.2 22.8 + - + +
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Residues in contact with ALA 302 (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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93A ILE* 4.4 15.7 - - + +
180A MET* 3.8 18.6 - - - -
298A GLN* 2.8 20.7 + - - +
299A PHE* 3.4 4.9 - - - +
300A HIS 3.1 0.2 - - - -
301A VAL* 1.3 76.4 - - - +
303A THR* 1.3 67.0 + - + +
305A MET* 2.8 17.3 + - - +
306A ASP* 2.9 12.4 + - - +
309A ILE* 3.7 24.0 - - + -
312A GLN* 5.4 0.7 - - - +
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Residues in contact with THR 303 (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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266A LYS* 3.5 22.9 + - - -
299A PHE* 2.9 40.8 + - + +
300A HIS* 3.2 10.4 + - - -
302A ALA* 1.3 71.0 - - - +
304A TYR* 1.3 59.3 + - - +
306A ASP 2.7 25.6 + - - +
307A ASN* 3.9 10.0 + - - +
309A ILE* 5.1 0.4 - - - -
312A GLN* 4.2 12.3 - - - +
315A ALA* 3.7 30.2 - - + +
323A VAL* 5.8 3.0 - - - +
325A ALA* 4.1 6.4 - - - +
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Residues in contact with TYR 304 (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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240A LEU* 4.4 23.8 - - + -
241A PRO 4.8 1.7 + - - -
243A PRO* 4.0 15.2 - - - +
263A LEU* 4.0 25.5 - - + +
266A LYS* 3.5 29.6 - - + +
267A LEU* 4.4 19.7 - - + -
270A ILE* 4.2 6.5 - - + -
300A HIS 2.9 18.6 + - - +
301A VAL* 3.6 6.3 - - + +
302A ALA 2.8 4.6 + - - -
303A THR* 1.3 76.3 + - - +
305A MET* 1.3 72.9 + - + +
306A ASP 3.2 0.7 + - - -
325A ALA* 4.1 2.5 - - - +
326A ILE* 3.5 40.0 + - + +
1209B ALA* 3.6 29.7 - - - +
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Residues in contact with MET 305 (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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92A HIS* 3.5 28.9 - - + +
93A ILE* 3.5 23.1 - - + +
237A ILE* 3.6 29.8 - - + -
240A LEU* 3.8 15.5 - - + -
301A VAL* 3.2 10.2 + - + +
302A ALA 2.8 6.8 + - - -
304A TYR* 1.3 87.5 - - + +
306A ASP* 1.3 62.9 + - - +
325A ALA* 4.6 2.5 - - - -
326A ILE* 5.1 1.3 - - - +
327A ARG* 4.0 13.0 + - - +
1413A PHE* 5.0 4.2 - - + -
1209B ALA 3.3 23.8 - - - +
1210B MET* 3.5 36.2 - - + +
1211B ASN* 4.3 2.7 - - - +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.1 15.4 - - + +
302A ALA 2.9 4.0 + - - +
303A THR* 2.7 32.7 - - - +
304A TYR 3.2 2.6 + - - -
305A MET* 1.3 82.3 - - - +
307A ASN* 1.3 64.1 + - - +
308A ASP* 2.2 43.5 + - - +
309A ILE* 3.6 24.4 + - + +
325A ALA* 3.7 8.3 - - - -
327A ARG* 3.5 26.7 + - - +
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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
------------------------------------------------------------
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