Contacts of the helix formed by residues 287 - 306 (chain A) in PDB entry 6S7T
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 SER 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 3.2 12.1 + - - +
286A TYR* 1.3 97.6 + - - +
288A LYS* 1.3 66.0 + - - +
289A ARG* 3.2 38.4 + - - -
290A VAL* 3.6 15.9 + - - +
291A TYR 3.8 0.3 + - - -
438A ASP* 5.0 1.3 + - - -
84D ASP* 5.1 6.4 + - - -
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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
----------------------------------------------------------
286A TYR* 4.9 13.4 + - + +
287A SER* 1.3 74.7 - - - +
289A ARG* 1.3 65.6 + - - +
291A TYR* 3.1 9.9 + - + +
292A ILE* 3.0 25.1 + - - +
335A ALA* 5.5 2.8 + - - +
338A GLN* 4.7 20.2 - - - +
339A TYR* 5.4 11.5 - - - +
342A ASP* 5.1 7.6 + - - -
75D ILE* 4.0 30.5 - - + -
81D ASN* 4.2 22.0 - - - +
84D ASP* 3.5 23.3 + - - +
85D PHE* 4.2 8.3 - - + -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 3.5 22.4 + - - +
242A LYS* 3.8 18.8 + - - +
243A THR 4.3 8.7 - - - -
244A GLY* 3.9 12.8 - - - -
287A SER* 3.2 25.0 + - - -
288A LYS* 1.3 78.3 - - - +
290A VAL* 1.3 57.2 + - + +
292A ILE* 3.3 4.0 + - - +
293A ALA* 2.9 31.3 + - - +
438A ASP* 3.0 29.9 + - - -
84D ASP* 4.5 25.0 + - + +
85D PHE* 3.5 29.6 - - + -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 5.8 0.7 - - + -
241A VAL* 4.6 14.6 - - + -
277A VAL* 4.4 26.9 - - + +
280A LEU* 3.9 33.7 - - + -
281A LEU* 5.9 1.6 - - + -
285A ARG 4.7 4.0 - - - +
286A TYR* 4.9 7.2 - - + -
287A SER* 3.6 22.8 + - - +
288A LYS 3.2 0.8 - - - -
289A ARG* 1.3 76.3 - - + +
291A TYR* 1.3 63.0 + - - +
293A ALA* 3.7 5.0 - - - +
294A TYR* 2.9 25.1 + - - +
331A LEU* 4.6 5.8 - - + -
438A ASP* 4.5 12.6 - - - +
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 3.5 27.9 - - + +
287A SER 3.8 1.6 + - - -
288A LYS* 3.1 11.9 + - + +
290A VAL* 1.3 78.2 - - - +
292A ILE* 1.3 66.1 + - + +
295A SER* 3.0 37.3 + - - -
331A LEU* 3.5 24.2 - - + -
332A GLN* 2.8 43.1 + - - -
335A ALA* 4.0 17.0 - - + -
67D PHE* 5.7 1.0 - - - -
68D ILE* 4.1 8.7 - - + +
71D VAL* 3.8 23.3 - - + +
72D CYS* 4.7 7.6 - - - -
75D ILE* 3.5 30.1 - - + -
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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
----------------------------------------------------------
244A GLY 3.6 18.2 - - - +
245A SER 4.9 0.7 - - - -
246A VAL* 3.9 12.7 - - + +
249A THR* 4.0 3.3 + - - -
288A LYS 3.0 11.3 + - - +
289A ARG 3.3 4.2 + - - +
291A TYR* 1.3 75.9 - - - +
293A ALA* 1.3 61.8 + - - +
296A THR* 3.2 20.3 + - - -
72D CYS* 3.7 27.6 - - + +
75D ILE* 3.7 33.0 - - + -
76D GLN* 3.7 25.1 - - + +
85D PHE* 3.5 33.2 - - + -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 3.7 22.0 - - + -
240A SER* 3.8 16.4 - - - +
241A VAL* 3.9 16.4 - - + -
244A GLY* 5.3 1.3 + - - -
245A SER 5.5 0.4 - - - -
249A THR* 3.5 12.1 - - - +
289A ARG 2.9 17.7 + - - +
290A VAL 3.7 2.9 - - - +
292A ILE* 1.3 79.1 - - - +
294A TYR* 1.3 66.4 + - - +
297A PHE* 3.0 25.5 + - - +
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Residues in contact with TYR 294 (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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237A TRP* 3.7 12.8 - + + -
273A ILE* 3.7 19.7 - - + -
274A PRO* 3.5 28.3 - - + +
277A VAL* 3.9 16.6 - - + -
290A VAL 2.9 18.9 + - - +
293A ALA* 1.3 75.4 - - - +
295A SER* 1.3 63.1 + - - +
297A PHE* 4.4 7.2 - + - -
298A TYR* 2.9 42.4 + + + +
324A ALA* 2.8 38.3 + - - +
327A VAL* 4.1 8.3 - - + -
328A PHE* 3.7 28.4 + - + -
331A LEU* 4.2 24.2 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 3.0 23.9 + - - -
292A ILE* 5.4 0.4 - - - -
294A TYR* 1.3 80.1 - - - +
296A THR* 1.3 63.7 + - - +
298A TYR* 3.3 1.4 + - - +
299A ILE* 3.1 27.2 + - - +
328A PHE* 3.3 12.3 - - - -
331A LEU* 4.5 6.2 - - - +
332A GLN* 3.1 28.4 + - - -
68D ILE* 3.2 26.1 - - - +
72D CYS* 5.5 0.7 - - - -
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.9 14.2 - - + +
249A THR* 3.6 14.8 - - + -
250A MET* 4.2 13.9 - - - -
292A ILE 3.2 20.4 + - - -
293A ALA 3.6 0.6 + - - -
294A TYR 3.4 0.2 - - - -
295A SER* 1.3 78.2 - - - +
297A PHE* 1.3 62.3 + - - +
299A ILE* 4.9 2.0 - - - -
300A VAL* 3.0 28.4 + - + +
68D ILE* 4.3 6.6 - - - +
69D LEU* 3.9 25.9 - - + +
72D CYS* 3.4 19.9 - - - -
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Residues in contact with PHE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 5.3 0.7 - - + -
237A TRP* 4.1 11.2 - + + -
249A THR* 3.2 7.3 - - + +
252A CYS* 3.5 34.3 - - + -
253A CYS* 3.4 18.7 - - - -
256A TYR* 4.1 41.3 - + + -
270A ILE* 5.5 9.9 - - + -
273A ILE* 3.3 43.7 - - + -
274A PRO* 5.6 0.2 - - + -
293A ALA 3.0 20.5 + - - +
294A TYR* 3.7 10.1 - + - +
296A THR* 1.3 76.5 - - - +
298A TYR* 1.3 65.9 + + - +
301A GLY* 2.8 30.1 + - - -
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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
----------------------------------------------------------
270A ILE* 5.0 9.2 - - + -
294A TYR* 2.9 36.9 + + + +
295A SER 3.8 2.5 - - - +
297A PHE* 1.3 85.9 - + - +
299A ILE* 1.3 63.4 + - + +
301A GLY* 5.2 0.2 - - - -
302A LEU* 2.8 64.2 + - + +
315A PRO 5.3 3.5 + - - -
321A HIS 5.0 3.0 + - - -
324A ALA* 3.6 31.0 - - + -
325A ALA* 3.5 26.0 + - + +
328A PHE* 3.7 40.2 - + + -
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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
----------------------------------------------------------
295A SER 3.1 12.4 + - - +
296A THR* 4.1 3.1 - - - +
298A TYR* 1.3 82.8 - - + +
300A VAL* 1.3 68.6 + - + +
302A LEU* 3.2 7.5 + - + +
303A ILE* 3.1 22.7 + - - +
328A PHE* 4.2 11.7 - - + -
61D ILE* 4.4 15.7 - - + +
64D VAL* 3.6 27.8 - - + +
65D GLY* 3.7 22.9 - - - +
68D ILE* 3.4 44.0 - - + -
104D LEU* 5.0 4.3 - - + -
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Residues in contact with VAL 300 (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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250A MET* 3.6 34.8 - - + -
253A CYS* 3.5 25.1 - - + -
296A THR* 3.0 23.2 + - + +
299A ILE* 1.3 81.0 - - + +
301A GLY* 1.3 58.3 + - - +
303A ILE* 3.2 12.2 - - + +
304A LEU* 3.0 39.4 + - + +
69D LEU* 5.5 6.5 - - + -
100D ALA 5.5 0.4 - - - +
103D ILE* 4.8 4.5 - - + -
104D LEU* 5.0 17.5 - - + -
107D VAL* 6.1 0.4 - - + -
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Residues in contact with GLY 301 (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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253A CYS* 3.7 9.3 - - - -
256A TYR* 3.8 25.9 - - - -
297A PHE* 2.8 18.9 + - - -
300A VAL* 1.3 74.6 - - - +
302A LEU* 1.3 61.0 + - - +
304A LEU* 3.7 5.7 - - - +
305A SER* 2.8 32.7 + - - -
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Residues in contact with LEU 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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256A TYR* 5.7 0.2 - - - -
298A TYR* 2.8 50.9 + - + +
299A ILE* 3.6 7.4 - - + +
301A GLY* 1.3 76.3 - - - +
303A ILE* 1.3 63.1 + - - +
305A SER* 3.2 5.5 + - - -
306A MET* 3.0 49.7 + - + +
315A PRO* 3.7 25.1 - - + +
316A ILE* 5.2 3.4 - - + -
61D ILE* 3.9 26.7 - - + -
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE 3.1 9.0 + - - +
300A VAL* 3.2 20.9 - - + +
302A LEU* 1.3 83.0 - - - +
304A LEU* 1.3 63.0 + - + +
306A MET* 3.6 9.0 + - - +
307A GLN* 3.3 22.8 + - - +
58D SER* 5.3 2.0 - - - +
61D ILE* 3.9 30.1 - - + -
104D LEU* 4.3 15.0 - - + -
107D VAL* 3.6 26.5 - - + +
108D VAL* 3.6 35.7 - - + +
111D PHE* 4.8 13.7 - - + -
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Residues in contact with LEU 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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253A CYS* 3.7 26.5 - - + +
254A LEU* 4.2 16.2 - - + -
256A TYR* 5.9 0.2 - - + -
257A PHE* 3.2 51.8 - - + -
300A VAL* 3.0 37.5 + - + +
301A GLY* 3.8 4.5 - - - +
303A ILE* 1.3 76.5 - - + +
305A SER* 1.3 63.4 + - - +
307A GLN* 3.2 15.8 + - + +
103D ILE* 5.2 1.8 - - + -
107D VAL* 3.4 34.3 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 4.1 19.9 + - - -
257A PHE* 4.9 1.3 - - - +
260A VAL* 4.1 20.6 - - - +
266A TYR* 4.5 3.8 - - - -
301A GLY 2.8 19.5 + - - -
302A LEU* 3.2 6.3 + - - -
304A LEU* 1.3 72.6 - - - +
306A MET* 1.3 62.3 + - - +
307A GLN 3.0 6.9 + - - -
308A ILE* 3.6 11.3 + - - +
311A VAL* 3.6 21.0 - - - +
315A PRO* 3.7 18.1 - - - +
321A HIS* 5.5 0.5 + - - -
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.0 38.0 + - + +
303A ILE* 4.0 7.9 - - - +
304A LEU 3.3 0.8 - - - -
305A SER* 1.3 75.9 - - - +
307A GLN* 1.3 62.1 + - - +
308A ILE 3.5 5.7 + - - +
312A GLY* 3.5 30.3 - - - +
313A PHE* 5.0 3.3 - - + -
315A PRO* 4.1 15.0 - - + -
316A ILE* 3.6 39.5 - - + +
57D LEU* 3.6 26.5 - - + -
61D ILE* 4.5 11.2 - - + -
111D PHE* 3.9 28.9 - - + -
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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