Contacts of the helix formed by residues 288 - 308 (chain J) in PDB entry 6PSU
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 PRO 288 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J ALA* 1.3 90.0 - - + +
289J ASP* 1.3 66.2 + - - +
290J ILE* 3.1 16.2 + - + +
291J ILE* 3.1 34.6 + - + +
292J VAL* 3.2 12.7 + - - +
377L LYS* 4.5 28.9 - - + +
380L VAL* 4.1 24.0 - - + -
381L GLU* 5.8 2.9 - - + +
413L MET* 4.1 11.2 - - + -
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Residues in contact with ASP 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J ALA 3.6 4.4 + - - +
288J PRO* 1.3 72.3 - - - +
290J ILE* 1.3 63.2 + - + +
292J VAL* 3.2 17.8 - - - +
293J ARG* 2.9 53.3 + - - +
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Residues in contact with ILE 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J PRO* 3.1 9.8 + - + -
289J ASP* 1.3 85.5 - - + +
291J ILE* 1.3 64.6 + - + +
293J ARG* 3.3 7.2 + - - +
294J ASN* 2.9 27.7 + - - +
101L TYR* 4.7 12.3 - - + +
104L GLU* 3.1 44.5 - - + +
381L GLU* 5.3 15.0 - - + +
384L LEU* 5.2 7.6 - - + -
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Residues in contact with ILE 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282J LEU* 3.9 12.1 - - + -
288J PRO* 3.1 22.6 + - + +
290J ILE* 1.3 80.8 - - + +
292J VAL* 1.3 59.3 + - + +
294J ASN* 3.3 7.7 + - - +
295J GLU* 2.9 24.9 + - - +
101L TYR* 4.7 8.3 - - - +
380L VAL* 4.4 13.9 - - + -
384L LEU* 4.8 6.5 - - + -
406L GLN* 3.2 23.4 - - - +
409L ASN* 3.3 31.0 - - + +
410L ILE* 5.4 0.2 - - + -
413L MET* 3.3 35.4 - - + -
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Residues in contact with VAL 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J LEU* 4.3 1.5 - - + +
282J LEU* 4.0 32.5 - - + +
283J LEU* 4.9 14.1 - - + -
287J ALA* 4.0 20.6 - - + +
288J PRO 3.3 13.0 - - - +
289J ASP* 3.2 31.4 - - - +
291J ILE* 1.3 76.6 - - - +
293J ARG* 1.3 66.2 + - + +
295J GLU* 3.2 2.8 + - - +
296J LYS* 2.9 39.3 + - + +
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Residues in contact with ARG 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J PHE* 3.2 48.0 + - + +
144J TYR* 4.4 15.7 + - - -
162J GLU* 4.6 5.5 + - - -
180J MET* 2.6 46.0 - - - +
289J ASP* 2.9 41.9 + - + +
290J ILE* 3.8 7.3 - - - +
292J VAL* 1.3 79.6 - - + +
294J ASN* 1.3 60.8 + - - +
296J LYS* 3.3 6.9 + - - +
297J ARG* 2.9 31.6 + - - +
104L GLU* 5.9 8.2 + - - +
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Residues in contact with ASN 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J ILE 2.9 14.3 + - - +
291J ILE 3.6 7.6 - - - +
293J ARG* 1.3 78.1 - - - +
295J GLU* 1.3 55.0 + - - +
297J ARG* 3.4 24.3 + - - +
298J MET* 2.8 39.4 + - - +
97L PRO 4.6 4.0 - - - +
101L TYR* 3.1 39.2 - - + +
402L LEU* 4.6 2.4 - - - +
405L ILE* 4.0 11.9 - - - +
406L GLN* 2.9 24.5 - - - +
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Residues in contact with GLU 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ARG* 2.7 42.5 - - - +
278J ARG* 3.3 30.9 + - - +
279J LEU* 3.3 36.1 - - + +
282J LEU* 3.7 11.8 - - + +
291J ILE 2.9 13.3 + - - +
292J VAL 3.2 8.7 + - - +
294J ASN* 1.3 77.1 - - - +
296J LYS* 1.3 57.1 + - - +
298J MET* 3.1 7.3 + - - +
299J LEU* 2.9 27.0 + - - +
406L GLN* 3.9 11.7 - - - +
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Residues in contact with LYS 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J SER* 2.8 42.1 + - - +
110J PRO 5.5 2.7 - - - +
111J THR* 6.0 0.2 - - - -
141J PHE* 3.3 34.5 - - + -
183J GLU* 3.9 24.4 + - - -
279J LEU* 3.3 20.2 - - + -
283J LEU* 4.8 11.2 - - - +
292J VAL* 2.9 27.8 + - + +
293J ARG* 3.7 0.7 - - + +
295J GLU* 1.3 74.3 - - - +
297J ARG* 1.3 63.0 + - - +
299J LEU* 3.2 4.8 + - - +
300J GLN* 3.0 23.9 + - - +
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Residues in contact with ARG 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J LEU 5.5 1.1 - - - -
140J TYR* 3.3 33.1 + - + +
141J PHE* 4.1 21.9 + - + +
142J GLU* 4.4 2.8 + - - -
293J ARG* 2.9 19.1 + - - +
294J ASN* 3.5 33.2 + - - +
296J LYS* 1.3 76.2 - - - +
298J MET* 1.3 57.9 + - - +
300J GLN* 3.3 7.6 + - - +
301J GLU* 2.9 26.9 + - - +
97L PRO* 3.5 36.5 + - + -
100L MET* 3.2 52.9 + - - +
101L TYR* 4.2 8.5 - - - +
104L GLU* 4.7 11.9 + - - +
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Residues in contact with MET 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ARG* 3.1 36.6 + - - +
278J ARG* 4.5 1.8 - - - +
294J ASN* 2.8 39.5 + - - +
295J GLU* 3.1 8.5 + - - +
297J ARG* 1.3 76.6 - - - +
299J LEU* 1.3 58.6 + - - +
301J GLU* 3.2 5.7 - - - +
302J ALA* 2.9 23.0 + - - +
97L PRO* 4.9 4.5 - - + -
402L LEU* 2.9 60.6 - - + +
403L ASP* 3.5 17.9 - - - +
406L GLN* 3.6 20.4 - - + -
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Residues in contact with LEU 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J LEU* 4.4 15.5 - - + -
108J ALA* 5.3 3.4 - - + +
109J SER 5.3 4.0 - - - +
111J THR* 4.5 13.9 - - + -
272J VAL* 4.4 7.0 - - + +
275J ARG* 3.8 13.7 - - + +
276J ASN* 3.4 48.2 - - + +
279J LEU* 5.0 9.2 - - + -
295J GLU* 2.9 15.8 + - - +
296J LYS* 3.2 6.7 + - - +
298J MET* 1.3 73.1 - - - +
300J GLN* 1.3 67.8 + - - +
302J ALA* 3.1 5.0 + - - +
303J VAL* 2.9 41.9 + - + +
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Residues in contact with GLN 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J THR* 2.1 42.8 + - - +
112J ALA* 2.5 35.5 + - - +
117J LEU* 4.2 7.5 - - - +
139J LEU* 5.5 9.0 - - + +
140J TYR* 4.0 24.9 - - + -
296J LYS 3.0 13.5 + - - +
297J ARG* 3.6 9.6 - - - +
299J LEU* 1.3 76.6 - - - +
301J GLU* 1.3 61.1 + - - +
303J VAL* 4.1 0.8 - - - +
304J ASP* 2.9 58.8 + - - +
312J ARG* 4.4 2.0 - - - +
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Residues in contact with GLU 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J TYR* 5.9 0.2 - - - -
275J ARG* 4.2 7.7 + - - +
297J ARG 2.9 13.8 + - - +
298J MET* 3.2 14.6 - - - +
300J GLN* 1.3 77.8 - - - +
302J ALA* 1.3 58.8 + - - +
304J ASP* 3.2 5.1 + - - +
305J ALA* 2.9 27.6 + - - +
312J ARG* 3.0 45.8 - - - +
314J ARG 4.8 0.2 - - - +
316J ILE* 3.6 34.6 - - - +
97L PRO* 4.0 25.8 - - + -
400L GLN* 5.8 0.2 + - - -
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Residues in contact with ALA 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J LEU* 5.8 1.3 - - - +
271J ARG* 4.7 10.1 + - - +
272J VAL* 4.2 25.1 - - + +
275J ARG* 4.0 23.3 - - - +
298J MET 2.9 18.6 + - - +
299J LEU* 3.1 6.3 + - - +
301J GLU* 1.3 78.0 + - - +
303J VAL* 1.3 58.4 + - - +
305J ALA* 3.2 5.5 + - - +
306J LEU* 2.9 27.6 + - - +
316J ILE* 5.7 0.2 - - - +
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Residues in contact with VAL 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J LEU* 4.8 2.2 - - + -
111J THR* 4.0 21.3 - - + -
112J ALA 4.9 7.2 - - - +
239J LEU* 4.7 3.6 - - + -
242J LEU* 3.5 35.0 - - + -
272J VAL* 3.6 22.7 - - + -
299J LEU* 2.9 26.6 + - + +
300J GLN 4.2 1.3 - - - +
302J ALA* 1.3 76.4 - - - +
304J ASP* 1.3 64.9 + - - +
306J LEU* 3.0 8.5 + - + +
307J LEU* 3.0 37.3 + - + +
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Residues in contact with ASP 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ALA 3.4 3.1 - - - +
114J ILE* 2.9 63.8 - - - +
117J LEU* 4.4 2.9 - - - +
118J LYS* 4.6 4.9 - - - +
300J GLN* 2.9 41.5 + - - +
301J GLU 3.7 3.4 - - - +
303J VAL* 1.3 78.2 - - - +
305J ALA* 1.3 51.9 + - - +
307J LEU* 3.8 1.1 + - - -
308J ASP 2.7 30.5 + - - +
312J ARG* 3.5 28.8 + - - +
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Residues in contact with ALA 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J LEU* 4.7 6.8 - - + +
271J ARG* 5.5 1.1 - - - +
301J GLU* 2.9 24.1 + - - +
302J ALA 3.6 3.6 - - - +
304J ASP* 1.3 74.3 - - - +
306J LEU* 1.3 62.6 + - - +
308J ASP 3.1 10.0 - - - +
309J ASN* 3.0 30.5 + - - +
312J ARG* 5.0 8.0 - - + +
314J ARG 5.8 1.1 - - - +
315J ALA* 6.3 0.4 - - - -
316J ILE* 4.0 31.0 - - + +
326J SER* 3.3 4.2 - - - -
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Residues in contact with LEU 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J LEU* 4.7 13.2 - - + -
265J LEU* 5.5 1.7 - - + +
268J LEU* 4.4 23.2 - - + +
269J TYR* 3.7 38.8 - - + +
272J VAL* 4.0 21.1 - - + -
302J ALA 2.9 12.4 + - - +
303J VAL* 3.0 12.1 + - - +
305J ALA* 1.3 76.0 - - - +
307J LEU* 1.3 94.0 + - + +
326J SER* 3.0 20.7 - - - -
327J LEU* 3.1 27.9 + - + +
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Residues in contact with LEU 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332I SER 5.3 0.2 - - - +
1333I LEU* 3.8 27.4 - - + +
113J HIS* 3.3 47.3 - - + +
114J ILE* 4.1 17.9 - - + +
115J TRP* 4.3 3.5 + - - +
239J LEU* 4.4 11.4 - - + -
242J LEU* 4.9 8.5 - - + -
303J VAL* 3.0 21.4 + - + +
304J ASP* 5.1 0.4 - - - -
306J LEU* 1.3 101.9 - - + +
308J ASP* 1.3 63.2 + - - +
326J SER* 4.1 0.7 - - - -
327J LEU* 4.0 5.6 - - + +
328J ALA* 3.2 24.5 + - - +
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Residues in contact with ASP 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J ILE* 4.2 15.3 - - + +
115J TRP* 3.8 11.4 + - - +
304J ASP 2.7 23.4 + - - +
305J ALA* 3.1 10.9 - - - -
306J LEU 3.1 1.6 - - - -
307J LEU* 1.3 79.1 - - - +
309J ASN* 1.3 65.1 + - - +
310J GLY 3.7 1.1 - - - -
311J ARG* 2.4 42.4 + - - +
312J ARG* 5.2 1.2 - - - +
326J SER* 3.3 10.3 + - - -
328J ALA* 3.0 25.3 - - - +
329J ASP* 3.5 14.9 - - - +
332J LYS* 4.1 5.5 - - - -
1329J THR* 4.1 1.9 + - - -
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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