Contacts of the strand formed by residues 310 - 330 (chain A) in PDB entry 3I5D
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 GLU 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR* 3.6 17.3 - - - +
116A GLN* 4.7 3.7 + - + +
167A TRP* 3.7 14.9 - - + -
302A TYR* 4.0 14.7 - - - +
303A TYR 4.0 8.3 - - - +
304A LYS* 5.0 2.9 - - + +
308A GLY 4.0 1.7 + - - +
309A THR* 1.3 76.8 - - - +
311A THR* 1.3 68.0 + - - +
85B ARG* 3.0 28.8 + - - -
92B TYR* 3.8 1.8 + - - -
301B LYS* 3.7 15.8 + - - -
303B TYR* 3.0 29.3 + - + +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 4.5 17.5 - - - +
114A GLN 3.0 9.2 - - - -
115A THR* 3.3 23.1 - - + -
167A TRP* 4.6 2.7 - - - -
302A TYR* 3.7 2.0 - - - +
303A TYR* 2.8 52.4 + - - +
305A ASN* 4.4 21.6 - - + +
309A THR* 4.5 2.5 - - - +
310A GLU* 1.3 76.2 - - - +
312A ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN 3.7 3.7 + - - -
114A GLN* 2.6 66.0 + - + +
167A TRP* 3.3 37.8 - - + +
300A ALA* 3.9 7.4 - - + -
301A LYS 3.1 12.6 - - - +
302A TYR* 3.6 32.5 + - + -
303A TYR* 4.9 2.5 - - - -
311A THR* 1.3 75.8 - - - +
313A THR* 1.3 62.8 + - - +
314A LEU* 3.1 25.7 + - - +
88B ASP* 2.5 43.8 + - - -
91B ASP* 3.5 14.8 - - - +
92B TYR* 4.2 0.4 - - - +
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Residues in contact with THR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.7 24.9 - - + -
111A THR 3.5 11.2 - - - +
112A THR* 3.9 15.7 - - + +
113A ASN 4.5 1.9 + - - -
299A PHE 3.8 0.2 - - - +
300A ALA* 3.3 8.1 - - - -
301A LYS* 2.9 41.4 + - + -
303A TYR* 3.6 18.2 + - - +
312A ARG* 1.3 73.5 + - - +
314A LEU* 1.3 60.9 + - - +
315A ILE* 3.7 15.9 + - + +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE 3.8 1.0 - - - +
110A ILE* 3.5 2.4 - - - -
111A THR* 2.7 45.7 + - - +
114A GLN* 3.4 30.5 + - - +
171A GLU* 4.1 24.2 - - + +
298A ARG* 3.9 33.9 - - + +
299A PHE 3.5 11.4 - - - +
300A ALA* 4.6 1.6 - - - -
312A ARG* 3.1 30.2 + - - +
313A THR* 1.3 72.2 - - - +
315A ILE* 1.3 71.0 + - - +
316A LYS 4.2 0.2 - - - -
88B ASP* 4.4 3.4 - - - +
91B ASP* 4.1 9.2 - - + -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 5.5 4.9 - - + -
92A TYR* 5.2 7.4 - - + +
108A MET* 4.5 17.7 - - + -
109A ILE 3.9 2.7 - - - -
110A ILE* 4.5 19.1 - - + +
297A PHE 3.6 0.2 - - - +
298A ARG* 3.3 5.2 - - - -
299A PHE* 2.9 73.7 + - + +
301A LYS* 4.5 17.7 - - + +
313A THR* 3.8 23.3 - - + +
314A LEU* 1.3 83.7 - - - +
316A LYS* 1.3 61.3 + - - +
317A GLY* 3.3 11.0 + - - +
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Residues in contact with LYS 316 (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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108A MET* 3.3 4.2 - - - -
109A ILE* 3.2 43.1 + - + +
171A GLU* 3.4 27.0 + - - +
296A ASN* 3.2 27.1 - - - +
297A PHE 3.7 4.7 - - - +
298A ARG* 3.7 30.8 - - + +
314A LEU* 4.2 1.2 - - - +
315A ILE* 1.3 69.8 - - - +
317A GLY* 1.3 61.0 + - - +
318A TYR* 3.1 33.9 + - + +
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Residues in contact with GLY 317 (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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103A PHE* 4.4 6.5 - - - -
105A LEU* 3.6 15.9 - - - -
107A ASN 3.6 6.7 - - - -
108A MET* 4.4 1.3 - - - -
296A ASN* 3.0 6.2 - - - +
297A PHE* 3.0 35.3 + - - +
299A PHE* 4.8 5.6 - - - -
315A ILE* 3.3 10.5 + - - -
316A LYS* 1.3 71.9 - - - +
318A TYR* 1.3 62.7 + - - -
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Residues in contact with TYR 318 (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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103A PHE* 4.2 1.3 - - - -
105A LEU* 3.2 6.0 - - - +
106A THR* 2.9 21.0 + - - +
107A ASN* 2.7 29.6 + - + +
108A MET 4.0 0.9 - - - -
109A ILE* 3.6 21.2 - - + +
174A VAL 5.2 0.7 + - - -
176A PRO* 3.6 32.5 - - + +
251A VAL 3.8 15.3 - - - +
252A ARG* 3.4 36.6 - - + -
253A GLY 4.4 0.4 - - - +
295A TYR 3.7 3.8 - - - -
296A ASN* 3.6 19.5 - - + -
316A LYS* 3.1 49.2 + - + +
317A GLY* 1.3 75.2 - - - -
319A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.7 12.0 - - - -
104A VAL 3.2 11.2 - - - -
106A THR* 2.9 14.8 + - - -
253A GLY* 3.1 20.0 - - - -
254A GLY 3.1 6.2 + - - +
295A TYR* 3.3 12.6 + - - +
318A TYR* 1.3 76.8 - - - +
320A ILE* 1.3 65.5 + - - -
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Residues in contact with ILE 320 (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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103A PHE* 4.1 2.0 - - - -
104A VAL* 3.1 27.4 + - + +
106A THR* 4.4 8.1 - - + -
239A VAL* 4.3 3.6 - - + -
246A PHE* 3.4 45.3 - - + -
249A MET* 3.9 25.1 - - + -
250A ALA* 4.4 14.1 - - + +
254A GLY 3.1 14.8 - - - +
256A MET* 3.8 30.1 - - + +
319A GLY* 1.3 76.3 - - - +
321A ARG* 1.3 60.3 + - - +
322A PHE* 3.6 23.6 - - + -
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Residues in contact with ARG 321 (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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101A SER* 4.4 8.3 - - - -
102A PHE 3.5 11.7 - - - +
103A PHE* 4.0 15.7 - - + -
254A GLY 2.9 7.9 + - - -
255A VAL* 3.2 21.7 - - + +
256A MET 2.9 23.7 + - - +
295A TYR* 3.3 39.6 + - + +
319A GLY 4.0 1.0 + - - -
320A ILE* 1.3 73.6 - - - +
322A PHE* 1.3 62.3 + - - +
323A ASP* 2.7 53.2 + - - -
66B SER* 4.5 0.6 + - - -
67B VAL 2.8 28.5 + - - -
68B THR* 3.2 18.2 + - - +
99B ASP* 4.1 27.9 + - - +
100B GLY 5.3 0.2 - - - +
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Residues in contact with PHE 322 (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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101A SER* 3.1 6.8 - - - -
102A PHE* 2.7 76.4 + + + -
104A VAL* 3.9 15.5 - - + -
235A LEU* 3.6 29.8 - - + -
238A ILE* 3.7 31.0 - - + -
239A VAL* 4.8 2.7 - - + -
246A PHE* 4.8 2.5 - + - -
256A MET* 3.5 23.1 - - + +
258A VAL* 4.3 12.1 - - + -
320A ILE* 3.6 41.1 - - + -
321A ARG* 1.3 71.5 - - - +
323A ASP* 1.3 61.7 + - - +
324A VAL 3.7 0.9 + - - -
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Residues in contact with ASP 323 (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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101A SER* 3.4 14.8 + - - +
255A VAL* 5.4 2.9 - - - +
256A MET 2.9 12.9 + - - +
257A GLY* 3.6 1.7 - - - -
258A VAL* 2.9 25.7 + - - -
282A LEU* 4.4 10.3 - - + -
321A ARG* 2.7 53.6 + - - -
322A PHE* 1.3 69.2 - - - +
324A VAL* 1.3 60.5 - - - +
325A MET* 3.3 18.7 + - + +
66B SER* 2.9 23.9 + - - -
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Residues in contact with VAL 324 (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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67A VAL* 3.6 37.4 - - + +
69A THR* 4.3 22.9 - - + -
100A GLY* 4.4 8.0 - - - +
101A SER* 3.9 8.6 + - - +
102A PHE* 4.7 9.6 - - + -
192A ILE* 4.5 14.6 - - + -
258A VAL* 3.5 18.6 - - + +
260A ILE* 4.1 15.0 - - + -
322A PHE 3.7 2.0 + - - +
323A ASP* 1.3 69.8 - - - +
325A MET* 1.3 60.2 + - - +
326A VAL* 3.7 13.8 + - + +
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Residues in contact with MET 325 (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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257A GLY* 3.3 35.4 - - - -
258A VAL 3.0 7.6 + - - +
259A GLN* 3.3 34.4 - - + +
260A ILE 3.0 24.1 + - - +
280A ARG* 4.6 4.0 - - - +
282A LEU* 3.8 21.5 - - + -
323A ASP* 3.7 12.6 - - + +
324A VAL* 1.3 73.0 - - - +
326A VAL* 1.3 60.0 + - - +
327A PHE* 4.1 6.7 + - + -
64B LEU* 5.7 9.0 - - + -
65B SER 4.2 21.8 - - - +
66B SER* 4.5 5.6 - - - -
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Residues in contact with VAL 326 (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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63A VAL* 4.8 2.8 - - + +
65A SER* 3.1 38.0 - - - +
67A VAL* 3.8 18.2 - - + -
194A ASN* 3.5 22.4 - - - +
196A ILE* 4.1 2.2 - - + -
260A ILE* 3.5 14.8 - - + +
262A TRP* 3.8 20.2 - - + +
324A VAL* 3.7 11.2 + - + +
325A MET* 1.3 76.0 - - - +
327A PHE* 1.3 70.9 + - - +
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Residues in contact with PHE 327 (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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63A VAL* 4.0 10.8 - - - -
259A GLN* 4.4 28.9 - - + -
260A ILE 3.1 15.4 + - - +
261A ARG* 3.4 40.4 - - + -
262A TRP* 3.0 22.5 + - - -
263A ASP* 5.6 0.4 - - - -
325A MET* 4.2 8.5 - - + -
326A VAL* 1.3 81.2 - - - +
328A GLY* 1.3 65.6 - - - +
64B LEU* 5.6 9.6 - - + -
197B ARG* 5.5 2.2 - - - -
199B PRO* 4.0 35.9 - - + -
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Residues in contact with GLY 328 (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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62A THR* 3.5 9.5 - - - +
63A VAL* 3.4 29.7 + - - +
261A ARG* 4.8 0.2 - - - -
262A TRP 3.3 12.3 - - - -
263A ASP* 3.7 8.1 - - - -
327A PHE* 1.3 87.0 - - - +
329A GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 329 (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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60A THR* 5.5 5.8 - - - -
61A ASP 3.4 14.8 - - - +
62A THR* 5.3 2.7 - - + -
198A TYR* 4.0 2.5 - - - -
262A TRP 3.1 13.7 + - - +
263A ASP* 3.3 13.1 + - - +
264A CYS 3.3 10.4 + - - +
328A GLY* 1.3 75.8 - - - +
330A ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 330 (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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59A ASP 3.2 4.5 - - - +
60A THR* 3.4 4.2 - - - -
61A ASP 3.2 26.1 + - - -
198A TYR* 3.7 23.8 - - + +
201A PHE* 3.6 5.8 - - + -
264A CYS* 3.2 20.2 - - + +
266A LEU* 3.6 22.2 - - + -
329A GLN* 1.3 77.6 - - - +
331A GLY* 1.3 59.7 + - - +
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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
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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