Contacts of the helix formed by residues 387 - 407 (chain B) in PDB entry 1Y8Q
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 ILE 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.6 18.8 - - + +
25A LEU* 4.4 8.5 - - + -
26A TRP* 3.6 31.0 - - + -
58B ASN* 4.2 4.9 - - - +
59B ARG* 3.9 5.2 - - - -
143B GLY 3.9 8.2 + - - +
144B TYR* 3.9 29.4 - - + -
386B ALA* 1.3 79.8 - - - +
388B ALA* 1.3 63.2 + - - +
389B THR* 3.3 27.8 - - + -
390B THR* 3.4 20.9 - - - +
391B ASN* 3.1 23.2 + - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 5.2 0.8 + - - -
54A ASN* 3.9 20.6 - - - +
57A LEU* 4.0 22.4 - - + -
58A ALA* 5.7 0.9 - - - +
31B GLU* 4.6 5.9 - - - +
58B ASN 3.6 19.0 + - - +
59B ARG* 3.7 15.8 - - - +
387B ILE* 1.3 74.1 - - - +
389B THR* 1.3 64.2 + - - +
391B ASN* 3.2 6.0 + - - +
392B ALA* 3.0 21.8 + - - +
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 5.8 2.0 - - + -
54A ASN* 4.2 15.6 + - - +
308A GLY* 2.2 35.8 + - - -
311A ALA* 5.1 0.4 - - - -
312A GLN* 2.9 42.9 + - + +
387B ILE* 3.3 23.3 - - + -
388B ALA* 1.3 80.0 - - - +
390B THR* 1.3 62.5 + - - +
392B ALA* 3.3 5.5 + - - +
393B VAL* 3.1 24.8 + - - +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLN* 3.5 12.0 + - - +
141B THR* 4.1 11.4 - - + -
143B GLY 2.8 25.0 + - - +
144B TYR* 3.6 13.4 - - - +
145B LEU 3.5 27.8 - - - +
146B GLY 4.6 0.2 - - - +
387B ILE* 3.4 19.2 + - - +
388B ALA 3.4 1.0 - - - -
389B THR* 1.3 77.6 - - - +
391B ASN* 1.3 64.3 + - - +
393B VAL* 3.3 6.8 + - - +
394B ILE* 3.1 22.9 + - + +
418B LEU* 4.0 9.4 - - + -
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY* 3.8 33.8 - - - +
28B ILE* 3.2 20.8 + - - +
31B GLU* 4.2 4.5 - - + +
59B ARG* 4.0 15.4 - - - +
141B THR* 2.8 30.7 + - - +
386B ALA* 4.6 4.4 - - - +
387B ILE 3.1 21.4 + - - +
388B ALA* 3.2 8.6 + - - +
390B THR* 1.3 78.3 - - - +
392B ALA* 1.3 58.4 + - - +
394B ILE* 3.4 1.4 + - - +
395B ALA* 3.0 31.0 + - - +
802B ATP 5.2 2.6 + - - -
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 4.8 1.8 - - - +
53A LYS* 4.2 8.1 - - - +
54A ASN* 4.2 10.8 - - - +
304A ALA* 3.8 25.4 - - + +
308A GLY* 4.7 0.4 - - - -
31B GLU* 3.7 30.4 - - - +
388B ALA 3.0 16.1 + - - +
389B THR* 3.6 6.7 - - - +
390B THR 3.2 0.2 - - - -
391B ASN* 1.3 77.2 - - - +
393B VAL* 1.3 62.9 + - - +
395B ALA* 3.4 1.4 + - - +
396B GLY 3.1 18.2 + - - -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA 4.2 4.7 - - - -
305A VAL* 3.8 28.4 - - + +
308A GLY* 3.9 8.1 - - - -
309A ILE* 3.6 29.4 - - + -
312A GLN* 5.3 1.6 - - - +
389B THR* 3.1 17.2 + - - +
390B THR* 3.3 7.8 + - - +
392B ALA* 1.3 76.1 - - - +
394B ILE* 1.3 62.7 + - - +
396B GLY* 3.2 3.6 + - - -
397B LEU* 3.1 35.4 + - + +
418B LEU* 3.6 27.4 - - + -
429B LEU* 4.5 2.9 - - + -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 4.0 10.1 - - + -
139B SER* 3.8 20.4 - - - -
140B GLY 4.6 0.2 - - - +
141B THR* 3.3 27.8 - - + -
146B GLY* 3.7 30.3 - - - -
147B GLN* 3.8 3.8 - - - +
148B VAL* 3.5 23.1 - - + -
390B THR* 3.1 10.6 + - + +
391B ASN 3.9 3.1 - - - +
393B VAL* 1.3 75.0 - - - +
395B ALA* 1.3 61.2 + - - +
397B LEU* 3.0 12.0 + - + +
398B ILE* 2.8 36.2 + - + +
416B ILE 5.7 0.2 - - - +
418B LEU* 4.2 17.0 - - + -
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 4.0 8.0 - - + +
31B GLU* 3.4 33.2 - - + -
32B LEU* 3.7 13.9 - - + +
35B ASN* 3.4 10.8 - - - +
391B ASN 3.0 11.9 + - - +
392B ALA 3.9 1.1 - - - +
394B ILE* 1.3 76.6 - - - +
396B GLY* 1.3 61.9 + - - +
398B ILE* 3.3 14.3 + - - +
399B VAL* 3.3 26.7 + - - +
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Residues in contact with GLY 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 3.4 34.6 - - - +
304A ALA* 4.1 2.7 - - - -
305A VAL* 4.2 7.2 - - - -
35B ASN* 3.7 8.7 - - - +
392B ALA 3.1 14.4 + - - -
393B VAL 3.2 4.2 + - - -
395B ALA* 1.3 78.7 - - - +
397B LEU* 1.3 60.0 + - - +
399B VAL 3.5 1.6 + - - -
400B LEU* 3.3 18.2 + - - +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 3.9 8.3 - - + -
331A PHE* 3.9 33.0 - - + -
336A GLY* 5.7 0.7 - - - -
148B VAL* 4.1 11.0 - - + -
393B VAL* 3.1 19.4 + - + +
394B ILE* 3.0 20.9 + - + +
396B GLY* 1.3 72.6 - - - +
398B ILE* 1.3 68.3 + - - +
400B LEU* 3.0 12.0 + - + +
401B GLU* 3.0 26.5 + - - +
416B ILE* 3.9 42.6 - - + +
418B LEU* 5.5 0.4 - - + -
429B LEU* 4.2 19.3 - - + -
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.7 25.8 - - + -
32B LEU* 3.9 22.7 - - + -
113B MET* 3.9 20.8 - - + +
114B ASN 4.7 3.4 - - - +
137B ILE* 3.6 17.4 - - + +
139B SER* 3.1 37.2 - - - +
148B VAL* 4.1 14.1 - - + -
394B ILE* 2.8 21.2 + - + +
395B ALA* 3.4 9.6 - - - +
396B GLY 3.2 0.4 - - - -
397B LEU* 1.3 78.9 - - - +
399B VAL* 1.3 62.5 + - - +
401B GLU* 3.2 0.9 + - - +
402B GLY* 3.0 18.5 + - - -
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PRO* 3.6 25.6 - - + -
32B LEU* 3.9 16.6 - - + -
35B ASN* 3.6 33.2 - - + +
36B LEU* 4.2 7.4 - - + -
39B THR* 3.6 23.1 - - + +
41B PHE* 4.4 12.3 - - + -
113B MET* 5.8 1.3 - - - -
395B ALA 3.3 9.6 + - - +
396B GLY 3.5 2.4 + - - +
398B ILE* 1.3 76.8 - - - +
400B LEU* 1.3 63.1 + - - +
402B GLY* 3.7 2.3 - - - +
403B LEU* 3.0 26.6 + - + +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.1 31.4 - - + -
299A MET* 5.4 1.8 - - + -
301A PRO* 3.9 19.7 - - + -
302A VAL* 4.6 8.3 - - + -
305A VAL* 4.8 2.0 - - + -
331A PHE* 3.8 31.0 - - + -
333A GLY* 4.1 18.2 - - - +
396B GLY 3.3 15.6 + - - +
397B LEU* 3.0 17.8 + - + +
399B VAL* 1.3 80.4 - - - +
401B GLU* 1.3 64.1 + - - +
403B LEU* 3.5 12.0 + - + +
404B LYS* 3.4 27.3 + - + +
416B ILE* 6.5 0.2 - - + -
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLY 5.7 0.2 - - - +
336A GLY* 5.8 0.3 - - - -
137B ILE* 4.2 7.2 - - + -
148B VAL* 4.2 18.4 - - + -
150B THR* 4.2 13.9 + - - +
397B LEU 3.0 17.7 + - - +
398B ILE* 3.7 6.5 - - - +
400B LEU* 1.3 75.7 - - - +
402B GLY* 1.3 66.7 + - - +
404B LYS* 3.0 27.8 + - - +
405B ILE* 2.9 26.9 + - - +
413B CYS* 3.1 15.2 - - - +
414B ARG* 2.9 37.8 + - - +
416B ILE* 3.5 21.1 - - + +
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 5.4 1.8 - - - -
111B LEU* 4.0 15.0 - - - -
113B MET* 6.1 0.2 - - - -
137B ILE* 3.6 17.1 - - - +
398B ILE 3.0 11.0 + - - -
399B VAL* 3.3 4.9 + - - -
401B GLU* 1.3 77.9 - - - +
403B LEU* 1.3 56.1 + - - +
405B ILE* 3.1 5.6 + - - +
406B LEU* 2.8 38.9 + - - +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.7 8.7 - - + +
299A MET* 4.4 20.0 - - + -
301A PRO* 5.1 1.6 - - + -
7B LEU* 4.6 7.6 - - + -
11B LEU* 3.8 32.6 - - + +
15B VAL* 4.2 12.3 - - + -
39B THR* 4.2 27.8 - - + -
41B PHE* 4.3 9.6 - - + -
399B VAL* 3.0 22.1 + - + +
400B LEU* 3.7 21.1 - - + +
401B GLU 3.2 0.2 - - - -
402B GLY* 1.3 76.1 - - - +
404B LYS* 1.3 59.6 + - + +
406B LEU* 3.7 3.0 + - - +
407B SER* 2.8 30.7 + - - -
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLY 4.9 7.0 + - - +
334A MET* 4.2 30.9 + - + +
335A LYS 5.9 1.2 - - - -
336A GLY* 5.9 0.6 - - - +
400B LEU* 3.4 18.0 + - + +
401B GLU* 3.0 33.8 + - - +
403B LEU* 1.3 75.8 - - + +
405B ILE* 1.3 65.7 - - - +
407B SER* 3.1 10.5 + - - -
408B GLY 3.1 0.2 + - - -
409B LYS* 2.8 47.8 + - + +
412B GLN* 3.1 45.0 + - + +
413B CYS* 3.7 11.7 - - - +
414B ARG* 4.6 4.4 - - - +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.7 24.9 - - + -
135B PRO* 3.7 31.2 - - + -
137B ILE* 3.8 20.2 - - + -
150B THR* 3.7 28.9 - - + +
401B GLU 2.9 14.5 + - - +
402B GLY* 3.4 6.7 - - - +
404B LYS* 1.3 75.1 - - - +
406B LEU* 1.3 64.0 + - + +
408B GLY* 2.9 22.0 + - - -
410B ILE* 4.4 17.4 + - + +
413B CYS* 3.6 13.7 - - - -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU 5.4 2.1 - - - +
11B LEU* 5.1 8.1 - - + +
14B ALA* 4.4 19.8 - - + +
15B VAL* 4.3 13.5 - - + +
41B PHE* 3.4 39.3 - - + -
110B ILE* 3.8 49.6 - - + +
111B LEU* 4.1 11.4 - - + -
402B GLY 2.8 21.2 + - - +
403B LEU* 3.8 4.7 - - - +
405B ILE* 1.3 76.9 - - + +
407B SER* 1.3 58.4 + - - +
408B GLY 3.2 1.7 + - - -
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 5.3 5.2 - - - +
11B LEU* 4.1 24.0 - - - +
403B LEU 2.8 20.6 + - - -
404B LYS* 3.5 8.3 - - - -
405B ILE 3.0 1.2 - - - -
406B LEU* 1.3 76.8 - - - +
408B GLY* 1.3 61.1 + - - +
409B LYS* 3.3 29.5 + - - +
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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