Contacts of the helix formed by residues 313 - 334 (chain B) in PDB entry 3GZN
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 VAL 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 3.7 20.9 - - + +
26A LEU* 3.6 20.3 - - + +
27A TRP* 3.8 21.1 - - + -
59A PRO* 6.2 1.1 - - + -
510A GLN* 4.6 0.7 - - - +
513A ILE* 6.4 0.2 - - + -
110B ASN* 4.6 4.5 - - - +
111B ARG* 4.2 4.0 - - - -
205B GLY 4.4 4.4 + - - +
206B PHE* 4.0 13.2 - - + -
312B ALA* 1.3 78.8 - - - +
314B ALA* 1.3 61.2 + - - +
315B SER* 3.3 24.0 - - - +
316B THR* 3.5 18.6 - - - +
317B ASN* 2.8 26.7 + - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 5.5 0.6 + - - -
54A LYS* 4.9 1.3 - - - +
55A ASN* 3.6 23.3 - - - +
58A LEU* 3.9 23.6 - - + -
59A PRO* 5.1 3.2 - - + +
83B GLU* 4.5 3.5 - - - +
110B ASN 4.1 6.0 + - - +
111B ARG* 3.8 24.8 - - + +
313B VAL* 1.3 73.4 - - - +
315B SER* 1.3 61.1 + - - +
317B ASN* 3.3 5.5 + - - +
318B ALA* 2.9 30.5 + - - +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 4.0 10.7 + - - +
506A GLY* 3.5 28.0 - - - -
509A ALA* 4.5 7.6 - - - -
510A GLN* 3.4 30.8 + - - +
513A ILE* 5.5 2.1 - - - +
313B VAL* 3.3 16.3 - - - +
314B ALA* 1.3 78.1 - - - +
316B THR* 1.3 68.0 + - - +
318B ALA* 3.3 2.8 + - - +
319B VAL* 3.1 26.1 + - - +
347B ASP* 4.6 1.5 + - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR* 3.4 18.8 - - - +
205B GLY 2.8 26.6 + - - +
206B PHE* 3.6 22.7 - - - +
207B LYS 3.8 15.5 - - - +
208B GLY* 4.4 2.5 - - - +
313B VAL* 3.5 15.7 - - - +
314B ALA 3.4 0.4 - - - -
315B SER* 1.3 77.4 + - - +
317B ASN* 1.3 64.6 + - - +
319B VAL* 3.2 9.7 + - - +
320B ILE* 3.2 21.2 + - + +
345B PHE* 4.2 15.7 - - + -
347B ASP* 4.4 2.5 + - - -
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 4.3 14.0 - - - +
80B LEU* 3.6 29.7 + - + +
83B GLU* 4.6 4.0 - - - +
111B ARG* 3.8 23.3 - - + +
203B THR* 3.1 32.4 + - - +
312B ALA* 4.5 3.6 - - - +
313B VAL 2.8 24.0 + - - +
314B ALA* 3.3 9.3 + - - +
316B THR* 1.3 78.0 - - - +
318B ALA* 1.3 56.6 + - - +
320B ILE* 3.3 2.0 + - - -
321B ALA* 2.9 33.4 + - - +
76I GLY 4.5 2.1 - - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 5.6 1.1 - - - +
55A ASN* 4.0 20.9 - - - +
502A ALA* 4.4 10.1 - - + +
506A GLY* 4.1 5.2 - - - -
83B GLU* 3.7 31.9 + - - +
314B ALA 2.9 16.8 + - - +
315B SER 3.4 9.6 - - - +
317B ASN* 1.3 73.1 - - - +
319B VAL* 1.3 64.5 + - - +
321B ALA* 3.8 0.9 - - - +
322B ALA* 2.9 26.5 + - - +
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 3.6 36.7 - - + +
506A GLY* 3.7 1.8 - - - -
507A ALA* 3.4 30.7 - - + +
315B SER 3.1 11.8 + - - +
316B THR 3.4 8.1 - - - +
318B ALA* 1.3 80.1 - - - +
320B ILE* 1.3 67.8 + - + +
322B ALA* 3.4 3.5 + - - +
323B VAL* 3.2 25.9 + - + +
343B LEU* 6.1 0.2 - - + -
345B PHE* 3.9 44.9 - - + -
347B ASP* 5.5 0.2 - - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.7 16.8 - - + -
201B GLY* 3.8 12.8 - - - -
202B GLY 3.9 14.1 - - - +
203B THR* 4.4 4.7 - - - +
208B GLY* 3.5 15.9 - - - +
209B ASN* 3.3 43.7 - - - +
210B ALA* 4.3 2.2 - - + +
316B THR* 3.2 13.8 + - + +
317B ASN* 3.9 5.4 - - - +
319B VAL* 1.3 75.3 - - + +
321B ALA* 1.3 66.6 + - - +
322B ALA 3.1 1.9 + - - -
323B VAL* 3.2 6.0 + - + +
324B CYS* 3.1 24.1 + - - -
343B LEU* 4.5 9.0 - - + -
345B PHE* 4.1 15.3 - - + -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.6 22.1 - - + +
83B GLU* 3.5 32.8 - - + -
84B LEU* 3.5 19.5 - - + +
87B ASN* 3.4 3.0 + - - +
317B ASN 2.9 19.5 + - - +
320B ILE* 1.3 73.3 - - - +
322B ALA* 1.3 57.2 + - - +
324B CYS* 4.5 0.9 - - - -
325B ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A THR* 3.4 24.6 - - - +
502A ALA* 3.9 8.1 - - + -
503A PHE* 3.6 19.3 - - + +
529A TYR* 5.7 0.2 - - - -
87B ASN* 3.5 10.2 - - - +
318B ALA 2.9 17.2 + - - +
319B VAL 3.5 5.6 - - - +
320B ILE 3.1 0.2 - - - -
321B ALA* 1.3 74.0 - - - +
323B VAL* 1.3 56.5 + - - +
325B ALA* 3.1 4.0 + - - +
326B THR* 2.8 38.6 + - - -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 3.8 24.0 - - + -
529A TYR* 4.9 0.7 - - - -
534A GLN* 3.3 39.3 + - + +
210B ALA* 4.0 20.2 - - + -
319B VAL* 3.2 17.9 - - + +
320B ILE* 3.5 8.1 - - - +
322B ALA* 1.3 76.1 - - - +
324B CYS* 1.3 64.4 + - - +
326B THR* 3.2 3.9 + - - -
327B GLU* 3.0 27.2 + - + +
339B LEU* 4.8 5.2 - - + -
343B LEU* 4.4 21.5 - - + -
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Residues in contact with CYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.7 0.7 - - - -
84B LEU* 3.7 21.8 - - + -
163B VAL* 3.9 3.1 - - + -
164B CYS 5.7 0.2 - - - -
199B ILE* 3.4 30.5 - - + +
201B GLY* 3.9 22.4 - - - -
210B ALA* 3.9 18.2 - - - -
320B ILE* 3.1 15.8 + - - -
321B ALA* 3.7 2.7 - - - +
323B VAL* 1.3 77.6 - - - +
325B ALA* 1.3 63.6 + - - +
327B GLU* 3.0 7.3 + - - +
328B VAL* 2.9 26.8 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A THR* 3.5 10.3 - - + -
84B LEU* 4.4 4.4 - - + +
87B ASN* 3.4 29.6 - - + -
88B LEU* 4.2 20.6 - - + +
91B SER* 5.3 0.9 - - - +
321B ALA 3.0 19.1 + - - +
322B ALA 3.1 4.2 + - - +
324B CYS* 1.3 73.7 - - - +
326B THR* 1.3 65.1 + - - +
328B VAL* 2.9 16.1 + - - +
329B PHE* 3.0 14.1 + - - +
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 5.4 4.7 - - + -
499A THR* 2.9 31.2 + - - +
500A ILE* 4.4 11.6 - - + +
529A TYR* 4.3 4.9 + - - -
531A GLY 4.1 10.5 - - - +
534A GLN* 3.6 11.8 + - - +
322B ALA 2.8 19.0 + - - -
323B VAL 3.4 7.9 - - - -
325B ALA* 1.3 71.0 - - - +
327B GLU* 1.3 69.1 + - - +
329B PHE* 3.4 10.8 + - + +
330B LYS* 2.9 37.4 + - + +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLN* 2.6 33.1 + - - +
199B ILE* 4.6 4.0 - - + -
212B VAL* 3.9 21.5 - - + -
323B VAL* 3.0 18.0 + - + +
324B CYS* 3.0 8.9 + - - +
326B THR* 1.3 73.4 - - - +
328B VAL* 1.3 60.7 + - - +
330B LYS* 3.1 30.7 + - - +
331B ILE* 2.8 37.1 + - + +
338B PRO* 3.4 3.1 - - - +
339B LEU* 2.6 51.2 + - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.2 11.7 - - + -
88B LEU* 3.9 17.9 - - + -
93B PHE* 3.8 15.9 - - + -
161B ILE* 3.5 26.6 - - + +
163B VAL* 3.3 28.9 - - + -
199B ILE* 4.1 16.4 - - + +
324B CYS 2.9 22.3 + - - +
325B ALA* 3.4 5.4 - - - +
327B GLU* 1.3 74.3 - - - +
329B PHE* 1.3 59.4 + - - +
331B ILE* 3.3 1.2 + - - -
332B ALA* 2.8 31.2 + - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A THR* 6.0 0.4 - - - +
41B VAL* 3.8 23.1 - - + -
44B PHE* 4.4 18.4 - + + -
45B LEU* 4.3 9.0 - - + -
66B LEU* 4.5 3.4 - - + -
91B SER* 3.6 35.2 - - - +
93B PHE* 3.9 18.3 - + + -
325B ALA 3.0 11.0 + - - +
326B THR* 3.4 14.8 - - + +
328B VAL* 1.3 76.6 - - - +
330B LYS* 1.3 59.4 + - + +
333B THR* 2.7 70.3 + - + +
335B ALA* 4.1 13.0 - - + -
336B TYR* 5.8 3.1 - + - -
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Residues in contact with LYS 330 (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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165A LEU* 4.8 1.3 - - - -
531A GLY 3.0 20.4 + - - -
532A MET* 2.9 25.8 + - - +
533A SER 5.2 0.2 - - - -
534A GLN* 4.2 2.6 - - - +
326B THR* 2.9 20.3 + - + +
327B GLU* 3.1 45.1 + - - +
329B PHE* 1.3 80.2 - - + +
331B ILE* 1.3 57.4 + - - +
333B THR* 4.1 4.3 - - - -
334B SER* 2.8 31.4 + - - -
335B ALA 3.8 1.9 + - - +
336B TYR* 3.6 53.0 - - + +
337B ILE 3.7 8.8 + - - +
338B PRO* 4.6 6.7 - - + +
339B LEU 4.4 1.4 - - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 4.3 10.3 - - + -
197B PRO* 4.0 30.1 - - + -
199B ILE* 3.6 28.7 - - + -
212B VAL* 4.1 21.5 - - + -
214B LEU* 5.4 2.9 - - + -
327B GLU 2.8 25.9 + - - +
328B VAL* 3.9 3.1 - - - +
330B LYS* 1.3 74.1 - - - +
332B ALA* 1.3 66.8 + - - +
333B THR 3.2 0.2 + - - -
334B SER* 3.6 10.2 + - - -
338B PRO* 3.8 23.6 - - + -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.1 7.6 - - + +
70B CYS* 4.0 11.9 - - - -
93B PHE* 3.7 24.5 - - + -
161B ILE* 3.6 17.2 - - + +
328B VAL 2.8 20.5 + - - +
331B ILE* 1.3 76.0 - - - +
333B THR* 1.3 59.7 + - - +
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 23.2 - - + +
56B PHE* 4.0 11.3 - - - -
66B LEU* 4.1 23.1 - - + -
329B PHE* 2.7 54.9 + - + +
332B ALA* 1.3 77.7 - - + +
334B SER* 1.3 67.6 + - - +
335B ALA* 3.2 22.7 + - - +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 3.3 36.5 + - - +
55B ASP* 4.4 8.3 + - - +
56B PHE* 3.4 26.9 - - - +
330B LYS 2.8 19.0 + - - -
331B ILE 3.6 8.2 + - - -
332B ALA 5.4 0.2 + - - -
333B THR* 1.3 74.4 - - - +
335B ALA* 1.3 63.1 + - - +
336B TYR 3.2 4.7 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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