Contacts of the helix formed by residues 330 - 345 (chain B) in PDB entry 6T2C
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 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLU* 5.2 8.7 - - + +
111B ILE* 4.4 13.5 - - + -
328B GLY 4.5 1.6 - - - +
329B GLN* 1.3 96.3 - - + +
331B GLU* 1.3 65.6 + - + +
332B TRP* 3.3 28.7 - - + +
333B PHE* 3.1 19.0 + - + +
334B ARG* 3.4 5.5 + - - +
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Residues in contact with GLU 331 (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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230A LYS* 3.7 23.9 + - - +
329B GLN 4.0 7.2 - - - +
330B PRO* 1.3 70.6 - - + +
332B TRP* 1.3 61.1 + - - +
334B ARG* 3.3 33.5 + - - +
335B ASP* 3.0 39.9 + - - +
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Residues in contact with TRP 332 (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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202A GLU* 4.7 11.1 + - + -
203A GLU* 3.6 52.5 + - + +
204A GLU* 4.4 0.2 - - - -
205A PHE* 3.8 39.9 - - + +
111B ILE* 3.8 34.3 - - + -
114B ILE* 3.9 33.7 - - + -
115B GLN* 4.2 8.7 - - - -
164B ILE* 4.0 9.4 - - + -
330B PRO* 3.5 28.5 - - + +
331B GLU* 1.3 77.7 - - - +
333B PHE* 1.3 65.2 + + + +
335B ASP* 3.5 2.0 + - - +
336B LEU* 2.9 39.4 + - + +
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Residues in contact with PHE 333 (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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107B CYS* 3.6 37.9 - - + -
110B THR* 3.8 24.0 - - + -
111B ILE* 3.6 31.2 - - + -
114B ILE* 3.6 30.3 - - + -
258B LEU* 4.9 0.4 - - + -
326B THR* 3.8 11.6 - - + +
329B GLN* 3.9 15.9 - - + -
330B PRO 3.1 12.7 + - - +
332B TRP* 1.3 90.2 - + + +
334B ARG* 1.3 57.5 + - - +
336B LEU* 3.4 2.5 + - + +
337B LEU* 3.0 54.1 + - + +
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Residues in contact with ARG 334 (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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226A TYR* 4.4 0.7 - - - -
230A LYS* 3.5 31.6 + - + +
234A SER* 3.4 33.9 + - - +
322B VAL 5.5 0.9 - - - +
323B LEU* 2.7 40.7 + - + +
326B THR* 3.1 42.6 + - - +
327B ALA* 3.8 9.3 - - - +
328B GLY 4.8 2.2 - - - +
329B GLN* 4.2 7.4 - - + +
330B PRO 3.6 11.2 - - - +
331B GLU* 3.3 34.1 + - - +
333B PHE* 1.3 76.2 - - - +
335B ASP* 1.3 61.7 + - - +
337B LEU* 3.8 1.8 - - - +
338B ALA* 2.9 33.2 + - - +
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Residues in contact with ASP 335 (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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205A PHE* 3.7 21.5 - - + +
206A SER* 4.7 4.9 - - - -
207A TYR* 2.9 42.7 + - + -
226A TYR* 3.6 5.5 + - - -
227A HIS* 5.6 3.5 - - - -
230A LYS* 2.6 33.3 + - - -
331B GLU* 3.0 19.9 + - - +
332B TRP 3.9 3.6 - - - +
334B ARG* 1.3 77.3 - - - +
336B LEU* 1.3 61.7 + - - +
338B ALA 3.1 0.7 + - - -
339B VAL* 3.1 16.9 + - - +
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Residues in contact with LEU 336 (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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205A PHE* 3.7 34.2 - - + -
114B ILE* 3.7 38.1 - - + -
164B ILE* 4.5 10.3 - - + -
167B LEU* 3.7 24.0 - - + -
251B PHE* 4.0 12.9 - - + +
254B PHE* 4.3 15.8 - - + +
255B VAL* 5.3 0.5 - - - +
332B TRP* 2.9 28.0 + - + +
333B PHE* 3.9 3.1 - - - +
335B ASP* 1.3 76.0 - - - +
337B LEU* 1.3 66.6 + - + +
338B ALA 3.6 0.2 + - - -
339B VAL* 3.7 14.9 + - - +
340B ALA 4.7 0.9 + - - -
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Residues in contact with LEU 337 (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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110B THR* 5.0 1.6 - - + -
114B ILE* 4.9 1.8 - - + -
254B PHE* 3.9 38.8 - - + +
255B VAL* 3.5 26.6 - - + +
258B LEU* 3.6 32.3 - - + -
322B VAL* 3.9 17.4 - - + +
326B THR* 4.1 8.1 - - + -
333B PHE* 3.0 56.6 + - + +
334B ARG 4.4 1.3 - - - +
336B LEU* 1.3 82.3 - - + +
338B ALA* 1.3 60.8 + - - +
339B VAL 3.3 0.8 + - - -
340B ALA 4.6 0.2 - - - -
341B PRO* 3.7 7.6 - - - +
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Residues in contact with ALA 338 (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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207A TYR* 4.0 3.4 - - - +
226A TYR* 3.4 22.0 - - + +
319B LEU* 3.6 21.8 - - + +
322B VAL* 4.3 3.6 - - + -
323B LEU* 4.3 7.9 - - + -
334B ARG 2.9 20.8 + - - +
335B ASP 3.1 3.5 + - - +
337B LEU* 1.3 76.2 - - - +
339B VAL* 1.3 64.4 + - - +
340B ALA 3.4 0.9 - - - -
341B PRO* 3.4 8.2 - - - +
342B ILE* 3.3 20.3 - - - +
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Residues in contact with VAL 339 (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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205A PHE* 4.4 9.0 - - + -
207A TYR* 3.7 17.0 - - + +
211A PHE* 3.7 23.1 - - + -
171B LEU* 4.3 3.1 - - + -
251B PHE* 3.6 48.9 - - + -
335B ASP 3.1 20.7 + - - +
336B LEU 3.8 4.9 - - - +
337B LEU 3.3 0.8 - - - -
338B ALA* 1.3 77.0 - - - +
340B ALA* 1.3 53.1 + - - +
342B ILE* 2.9 7.7 + - - +
343B MET* 2.8 43.9 + - + +
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Residues in contact with ALA 340 (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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248B ILE* 5.5 1.1 - - + -
251B PHE* 3.7 29.5 - - + +
252B VAL* 4.2 7.2 - - + +
255B VAL* 3.9 18.6 - - + -
336B LEU 4.7 0.4 + - - -
337B LEU 4.2 1.6 + - - -
339B VAL* 1.3 79.2 - - - +
341B PRO* 1.3 63.7 - - + +
343B MET* 3.5 5.9 + - - +
344B PHE* 2.9 33.6 + - - +
412B PHE* 4.1 13.0 - - + -
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Residues in contact with PRO 341 (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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218A SER* 4.9 1.0 - - - -
255B VAL* 5.0 2.2 - - + -
315B PRO* 3.5 24.3 - - + +
318B PHE* 4.1 13.2 - - + +
319B LEU* 3.8 30.7 - - + +
322B VAL* 4.3 7.6 - - + -
337B LEU 3.7 7.9 - - - +
338B ALA* 3.4 15.7 - - - +
340B ALA* 1.3 91.1 - - + +
342B ILE* 1.3 59.0 + - - +
344B PHE* 3.7 6.2 - - + +
345B SER* 2.9 32.1 + - - -
412B PHE* 4.8 8.1 - - + -
415B LEU* 5.9 0.4 - - + -
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Residues in contact with ILE 342 (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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207A TYR* 4.0 15.9 - - + +
211A PHE* 3.7 24.6 - - + -
214A LEU* 4.5 0.7 - - + -
215A ALA* 3.7 40.2 - - + +
218A SER* 3.8 16.1 + - - +
226A TYR* 4.1 20.9 - - + -
319B LEU* 4.1 16.8 - - + -
338B ALA 3.3 17.9 + - - +
339B VAL* 2.9 9.0 + - - +
341B PRO* 1.3 77.5 - - - +
343B MET* 1.3 60.8 + - - +
345B SER 3.7 1.6 + - - -
346B ASN* 2.6 33.6 + - - +
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Residues in contact with MET 343 (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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211A PHE* 3.9 21.5 - - + -
214A LEU* 6.4 0.7 - - - -
170B VAL* 5.5 0.4 - - + -
171B LEU* 5.6 0.9 - - - -
174B PHE* 4.3 19.7 - - + -
221B ALA 4.7 5.8 - - - +
222B LEU* 3.7 37.4 - - + +
247B GLN* 4.5 9.4 - - + +
248B ILE* 3.7 49.2 - - + +
251B PHE* 4.8 5.8 - - + -
339B VAL* 2.8 39.1 + - + +
340B ALA* 3.9 4.3 - - - +
342B ILE* 1.3 73.1 - - - +
344B PHE* 1.3 60.9 + - - +
346B ASN* 3.7 8.1 + - - +
347B LYS* 3.8 10.6 + - - +
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Residues in contact with PHE 344 (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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224B LEU* 4.3 10.5 - - + -
244B PRO* 5.2 4.0 - - + -
248B ILE* 4.0 17.0 - - + -
252B VAL* 3.6 27.4 - - + -
315B PRO* 4.0 13.9 - - + -
340B ALA 2.9 24.0 + - - +
341B PRO* 3.2 4.9 + - + +
343B MET* 1.3 75.6 - - - +
345B SER* 1.3 58.9 + - - +
346B ASN 3.2 5.6 - - - -
347B LYS* 2.7 57.8 + - + +
407B MET* 3.6 19.5 - - + -
411B MET* 3.6 44.9 - - + -
412B PHE* 3.8 17.7 - + + -
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Residues in contact with SER 345 (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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218A SER* 4.1 19.1 - - - -
65B GLN* 4.3 0.9 + - - -
315B PRO* 3.9 17.9 - - - +
316B ARG* 3.3 38.8 + - - +
341B PRO 2.9 16.4 + - - -
342B ILE 3.7 0.4 + - - -
343B MET 3.4 0.4 - - - -
344B PHE* 1.3 76.6 - - - +
346B ASN* 1.3 62.9 + - - +
347B LYS 3.6 0.7 - - - -
404B SER* 2.9 27.3 + - - -
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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