Contacts of the helix formed by residues 338 - 357 (chain B) in PDB entry 2GH0
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 ASN 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B CYS* 2.9 19.2 + - - +
274B PRO* 3.6 15.4 - - - +
333B GLY 4.0 0.7 - - - +
334B PHE* 3.0 45.4 - - - +
335B PHE 4.7 2.5 - - - +
336B SER 3.6 2.6 - - - -
337B HIS* 1.3 75.3 - - - +
339B PRO* 1.3 60.7 - - - +
340B CYS* 3.0 25.7 - - - +
341B LEU* 3.2 19.3 - - + +
342B THR* 2.9 34.0 + - - -
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Residues in contact with PRO 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B PRO* 3.9 15.0 - - + -
276B ASP 3.8 22.9 - - - +
277B ILE* 3.8 25.4 - - + +
279B GLY* 3.6 6.6 - - - -
337B HIS 3.5 10.8 - - - +
338B ASN* 1.3 82.9 - - - +
340B CYS* 1.3 57.1 + - - +
342B THR* 3.9 4.9 - - - -
343B GLU* 3.0 33.3 + - - +
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Residues in contact with CYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B CYS* 3.4 30.3 - - - +
274B PRO* 3.7 16.7 - - + +
279B GLY* 3.5 13.2 - - - +
280B THR 4.1 0.2 - - - +
281B CYS* 2.1 51.7 - - - -
288B CYS* 3.8 4.0 - - - -
338B ASN* 3.0 10.1 - - - +
339B PRO* 1.3 75.9 - - - +
341B LEU* 1.3 61.3 + - - +
343B GLU* 3.8 0.9 - - - +
344B ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 4.1 10.3 - - + -
272B CYS* 4.3 2.9 - - + -
288B CYS* 3.9 24.5 - - - -
289B LEU* 5.0 2.5 - - + -
292B TYR* 3.7 44.4 - - + -
312B VAL* 4.3 9.2 - - + -
334B PHE 3.9 16.6 - - - +
335B PHE* 4.2 15.0 - - + +
338B ASN* 3.2 19.6 - - + +
340B CYS* 1.3 78.4 - - - +
342B THR* 1.3 65.7 + - - +
344B ALA* 3.3 1.2 + - - -
345B ILE* 3.0 40.5 + - + +
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B THR* 6.1 0.9 - - - +
335B PHE 5.1 4.9 + - - -
336B SER 4.9 6.1 + - - -
338B ASN 2.9 23.1 + - - -
339B PRO* 3.9 6.1 - - - +
341B LEU* 1.3 79.0 - - - +
343B GLU* 1.3 61.0 + - + +
345B ILE* 3.5 6.2 + - - +
346B ALA* 2.9 30.3 + - + +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU 4.2 14.4 - - - +
279B GLY* 4.2 9.4 - - - +
285B GLN* 3.6 17.8 + - - +
339B PRO 3.0 19.4 + - - +
340B CYS 4.2 1.1 - - - +
342B THR* 1.3 75.8 - - + +
344B ALA* 1.3 61.0 + - - +
346B ALA* 4.2 7.9 - - - +
347B ALA* 2.8 31.7 + - - +
350B ARG* 2.8 29.2 + - - -
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B CYS* 4.8 0.2 - - - -
285B GLN* 3.9 40.8 - - + +
288B CYS* 4.6 5.8 - - + -
289B LEU* 3.9 23.0 - - + +
340B CYS 2.9 19.8 + - - +
341B LEU* 3.8 5.6 - - - +
343B GLU* 1.3 77.6 - - - +
345B ILE* 1.3 60.4 + - - +
347B ALA* 3.8 1.7 - - - +
348B LYS* 3.2 24.3 + - - +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 4.4 15.7 - - + +
289B LEU* 3.8 19.3 - - + -
292B TYR* 4.3 16.2 - - + +
304B PHE* 4.7 8.7 - - + -
310B THR* 5.0 10.3 - - - +
312B VAL* 4.2 20.2 - - + -
341B LEU* 3.0 38.2 + - + +
342B THR* 3.9 5.4 - - - +
344B ALA* 1.3 74.8 - - - +
346B ALA* 1.3 66.1 + - - +
348B LYS* 3.2 5.0 + - - +
349B MET* 3.0 52.1 + - + +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B THR* 5.8 3.4 - - - +
342B THR* 2.9 22.8 + - + +
343B GLU* 3.8 15.7 - - - +
345B ILE* 1.3 78.9 - - - +
347B ALA* 1.3 55.8 + - - +
349B MET* 3.3 9.5 + - - +
350B ARG* 2.9 38.5 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 3.6 21.5 - - - +
343B GLU* 2.8 22.3 + - - +
344B ALA 3.8 2.7 - - - +
346B ALA* 1.3 77.1 - - - +
348B LYS* 1.3 57.0 + - - +
350B ARG* 3.3 27.9 + - - +
351B PHE* 2.9 28.8 + - - +
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PRO* 6.2 1.2 - - - +
213B GLN* 3.2 24.6 + - - +
217B LEU* 4.1 16.6 - - + -
289B LEU* 3.8 20.9 - - + -
344B ALA 3.2 15.6 + - - +
345B ILE 3.2 4.2 + - - +
347B ALA* 1.3 76.7 - - - +
349B MET* 1.3 61.5 + - - +
351B PHE* 3.3 30.5 - - + +
352B HIS* 2.9 66.8 + - + +
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Residues in contact with MET 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.4 25.6 - - + +
218B CYS 3.7 10.5 - - - +
219B PRO* 3.6 14.9 - - + +
231B ARG* 3.5 30.5 - - - +
304B PHE* 3.7 31.2 - - + -
310B THR* 3.9 15.7 - - + -
345B ILE* 3.0 35.4 + - + +
346B ALA* 3.6 7.9 - - - +
348B LYS* 1.3 76.8 - - - +
350B ARG* 1.3 62.1 + - - +
352B HIS* 3.3 4.8 + - - +
353B SER* 3.0 25.3 + - - -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 2.8 33.7 + - - -
346B ALA* 2.9 18.0 + - - +
347B ALA* 3.5 26.3 + - - +
349B MET* 1.3 77.2 - - + +
351B PHE* 1.3 60.9 + - - +
353B SER* 3.3 7.8 - - - -
354B GLN* 2.9 47.8 + - - +
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ALA 2.9 14.7 + - - +
348B LYS* 3.3 34.5 - - + +
350B ARG* 1.3 75.7 - - - +
352B HIS* 1.3 68.1 + + - +
354B GLN* 3.2 13.9 + - + +
355B LEU* 2.7 73.6 + - + +
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Residues in contact with HIS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.1 1.5 - - - +
165B PHE* 3.7 30.9 - + + -
210B PRO* 4.8 3.4 + - - +
213B GLN* 3.3 22.4 - - - +
214B GLY* 3.5 15.6 + - - -
217B LEU 2.8 28.4 + - - -
218B CYS* 4.3 1.2 - - - -
219B PRO* 3.8 8.7 - - + -
348B LYS* 2.9 39.3 + - + +
349B MET 3.5 6.7 - - - +
351B PHE* 1.3 86.6 - + - +
353B SER* 1.3 66.1 + - - +
355B LEU* 3.6 7.8 - - + +
356B PHE* 3.3 28.2 + - - +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.9 13.7 - - - +
219B PRO* 3.4 24.4 - - - +
349B MET 3.0 8.7 + - - -
350B ARG* 3.3 12.6 - - - -
352B HIS* 1.3 74.5 - - - +
354B GLN* 1.3 61.1 + - - +
356B PHE* 3.4 5.0 + - - +
357B SER* 3.1 28.2 + - - -
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Residues in contact with GLN 354 (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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350B ARG* 2.9 49.0 + - - +
351B PHE* 3.3 11.7 + - + +
353B SER* 1.3 79.6 - - - +
355B LEU* 1.3 67.5 + - - +
357B SER* 3.1 25.6 + - - +
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Residues in contact with LEU 355 (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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165B PHE* 5.1 8.3 - - + -
351B PHE* 2.7 58.3 + - + +
352B HIS* 3.6 15.3 - - + +
354B GLN* 1.3 73.7 - - - +
356B PHE* 1.3 65.2 + - + +
357B SER 4.7 1.4 - - - -
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.0 17.3 - - + -
164B LYS* 3.4 51.4 - - + -
165B PHE* 3.4 46.2 - + - -
168B LEU* 3.9 22.7 - - + -
352B HIS 3.3 9.9 + - - +
353B SER 3.4 4.5 + - - +
355B LEU* 1.3 83.9 - - + +
357B SER* 1.3 62.2 + - - +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B SER 3.1 14.8 + - - -
354B GLN* 3.1 24.4 + - - +
355B LEU 4.7 1.3 - - - -
356B PHE* 1.3 81.7 - - - +
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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) + - + + + + + -
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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