Contacts of the helix formed by residues 328 - 347 (chain B) in PDB entry 2GTP
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 ASP 328 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 3.5 2.0 - - - -
271B LYS* 5.9 0.7 + - - -
325B CYS* 2.8 32.5 + - + +
327B THR* 1.3 77.3 + - - +
329B THR* 1.3 63.7 + - - +
330B LYS* 3.3 17.9 + - - +
331B ASN* 3.0 17.9 + - + +
332B VAL* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 2.6 33.8 + - - +
55B ILE* 4.1 17.7 - - + +
56B ILE* 4.1 18.6 - - + +
171B GLN* 4.8 2.6 + - - +
175B LEU* 3.8 11.8 - - - +
327B THR 3.6 1.6 + - - -
328B ASP* 1.3 70.9 + - - +
330B LYS* 1.3 60.2 + - - +
332B VAL* 3.2 2.9 + - - +
333B GLN* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASP* 3.3 9.2 + - - +
329B THR* 1.3 78.8 - - - +
331B ASN* 1.3 61.8 + - - +
333B GLN* 3.5 10.3 + - - +
334B PHE* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 2.8 28.7 - - - +
323B PHE 4.2 3.4 + - - -
324B THR* 3.3 15.8 - - - +
325B CYS* 3.1 24.2 + - + +
328B ASP* 3.0 30.3 + - + +
330B LYS* 1.3 77.1 - - - +
332B VAL* 1.3 59.5 + - - +
334B PHE* 3.4 10.6 + - - +
335B VAL* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.7 26.7 - - + -
52B GLN* 3.7 25.8 - - + -
53B MET* 3.8 21.3 - - + -
56B ILE* 4.1 2.9 - - + -
267B PHE* 5.5 3.4 - - + -
324B THR* 5.4 4.3 - - + -
325B CYS 3.7 15.0 - - - +
326B ALA* 3.7 12.8 - - - +
328B ASP 3.0 18.5 + - - +
329B THR 3.9 2.9 - - - +
331B ASN* 1.3 79.5 - - - +
333B GLN* 1.3 57.6 + - - +
335B VAL* 4.5 4.5 - - - +
336B PHE* 2.8 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.7 39.2 - - + +
191B PHE* 5.9 1.0 - - + -
329B THR* 2.8 21.0 + - - +
330B LYS* 3.7 10.2 - - - +
331B ASN 3.3 0.2 - - - -
332B VAL* 1.3 76.5 - - - +
334B PHE* 1.3 62.1 + - - +
336B PHE* 4.1 2.0 - - - +
337B ASP* 3.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B HIS* 5.8 3.6 - + - -
330B LYS 3.2 14.5 + - - +
331B ASN* 3.7 9.4 - - - +
333B GLN* 1.3 81.0 - - - +
335B VAL* 1.3 77.8 + - + +
337B ASP* 3.5 8.5 - - + +
338B ALA* 3.3 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 3.3 39.3 - - + -
322B HIS* 3.8 32.8 - - + +
323B PHE 4.5 4.7 - - - +
324B THR* 3.9 15.7 - - + -
331B ASN* 3.0 25.7 + - - +
332B VAL* 4.2 3.6 - - - +
334B PHE* 1.3 88.7 - - + +
336B PHE* 1.3 60.0 + - - +
338B ALA* 3.0 8.4 + - - +
339B VAL* 2.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.0 17.0 - - + -
53B MET* 3.6 32.5 - - + -
56B ILE* 5.6 0.7 - - + -
57B HIS* 3.5 30.5 - + + -
189B PHE* 4.1 8.5 - + - -
191B PHE* 3.8 11.7 - + - -
196B PHE* 3.7 27.6 - + - -
222B ILE* 4.0 18.4 - - + -
267B PHE* 5.1 3.6 - + + -
332B VAL* 2.8 20.1 + - + +
333B GLN* 4.2 3.6 - - - +
335B VAL* 1.3 77.7 - - - +
337B ASP* 1.3 56.6 + - - +
339B VAL* 3.5 14.5 - - + +
340B THR* 2.9 49.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 4.1 17.5 - - + -
192B LYS* 3.1 30.2 + - - -
333B GLN* 3.1 20.0 + - + +
334B PHE* 3.5 9.0 - - + +
336B PHE* 1.3 78.0 - - - +
338B ALA* 1.3 63.2 + - - +
340B THR* 3.4 1.6 + - - -
341B ASP* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B HIS* 3.9 21.5 - - + -
334B PHE* 3.3 15.9 + - + +
335B VAL* 3.0 9.4 + - - +
337B ASP* 1.3 77.9 + - - +
339B VAL* 1.3 67.4 + - - +
341B ASP* 3.2 11.2 + - - +
342B VAL* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.6 1.1 - - + -
222B ILE* 4.5 9.4 - - + -
265B ILE* 3.8 28.2 - - + +
267B PHE* 3.8 32.5 - - + -
322B HIS* 4.4 6.9 + - - +
335B VAL* 2.9 19.3 + - + +
336B PHE* 3.5 24.9 - - + +
338B ALA* 1.3 76.2 - - - +
340B THR* 1.3 58.4 + - - +
342B VAL* 3.1 10.6 + - - +
343B ILE* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 3.5 20.5 - - + +
192B LYS* 4.2 18.2 - - + -
194B LEU* 4.0 24.2 - - + -
196B PHE* 3.8 8.9 - - + -
336B PHE* 2.9 42.2 + - - -
337B ASP 3.8 4.3 - - - -
338B ALA 3.2 0.2 - - - -
339B VAL* 1.3 72.7 - - - +
341B ASP* 1.3 60.1 + - - +
343B ILE* 3.1 10.8 + - + +
344B ILE* 2.9 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 2.9 27.9 + - - +
337B ASP* 3.1 22.1 + - - +
338B ALA* 3.2 12.5 + - - +
340B THR* 1.3 75.7 - - - +
342B VAL* 1.3 57.8 - - + +
344B ILE* 3.3 10.2 + - - +
345B LYS* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER* 4.4 6.5 - - - +
265B ILE* 5.0 3.6 - - + -
320B TYR* 3.5 47.1 - - + -
322B HIS* 5.7 3.1 - - + +
338B ALA* 3.0 18.6 + - + +
339B VAL* 3.1 11.9 + - - +
341B ASP* 1.3 72.6 - - + +
343B ILE* 1.3 67.3 + - - +
345B LYS* 3.4 5.6 + - - +
346B ASN* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 4.2 27.8 - - + -
36B LEU* 5.3 1.8 - - + -
194B LEU* 5.2 1.8 - - + -
196B PHE* 4.3 13.7 - - + -
219B THR* 4.2 22.9 - - + +
220B ALA* 3.8 28.9 - - + -
263B SER* 4.7 11.9 - - - +
265B ILE* 5.2 1.3 - - + -
336B PHE* 5.9 0.2 - - + -
339B VAL* 3.0 28.5 + - + +
340B THR* 3.1 11.2 + - + +
342B VAL* 1.3 79.4 - - + +
344B ILE* 1.3 67.2 + - + +
346B ASN* 3.2 2.3 + - - +
347B ASN* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 5.5 5.6 - - + +
194B LEU* 2.9 45.1 - - + -
340B THR* 2.9 21.8 + - + +
341B ASP* 3.6 13.2 - - - +
343B ILE* 1.3 80.8 - - + +
345B LYS* 1.3 62.1 + - - +
347B ASN 3.3 1.9 + - - -
348B LEU* 2.7 42.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASP 2.9 17.4 + - - +
342B VAL* 3.9 7.2 - - - +
344B ILE* 1.3 78.4 - - - +
346B ASN* 1.3 64.0 + - - +
347B ASN 3.6 0.3 + - - -
348B LEU* 4.5 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER* 2.9 28.1 + - - +
320B TYR* 3.0 29.9 + - - -
342B VAL* 3.0 28.3 + - - +
343B ILE 3.2 2.9 + - - +
345B LYS* 1.3 80.2 - - - +
347B ASN* 1.3 59.1 - - + +
348B LEU 3.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 4.6 20.4 - - + -
343B ILE* 3.1 17.0 + - + +
344B ILE* 3.3 1.9 + - - -
346B ASN* 1.3 81.5 - - + +
348B LEU* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
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