Contacts of the helix formed by residues 342 - 359 (chain B) in PDB entry 2GPV
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 LEU 342 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 4.1 11.2 - - + -
268B LEU* 3.8 28.5 - - + -
326B TYR* 5.1 0.2 - - - +
332B MET* 4.0 12.6 - - - -
337B SER* 3.0 7.8 + - - +
340B ALA* 3.8 22.4 - - + +
341B GLY* 1.3 82.1 - - - +
343B LEU* 1.3 56.8 + - - +
344B ASP 3.3 2.5 - - - -
345B LEU* 3.2 15.1 + - + +
346B ASN* 2.7 55.6 + - - +
434B HIS* 4.2 10.8 - - + +
501B OHT 4.0 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LYS* 4.8 6.1 - - - +
343A LEU* 3.9 29.2 - - + -
347A ASN* 5.5 4.0 - - - +
334B GLU* 4.6 17.9 - - + -
337B SER* 3.4 24.3 + - - +
338B LYS* 4.2 31.0 - - + -
341B GLY* 3.5 3.6 - - - -
342B LEU* 1.3 78.4 - - - +
344B ASP* 1.3 65.1 + - - +
346B ASN* 4.0 0.6 - - + -
347B ASN* 3.1 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 5.2 10.4 - - - +
344A ASP* 4.8 9.2 - - - +
342B LEU 3.3 0.4 - - - -
343B LEU* 1.3 80.6 - - - +
345B LEU* 1.3 60.9 + - - +
347B ASN* 3.6 8.6 + - - +
348B ALA* 3.4 20.4 + - - +
380E MET* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.2 16.5 + - + +
344B ASP* 1.3 76.5 - - - +
346B ASN* 1.3 66.7 + - - +
348B ALA* 3.5 6.3 + - + +
349B ILE* 3.4 25.9 + - + +
427B THR* 4.4 7.9 - - + +
430B LYS* 4.0 13.5 - - + -
431B ALA* 3.8 41.7 - - + +
434B HIS* 4.1 30.5 - - + +
501B OHT 3.9 33.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
324B LEU* 3.2 16.2 - - + +
326B TYR* 2.7 26.9 + - - -
332B MET* 3.8 20.6 - - - +
337B SER* 2.8 33.9 + - - +
342B LEU* 2.7 36.0 + - - +
343B LEU 4.1 1.8 - - - +
345B LEU* 1.3 74.2 - - - +
347B ASN* 1.3 58.9 + - - +
349B ILE* 3.1 9.1 + - - +
350B LEU* 2.8 32.8 + - + +
501B OHT 4.8 1.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
338A LYS* 4.3 14.9 + - - +
343A LEU* 5.3 2.6 - - - +
334B GLU* 5.4 4.2 - - - +
343B LEU* 3.1 44.6 + - - +
344B ASP* 3.9 8.6 + - - +
346B ASN* 1.3 75.5 - - - +
348B ALA* 1.3 57.7 + - - +
350B LEU* 3.5 21.0 - - - +
351B GLN* 2.8 27.5 + - - +
380E MET* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ASP 3.4 11.4 + - - +
345B LEU* 3.6 14.6 - - + +
346B ASN 3.2 0.4 - - - -
347B ASN* 1.3 78.2 - - - +
349B ILE* 1.3 62.4 + - - +
351B GLN* 3.1 25.4 + - - +
352B LEU* 3.2 6.8 + - - +
423B LEU* 5.0 1.4 - - + +
427B THR* 4.0 27.4 + - + +
430B LYS* 5.2 11.0 - - + -
380E MET* 4.4 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 4.3 14.1 - - + -
313B VAL* 4.3 13.5 - - + -
314B VAL* 3.4 23.6 - - + -
324B LEU* 4.0 17.9 - - + -
326B TYR* 3.5 24.7 - - + +
345B LEU* 3.4 18.6 + - + +
346B ASN* 3.1 11.2 + - - +
348B ALA* 1.3 74.0 - - - +
350B LEU* 1.3 59.7 + - - +
352B LEU* 3.0 10.1 + - - +
353B VAL* 2.9 24.3 + - - +
427B THR* 4.0 19.5 - - + -
501B OHT 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 4.0 30.3 - - + +
323B GLU 4.0 19.7 - - - +
324B LEU* 3.4 28.7 - - + -
346B ASN* 2.8 18.0 + - + +
347B ASN* 3.3 26.4 + - - +
349B ILE* 1.3 72.7 - - - +
351B GLN* 1.3 60.1 + - - +
353B VAL* 3.3 15.3 + - + +
354B LYS* 3.0 28.2 + - - +
357B LYS* 5.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ASN 2.8 13.8 + - - +
348B ALA* 3.1 16.2 - - - +
350B LEU* 1.3 77.2 - - - +
352B LEU* 1.3 58.5 + - - +
354B LYS* 3.5 8.6 + - + +
355B LYS* 3.5 20.7 + - - +
423B LEU* 3.8 27.9 - - + +
378E ASP* 3.8 27.9 + - - +
379E SER 3.9 10.7 + - - -
380E MET* 3.2 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 4.1 7.9 - - + -
314B VAL* 3.9 11.7 - - + -
348B ALA 3.2 5.5 + - - +
349B ILE* 3.0 9.4 + - - +
351B GLN* 1.3 76.8 - - - +
353B VAL* 1.3 66.0 + - - +
355B LYS* 3.6 6.9 + - + +
356B TYR* 3.1 48.5 + - + +
420B THR* 4.2 8.7 - - - +
423B LEU* 3.6 34.5 - - + -
424B LEU* 3.7 34.1 - - + +
427B THR* 4.0 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B VAL* 4.1 20.6 - - + +
317B SER* 3.9 44.4 - - - +
318B LEU* 4.0 5.5 - - + +
323B GLU 5.7 0.2 - - - +
324B LEU* 4.0 9.6 - - + -
349B ILE 2.9 19.5 + - - +
350B LEU* 3.3 19.2 + - + +
352B LEU* 1.3 75.5 - - - +
354B LYS* 1.3 55.1 + - - +
356B TYR* 3.2 3.8 + - - +
357B LYS* 2.8 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU 3.0 16.5 + - - +
351B GLN* 3.7 10.8 - - + +
352B LEU 3.3 0.2 - - - -
353B VAL* 1.3 75.6 - - - +
355B LYS* 1.3 60.0 + - - +
357B LYS* 3.4 14.5 - - + +
358B SER* 2.9 33.6 + - - +
385E VAL* 4.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLN* 3.5 10.1 + - - +
352B LEU* 3.9 11.0 - - + +
353B VAL 3.2 0.4 - - - -
354B LYS* 1.3 79.5 - - - +
356B TYR* 1.3 60.8 + - + +
358B SER* 2.9 24.7 + - - -
359B MET* 3.2 22.8 + - + +
419B MET* 3.4 24.4 + - - +
420B THR* 3.6 31.8 - - + +
423B LEU* 4.5 13.1 - - - +
376E ASN* 3.8 8.1 + - - -
378E ASP* 3.2 30.8 + - - -
392E GLN* 5.3 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.9 29.0 - - + +
314B VAL* 3.6 17.7 - - + -
318B LEU* 3.6 19.9 - - + +
352B LEU* 3.1 34.0 + - + +
353B VAL 3.2 2.5 + - - +
355B LYS* 1.3 74.2 - - + +
357B LYS* 1.3 66.5 + - - +
359B MET* 3.4 10.5 + - - +
360B LYS 3.2 3.6 + - - -
361B LEU* 3.2 57.8 + - + +
369B LEU* 4.3 15.6 - - + +
417B MET* 4.5 4.5 - - - -
420B THR* 2.4 50.0 + - + -
421B LEU* 5.5 1.9 - - - +
424B LEU* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.2 31.9 - - - +
320B PHE 2.8 30.5 + - - -
321B GLU* 3.7 28.5 + - - +
322B ASP* 4.3 6.5 + - - +
350B LEU* 5.9 2.0 - - - +
353B VAL* 2.8 36.1 + - + +
354B LYS* 3.4 15.9 - - + +
356B TYR* 1.3 72.2 - - - +
358B SER* 1.3 63.0 + - - +
360B LYS* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LYS* 2.9 21.6 + - - +
355B LYS* 2.9 14.2 + - - -
357B LYS* 1.3 76.9 - - - +
359B MET* 1.3 60.0 + - - +
360B LYS* 3.3 8.0 + - - +
389E GLN* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 3.2 22.7 + - + +
356B TYR* 3.4 11.4 + - - +
357B LYS 3.3 0.2 - - - -
358B SER* 1.3 78.5 - - - +
360B LYS* 1.3 71.0 + - - +
361B LEU 2.9 1.9 + - - +
413B ARG* 2.8 33.8 + - + +
416B LYS* 3.5 39.3 - - + +
417B MET* 3.6 34.1 - - + +
420B THR* 4.4 19.7 - - - -
389E GLN* 6.2 0.4 - - - +
----------------------------------------------------------
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