Contacts of the helix formed by residues 347 - 358 (chain B) in PDB entry 6GXV
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 PHE 347 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.7 27.8 - + - -
299B ALA* 3.6 26.5 - - + -
300B ALA* 3.5 26.0 - - + -
308B MET* 4.2 12.8 - - + -
311B LEU* 4.2 14.4 - - + -
343B VAL* 3.8 10.3 - - + -
344B SER 3.0 5.5 + - - +
346B TRP* 1.3 108.1 - + + +
348B LYS* 1.3 66.5 + - - +
349B PRO* 3.3 1.8 - - - -
350B LEU* 2.9 42.6 + - + -
351B ALA* 3.1 21.0 + - + -
431B ASP* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 3.6 12.8 - - + -
329B ASP* 2.8 28.5 + - - -
342B TRP* 3.2 20.2 - - - -
343B VAL* 3.3 19.8 + - - +
344B SER 3.0 11.0 + - - +
345B ASP* 3.6 11.6 + - - +
347B PHE* 1.3 76.9 - - - +
349B PRO* 1.3 62.9 - - + +
351B ALA* 3.3 2.8 + - - +
352B TYR* 2.9 41.8 + - + -
369B ASP* 2.7 44.8 + - + +
381B LYS* 4.5 13.7 - - + -
384B TRP* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASP 3.2 15.5 - - - +
346B TRP 3.4 13.7 - - - +
347B PHE 3.4 0.9 - - - -
348B LYS* 1.3 93.8 - - + +
350B LEU* 1.3 57.8 + - + +
353B ALA* 3.0 17.2 + - - +
384B TRP* 3.4 35.2 - - + +
388B GLN* 3.0 29.0 + - - +
456B ASN* 5.9 2.5 - - - +
477B SER* 6.3 0.7 - - - -
478B VAL* 3.6 14.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
308B MET* 4.3 2.2 - - + -
346B TRP* 4.0 19.7 - - + +
347B PHE* 2.9 42.6 + - + +
349B PRO* 1.3 72.6 - - + +
351B ALA* 1.3 54.5 + - - +
353B ALA 3.4 0.7 + - - -
354B THR* 2.8 36.8 + - - -
429B MET* 3.4 40.7 - - + +
430B SER 3.5 29.2 - - - +
431B ASP* 4.4 1.3 - - - +
476B GLY 4.3 0.9 - - - +
477B SER* 3.6 30.3 - - - +
478B VAL* 3.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.5 44.7 - - + -
328B VAL* 3.7 22.2 - - + -
343B VAL* 4.5 0.4 - - + -
347B PHE* 3.1 18.6 + - + +
348B LYS* 3.6 8.5 - - - +
350B LEU* 1.3 76.3 - - - +
352B TYR* 1.3 61.3 + - - +
354B THR* 3.1 12.8 + - - -
355B ILE* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 3.7 24.7 + - + +
329B ASP 4.9 0.5 + - - -
348B LYS* 2.9 40.8 + - + +
351B ALA* 1.3 71.1 - - - +
353B ALA* 1.3 61.5 + - - +
355B ILE* 3.2 17.2 + - + -
356B LEU* 2.8 46.0 + - + +
364B CYS 4.4 1.5 + - - -
365B VAL* 3.9 22.9 - - + -
366B PHE* 3.2 20.8 + - - +
369B ASP* 2.5 38.0 + - + +
384B TRP* 3.9 16.6 - + + -
385B LEU* 3.7 20.4 - - + -
388B GLN* 3.2 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PRO 3.0 17.5 + - - +
350B LEU 3.7 4.7 - - - +
352B TYR* 1.3 75.5 - - - +
354B THR* 1.3 57.0 + - - +
356B LEU* 4.6 0.9 - - - +
357B THR* 2.6 39.9 + - - -
388B GLN* 2.9 18.5 + - - +
412B TRP* 3.7 2.6 - - - -
427B THR* 4.3 3.8 - - + -
429B MET* 4.2 4.0 - - + -
478B VAL* 3.8 25.1 - - + -
480B ILE* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.9 18.6 - - + -
311B LEU* 3.9 12.6 - - + +
312B LEU* 3.9 28.0 - - + -
317B MET* 3.3 12.8 - - - +
350B LEU 2.8 18.6 + - - -
351B ALA 3.3 9.9 - - - -
352B TYR 3.1 0.2 - - - -
353B ALA* 1.3 77.9 - - - +
355B ILE* 1.3 60.9 + - - +
358B ARG* 3.3 35.7 - - - +
412B TRP* 3.5 20.4 - - + -
429B MET* 3.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.0 5.2 - - + -
296B PHE* 3.7 24.0 - - + -
317B MET* 4.2 6.1 - - + -
326B THR* 3.6 40.0 + - + +
327B PHE* 4.1 3.4 - - - +
328B VAL* 4.1 10.1 - - + -
351B ALA 3.2 14.0 + - - +
352B TYR* 3.6 27.6 - - + +
354B THR* 1.3 77.2 - - - +
356B LEU* 1.3 68.0 + - + +
357B THR 3.7 0.2 - - - -
358B ARG 4.2 5.2 - - - +
360B GLU 4.7 5.2 - - - +
363B PRO* 3.5 34.2 - - + +
364B CYS 4.0 12.3 - - - +
392B ARG* 3.7 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 4.2 5.4 - - + -
352B TYR* 2.8 35.5 + - + +
353B ALA 4.6 0.4 - - - +
355B ILE* 1.3 82.5 - - + +
357B THR* 1.3 62.1 + - + +
363B PRO* 3.9 19.1 - - + -
365B VAL* 4.4 7.6 - - + -
385B LEU* 4.5 4.3 - - + -
388B GLN* 3.8 34.3 - - + +
389B LEU* 4.2 27.6 - - + -
392B ARG* 2.9 57.5 + - + +
396B ALA* 4.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 2.6 22.7 + - - +
356B LEU* 1.3 83.0 - - + +
358B ARG* 1.3 61.6 + - - +
388B GLN 5.0 0.4 - - - +
391B ALA* 4.3 10.3 - - + -
392B ARG 5.1 0.2 - - - +
396B ALA* 3.9 6.6 - - + +
412B TRP* 3.0 19.0 + - - -
414B ARG* 3.1 32.6 + - - +
425B LEU* 3.9 22.2 - - + -
427B THR* 3.1 13.0 + - - +
480B ILE* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.4 28.4 - - - +
317B MET* 3.6 19.9 - - + +
354B THR* 3.3 28.8 + - - +
355B ILE 4.2 2.4 - - - +
356B LEU 3.6 0.4 - - - -
357B THR* 1.3 79.8 - - - +
359B GLN* 1.3 63.2 + - - +
360B GLU* 3.3 22.1 + - - +
392B ARG* 3.6 21.1 + - - -
400B GLN* 3.2 20.1 - - - +
402B ASP* 2.7 41.2 + - - -
404B LEU* 4.1 1.8 - - - +
412B TRP* 3.4 52.3 - - + +
414B ARG* 3.6 2.8 + - - -
----------------------------------------------------------
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