Contacts of the helix formed by residues 357 - 371 (chain B) in PDB entry 3DGR
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 357 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 3.8 9.4 - - - -
355B GLY 4.8 2.0 - - - -
356B VAL* 1.3 75.5 - - - +
358B ILE* 1.3 67.6 + - + +
359B ASN* 2.9 25.1 + - - +
360B THR* 2.9 26.4 + - - +
361B LEU* 2.9 22.7 + - - +
382B SER* 4.7 0.4 - - - -
385B GLY* 4.1 11.2 - - - +
389B LYS* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TYR* 3.6 27.6 - - + +
164B ASN* 3.8 13.2 - - - +
167B GLU* 3.6 31.6 - - + +
168B GLN* 3.6 30.8 + - + +
171B ILE* 3.8 20.8 - - + +
357B ASP* 1.3 77.7 - - + +
359B ASN* 1.3 79.3 + - - +
361B LEU* 3.8 2.6 - - - +
362B GLN* 3.3 20.8 + - - +
389B LYS* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASP* 2.9 16.6 + - - +
358B ILE* 1.3 89.3 - - - +
360B THR* 1.3 64.0 + - + +
362B GLN* 3.4 8.7 + - - +
363B GLU* 3.3 31.7 + - - +
389B LYS* 5.1 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 5.2 10.1 - - + -
355B GLY 2.5 29.5 + - - +
356B VAL* 3.4 2.9 - - - +
357B ASP* 2.9 29.0 + - - +
359B ASN* 1.3 76.0 - - + +
361B LEU* 1.3 60.2 + - - +
363B GLU* 3.2 18.8 + - - +
364B ILE* 2.9 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 3.5 38.1 - - + +
171B ILE* 3.6 27.4 - - + -
172B LEU* 3.9 36.3 - - + -
190B LEU* 4.3 10.5 - - + -
356B VAL* 4.4 8.9 - - + +
357B ASP 2.9 17.7 + - - +
358B ILE 3.8 3.6 - - - +
360B THR* 1.3 78.5 + - - +
362B GLN* 1.3 62.4 + - - +
364B ILE* 3.4 8.0 + - - +
365B VAL* 3.1 25.6 + - + +
380B PHE* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.5 43.4 - - + +
174B LYS* 5.9 0.4 - - - +
175B TYR* 3.0 27.7 + - - -
358B ILE 3.3 11.1 + - - +
359B ASN* 3.5 11.2 - - - +
360B THR 3.3 0.2 - - - -
361B LEU* 1.3 79.7 - - - +
363B GLU* 1.3 65.4 + - + +
365B VAL* 3.5 2.3 - - - +
366B GLU* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.8 17.2 - - + +
359B ASN* 3.4 19.9 - - - +
360B THR* 3.2 21.7 + - - +
362B GLN* 1.3 79.1 - - + +
364B ILE* 1.3 60.0 + - + +
366B GLU* 3.9 4.4 - - - +
367B GLY* 2.9 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 3.9 25.1 - - + +
318B LEU* 4.0 27.0 - - + +
321B VAL* 4.4 15.5 - - + -
352B GLN* 4.1 13.9 - - + -
356B VAL* 5.0 4.7 - - + -
360B THR* 2.9 27.3 + - - +
361B LEU* 3.8 4.3 - - - +
363B GLU* 1.3 77.5 - - + +
365B VAL* 1.3 58.9 + - - +
367B GLY* 3.7 0.5 - - - -
368B MET* 2.9 42.9 + - + +
378B ILE* 4.4 1.6 - - + -
380B PHE* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.8 14.1 - - + +
172B LEU* 4.3 12.8 - - + -
175B TYR* 3.7 33.9 - - + -
361B LEU* 3.1 19.1 + - + +
362B GLN 3.5 6.3 - - - +
364B ILE* 1.3 73.1 - - + +
366B GLU* 1.3 64.0 + - - +
368B MET* 3.4 2.0 + - - +
369B LYS* 2.9 29.6 + - - +
375B ILE* 3.8 29.3 - - + +
380B PHE* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.0 37.9 + - - +
362B GLN* 3.1 23.1 + - - +
363B GLU* 4.0 4.7 - - - +
365B VAL* 1.3 77.2 - - - +
367B GLY* 1.3 57.9 + - - +
369B LYS* 3.3 13.8 + - - +
370B GLN* 2.9 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.8 22.2 - - - -
322B LEU* 3.9 2.5 - - - +
363B GLU 2.9 17.9 + - - -
364B ILE 3.8 0.7 - - - -
366B GLU* 1.3 75.3 - - - +
368B MET* 1.3 64.7 + - - +
370B GLN* 3.5 14.1 + - - +
371B LYS* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 4.2 0.8 - - + +
321B VAL* 4.1 15.3 - - + -
322B LEU* 4.1 10.5 - - + -
325B LEU* 3.8 23.6 - - + -
364B ILE* 2.9 28.7 + - + +
365B VAL* 3.7 4.7 - - - +
366B GLU 3.4 0.2 - - - -
367B GLY* 1.3 75.0 - - - +
369B LYS* 1.3 63.2 + - - +
371B LYS* 3.0 12.3 + - - +
373B TRP* 3.0 28.3 + - + +
374B SER 3.3 26.2 - - - +
375B ILE* 3.9 11.9 - - + -
377B ASN* 4.3 3.8 - - + -
378B ILE* 3.6 46.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.1 16.2 - - + -
178B GLU* 2.7 38.6 + - + +
179B THR* 4.2 15.0 - - + -
341B TYR* 3.6 24.5 - - + +
365B VAL 2.9 17.3 + - - +
366B GLU* 3.3 16.3 + - - +
368B MET* 1.3 74.9 - - - +
370B GLN* 1.3 54.0 + - + +
372B MET* 2.8 40.4 + - + +
373B TRP 4.1 8.7 + - - -
375B ILE* 4.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLU* 2.9 49.2 + - - +
367B GLY* 3.7 12.5 - - - +
368B MET 3.3 0.2 - - - -
369B LYS* 1.3 77.7 - - + +
371B LYS* 1.3 69.4 + - + +
372B MET* 3.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.2 22.9 - - + -
326B GLU* 5.5 2.0 - - - +
342B LYS* 3.5 10.9 + - - -
367B GLY 3.3 15.2 + - - +
368B MET 3.0 2.8 + - - -
370B GLN* 1.3 84.8 + - + +
372B MET* 1.3 71.3 + - - +
373B TRP* 3.3 25.8 - - + +
----------------------------------------------------------
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