Contacts of the helix formed by residues 381 - 391 (chain B) in PDB entry 3DLX
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 SER 381 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 3.6 12.0 - - - +
229B ASN* 3.6 12.6 - - - -
232B LEU* 3.9 29.6 - - - +
346B GLY* 4.8 0.4 - - - -
380B PHE* 1.3 78.9 - - - +
382B SER* 1.3 59.5 + - - +
383B ASP* 2.4 29.6 + - - -
384B GLU* 3.3 9.6 + - - +
385B SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLN* 4.8 0.2 + - - -
142B ALA* 3.7 3.0 - - - +
229B ASN* 2.9 42.7 + - - +
230B PHE* 3.3 36.2 - - - -
233B PRO* 5.1 0.4 - - - -
344B GLU 4.5 8.1 + - - -
345B ASN* 4.3 4.8 + - - -
381B SER* 1.3 71.4 - - - +
383B ASP* 1.3 62.2 + - - +
385B SER* 4.1 6.3 - - - -
386B PHE* 3.2 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 4.3 7.2 + - - +
142B ALA* 3.7 29.9 - - + +
143B GLU* 4.4 9.4 - - - +
146B ARG* 3.7 27.0 + - + +
232B LEU* 4.3 6.0 - - - +
233B PRO* 3.6 21.3 - - + +
236B LYS* 5.2 3.3 + - - -
381B SER* 2.4 31.6 + - - -
382B SER* 1.3 74.1 - - - +
384B GLU* 1.3 59.3 + - - +
386B PHE* 3.5 2.4 + - - +
387B ALA* 3.1 26.9 + - - +
390B ARG* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 5.3 6.6 + - - +
236A LYS* 2.7 32.7 + - - +
262A PRO* 5.8 3.8 - - + -
265A TYR* 2.6 36.2 + - + -
380B PHE* 4.0 24.5 - - + -
381B SER* 3.3 16.7 + - - +
383B ASP* 1.3 80.5 + - - +
385B SER* 1.3 64.2 + - - +
387B ALA* 3.4 9.5 + - - +
388B MET* 3.2 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLN* 3.2 16.8 + - - +
343B SER 3.8 0.2 + - - -
344B GLU* 2.7 34.6 + - - +
346B GLY* 4.1 2.2 - - - -
380B PHE* 3.8 22.6 - - - -
381B SER 2.9 20.8 + - - -
382B SER* 3.6 4.5 - - - -
384B GLU* 1.3 72.8 - - - +
386B PHE* 1.3 58.3 + - - +
388B MET* 3.2 8.5 - - - +
389B ILE* 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLN* 3.3 48.2 - - + -
139B GLY* 3.2 22.7 - - - +
142B ALA* 4.6 2.5 - - + -
344B GLU* 3.6 26.5 - - + -
382B SER* 3.2 28.3 + - - +
383B ASP 4.3 2.0 - - - +
385B SER* 1.3 74.2 - - - +
387B ALA* 1.3 56.6 + - - +
389B ILE* 3.9 20.9 - - + -
390B ARG* 2.7 51.3 + - - +
425B GLY* 3.9 11.9 - - - -
428B ASP* 3.5 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 4.4 9.2 - - - +
149A GLY 3.3 10.0 - - - +
150A ALA* 3.6 23.2 - - + +
236A LYS* 6.2 1.8 - - + -
265A TYR* 4.2 3.1 - - - +
383B ASP 3.1 18.5 + - - +
384B GLU* 3.4 18.1 + - - +
386B PHE* 1.3 73.9 - - - +
388B MET* 1.3 57.8 + - - +
390B ARG* 3.8 10.0 - - - +
391B GLY* 2.8 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 4.4 3.6 - - + -
264A ILE* 3.7 43.3 - - + -
265A TYR* 3.5 34.0 + - + +
342B GLN* 4.0 16.2 - - - +
348B LEU* 5.1 2.0 - - - -
380B PHE* 3.5 48.7 - - + -
384B GLU* 3.2 13.1 + - + +
385B SER 3.2 9.4 - - - +
387B ALA* 1.3 74.9 - - - +
389B ILE* 1.3 60.1 + - - +
392B GLY 3.5 0.3 + - - -
393B HIS* 2.9 41.3 + - + +
394B VAL* 3.8 6.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLN* 3.8 27.4 - - - +
344B GLU* 4.2 6.5 - - + -
385B SER* 3.2 21.9 + - - +
386B PHE* 3.8 25.1 - - + +
387B ALA 3.4 0.2 - - - -
388B MET* 1.3 73.6 - - - +
390B ARG* 1.3 66.0 + - - +
391B GLY 3.1 1.3 - - - -
392B GLY* 3.1 13.7 + - - -
393B HIS 4.6 0.2 + - - -
394B VAL* 4.3 13.0 - - + -
428B ASP* 3.2 37.1 - - + +
429B LEU* 3.7 32.3 - - + +
432B SER* 3.8 8.7 - - - -
435B THR* 4.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA* 3.1 27.5 + - - +
151A GLY* 3.6 25.6 - - - +
152A VAL* 3.8 15.0 - - - +
139B GLY* 2.9 34.8 + - - -
140B THR* 4.8 0.8 - - - +
143B GLU* 3.7 23.2 + - - +
155B PHE* 5.4 0.4 - - - -
157B THR* 3.5 23.2 + - - +
158B PRO* 3.8 18.6 - - + +
159B THR* 4.4 1.3 - - - +
383B ASP 5.2 0.6 + - - -
386B PHE* 2.7 43.8 + - - +
387B ALA* 3.8 5.1 - - - +
389B ILE* 1.3 74.4 - - + +
391B GLY* 1.3 59.4 + - - +
392B GLY 3.2 1.4 + - - -
428B ASP* 4.1 8.9 + - - +
431B SER* 4.4 13.1 + - - +
432B SER* 3.7 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY 5.4 0.2 - - - -
149A GLY 3.6 13.8 - - - +
150A ALA 3.5 0.6 + - - -
151A GLY* 3.6 13.0 - - - -
387B ALA 2.8 22.6 + - - -
389B ILE 3.1 0.2 - - - -
390B ARG* 1.3 76.9 - - - +
392B GLY* 1.3 59.9 + - - +
393B HIS* 3.5 12.5 + - - -
432B SER* 4.2 0.9 - - - -
434B LYS* 4.4 10.7 + - - +
----------------------------------------------------------
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