Contacts of the helix formed by residues 375 - 385 (chain A) in PDB entry 2DB3
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 THR 375 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 4.8 0.7 - - - -
325A SER 3.6 9.0 - - - +
327A THR* 3.5 37.5 - - - +
328A ARG* 3.6 12.8 - - + +
331A ALA* 4.3 5.8 - - + +
352A VAL 3.3 2.4 + - - +
353A TYR* 3.2 18.9 - - + +
354A GLY 3.7 0.3 + - - -
374A ALA* 1.3 78.0 - - - +
376A PRO* 1.3 73.2 - - - +
377A GLY 3.4 0.3 + - - -
378A ARG 3.7 0.7 + - - -
379A LEU* 3.4 17.4 + - - +
5E U 3.6 16.1 + - - -
6E U 2.9 18.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 3.7 5.2 - - + -
325A SER 3.2 15.3 - - - +
374A ALA 4.1 0.2 - - - -
375A THR* 1.3 85.1 - - - +
377A GLY* 1.3 63.5 + - - +
379A LEU* 3.0 4.9 + - + +
380A LEU* 2.9 29.2 + - - +
404A MET* 3.3 26.9 - - + -
409A PHE* 3.6 22.7 - - + -
412A ASP* 4.3 13.0 - - + -
413A MET* 3.5 16.8 - - + -
416A ILE* 4.2 11.2 - - + -
5E U 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR 3.4 1.0 + - - -
376A PRO* 1.3 72.0 - - - +
378A ARG* 1.3 58.4 + - - +
379A LEU 3.0 5.5 + - - -
380A LEU* 3.1 7.1 + - - +
381A ASP 3.1 16.6 + - - -
412A ASP* 4.3 8.9 + - - -
5E U 3.0 18.5 + - - -
6E U 3.0 37.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.1 20.4 - - + +
353A TYR* 3.5 15.0 - - - +
354A GLY* 3.4 10.8 - - - +
356A THR* 2.8 38.6 + - - +
358A PHE* 3.9 31.0 - - - +
361A GLN* 2.7 30.3 + - - +
375A THR* 3.7 0.9 + - - +
376A PRO 3.5 0.2 - - - -
377A GLY* 1.3 71.7 - - - +
379A LEU* 1.3 59.1 + - - +
381A ASP* 3.8 1.6 - - - -
382A PHE* 3.1 31.3 + - - -
6E U 2.7 48.0 + - - +
7E U 2.8 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.1 26.0 - - + -
324A VAL* 4.4 7.2 - - + -
352A VAL* 4.1 4.0 - - + +
372A VAL* 5.3 4.3 - - + -
374A ALA* 4.2 16.6 - - + -
375A THR 3.4 12.2 + - - +
376A PRO* 3.0 8.2 + - + +
377A GLY 3.0 1.2 - - - -
378A ARG* 1.3 74.7 - - - +
380A LEU* 1.3 59.5 + - - +
381A ASP 3.0 4.9 - - - -
382A PHE* 3.2 2.2 + - - +
383A VAL* 2.9 48.4 + - + +
388A ILE* 4.1 26.0 - - + -
390A PHE* 4.5 7.0 - - + -
416A ILE* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PRO 2.9 20.2 + - - +
377A GLY* 3.7 4.9 - - - +
379A LEU* 1.3 78.2 - - - +
381A ASP* 1.3 57.2 + - - +
383A VAL* 3.7 15.5 - - + -
384A ASP* 2.9 38.1 + - - +
390A PHE* 6.0 0.7 - - + -
412A ASP* 3.3 51.4 - - + +
415A ARG* 3.9 34.1 - - + +
416A ILE* 3.4 34.5 - - + +
419A HIS* 6.2 1.1 - - - +
6E U 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 2.9 29.7 - - + -
377A GLY 3.1 9.2 + - - +
378A ARG 3.9 4.0 - - - +
379A LEU 3.0 0.6 - - - -
380A LEU* 1.3 75.9 - - - +
382A PHE* 1.3 65.6 + - - +
383A VAL 3.0 1.1 - - - -
384A ASP* 3.4 4.2 + - - +
385A ARG* 3.1 59.2 + - - +
6E U 3.0 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.5 27.8 - - + -
358A PHE* 3.4 29.6 - + - -
361A GLN* 3.8 7.6 - - + -
362A ASN* 3.3 50.5 - - + -
365A ILE* 4.6 6.5 - - + -
378A ARG* 3.1 38.2 + - - +
379A LEU* 3.2 8.0 + - - +
381A ASP* 1.3 77.7 - - - +
383A VAL* 1.3 58.7 + - - +
385A ARG 3.7 0.7 + - - -
386A THR 3.5 2.1 + - - -
387A PHE* 2.9 44.7 + - + +
388A ILE* 3.2 32.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 2.9 27.3 + - + +
380A LEU* 3.9 14.1 - - + +
382A PHE* 1.3 74.4 - - - +
384A ASP* 1.3 63.1 + - - +
385A ARG 3.0 4.7 - - - -
386A THR* 2.8 23.9 + - - +
388A ILE* 3.6 26.5 - - + +
390A PHE* 3.5 30.7 - - + -
419A HIS* 3.6 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 2.9 28.8 + - - +
381A ASP* 3.4 5.3 + - - +
383A VAL* 1.3 80.5 - - - +
385A ARG* 1.3 60.9 + - + +
386A THR* 3.2 8.6 + - - +
415A ARG* 2.7 35.5 + - - -
419A HIS* 5.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 3.2 38.3 - - - +
381A ASP* 3.1 36.5 + - - +
382A PHE 4.1 0.2 - - - +
383A VAL 3.0 1.0 - - - -
384A ASP* 1.3 79.9 - - + +
386A THR* 1.3 70.0 + - - +
387A PHE* 3.0 53.3 - - + -
6E U 5.7 0.2 + - - -
----------------------------------------------------------
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