Contacts of the helix formed by residues 370 - 381 (chain A) in PDB entry 3P3B
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 370 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY* 2.9 30.1 + - - -
368A VAL 3.8 0.8 + - - -
369A PHE* 1.3 70.1 - - - +
371A ASP* 1.3 62.2 + - - +
372A GLU* 3.3 14.4 + - - +
373A LEU* 3.0 28.9 + - + +
374A VAL* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 3.3 7.3 + - - +
56A THR* 5.1 2.6 + - - -
58A TYR* 2.5 40.1 + - - +
369A PHE 3.2 9.5 + - - +
370A ASP* 1.3 71.3 + - - +
372A GLU* 1.3 73.7 + - - +
375A THR* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 3.3 9.4 - - - +
371A ASP* 1.3 87.1 + - - +
373A LEU* 1.3 66.6 + - - +
375A THR* 3.4 7.5 + - - -
376A TYR* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 6.0 0.2 - - + -
343A GLU* 4.0 15.9 - - + +
344A GLY* 3.8 30.3 - - - +
370A ASP* 3.0 28.8 + - + +
372A GLU* 1.3 76.3 - - - +
374A VAL* 1.3 60.4 + - + +
376A TYR* 3.2 19.6 + - + +
377A LEU* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.4 10.3 - - + -
22A LEU* 4.4 20.2 - - + -
47A ILE* 5.3 5.4 - - + -
49A ARG* 4.2 7.2 - - + +
58A TYR* 4.0 27.6 - - + -
344A GLY* 4.8 2.2 - - - +
369A PHE* 4.5 13.0 - - + -
370A ASP 2.9 22.8 + - - +
371A ASP 3.9 2.9 - - - +
373A LEU* 1.3 79.1 - - + +
375A THR* 1.3 57.1 + - - +
377A LEU* 3.0 8.0 + - + +
378A ILE* 2.7 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.7 1.1 - - - +
49A ARG* 2.9 27.9 + - - +
371A ASP 2.9 20.1 + - - -
372A GLU* 3.6 8.4 - - - -
373A LEU 3.3 0.2 - - - -
374A VAL* 1.3 76.2 - - - +
376A TYR* 1.3 57.4 + - - +
378A ILE* 3.2 4.3 + - + +
379A ASN* 2.8 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU 3.0 13.9 + - - +
373A LEU* 3.3 19.7 - - + +
375A THR* 1.3 76.5 - - - +
377A LEU* 1.3 70.9 + - + +
379A ASN* 3.7 3.0 - - - +
380A ARG* 2.8 84.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.0 13.8 - - + +
21A LYS 4.0 13.9 + - - +
22A LEU* 3.8 31.2 - - + -
23A THR 5.6 0.7 - - - +
343A GLU* 5.6 0.4 - - + +
373A LEU* 2.9 42.0 + - + +
374A VAL* 3.7 4.7 - - - +
376A TYR* 1.3 84.3 - - + +
378A ILE* 1.3 58.4 + - - +
380A ARG* 3.3 28.0 - - - +
381A SER* 2.9 29.1 + - - -
382A GLY* 2.9 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.6 29.4 - - + +
19A PHE 3.7 20.9 - - - +
20A ALA* 3.8 8.7 - - + -
49A ARG* 3.3 33.9 - - + +
374A VAL* 2.7 38.7 + - + +
375A THR* 3.5 4.0 - - + +
377A LEU* 1.3 72.7 - - - +
379A ASN* 1.3 70.8 + - - +
382A GLY 3.0 29.5 + - - +
383A TRP* 3.4 25.9 + - - +
384A SER* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.5 0.9 - - - +
375A THR* 2.8 37.6 + - - +
376A TYR* 4.1 3.3 - - - +
378A ILE* 1.3 91.5 - - - +
380A ARG* 1.3 60.6 + - - +
382A GLY 5.3 1.0 - - - +
384A SER* 5.2 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TYR* 2.8 72.6 + - + +
377A LEU* 3.3 21.8 - - - +
379A ASN* 1.3 76.1 - - - +
381A SER* 1.3 75.8 + - - +
382A GLY 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS 6.3 0.2 - - - -
377A LEU* 2.9 11.3 + - - -
380A ARG* 1.3 105.2 + - - +
382A GLY* 1.3 66.9 + - - +
383A TRP* 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