Contacts of the helix formed by residues 376 - 381 (chain D) in PDB entry 5ZR1
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 LEU 376 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A LEU* 3.8 29.8 - - + +
862A ARG* 5.0 15.5 - - + +
375D ASN* 1.3 85.2 + - - +
377D THR* 1.3 60.8 + - - +
378D GLY 3.4 0.9 - - - -
379D ARG* 3.5 25.1 + - - +
380D LEU* 3.4 21.5 + - - +
467D ASP 4.0 11.4 - - - +
468D PHE* 3.9 24.6 - - + -
507D GLN* 4.6 17.0 - - + +
508D ILE* 4.3 17.5 - - + -
512D GLU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A SER* 4.2 5.2 - - - -
859A GLU 4.0 13.5 - - - +
860A GLN* 3.4 39.4 - - + +
861A LEU* 3.8 14.5 + - - +
375D ASN* 3.3 4.8 + - - -
376D LEU* 1.3 76.2 - - - +
378D GLY* 1.3 59.7 + - - +
380D LEU* 3.3 5.6 + - - +
381D GLN* 3.1 50.6 + - - +
516D ILE* 3.8 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A GLN* 5.5 0.4 - - - +
372D LEU 5.0 1.4 + - - -
373D SER* 3.3 30.8 - - - +
374D ASN* 4.3 1.9 - - - +
375D ASN* 3.7 7.3 + - - -
376D LEU 3.4 0.4 - - - -
377D THR* 1.3 78.7 - - - +
379D ARG* 1.3 59.6 + - - +
381D GLN* 4.0 10.4 - - - +
382D SER* 3.0 25.6 + - - -
190E PRO* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D ASN* 3.7 19.3 + - + +
375D ASN 2.5 28.7 + - - -
376D LEU* 3.5 26.2 + - - +
377D THR 3.3 0.4 - - - -
378D GLY* 1.3 79.8 - - - +
380D LEU* 1.3 63.7 + - - +
381D GLN 3.2 0.2 - - - -
382D SER* 3.2 16.3 + - - +
383D LEU* 3.5 15.9 - - - +
466D LEU* 2.4 46.5 + - + +
467D ASP* 3.4 13.5 + - - +
468D PHE* 3.7 15.2 - - + -
507D GLN* 5.7 2.0 - - - +
38E TYR* 2.5 48.3 + - + -
173E THR* 3.8 10.4 - - - +
191E ARG* 5.0 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LEU 3.4 15.8 + - - +
377D THR* 3.3 5.7 + - - +
379D ARG* 1.3 79.3 - - - +
381D GLN* 1.3 60.3 + - + +
382D SER 3.4 0.9 + - - -
383D LEU* 3.7 15.2 + - + +
388D LEU* 3.8 20.0 - - + +
391D LEU* 3.7 29.6 - - + -
468D PHE* 3.8 10.0 - - + -
508D ILE* 3.8 13.9 - - + -
513D LEU* 3.7 24.5 - - + -
516D ILE* 3.7 32.1 - - + -
517D ILE* 3.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A SER* 3.1 35.8 + - - -
377D THR* 3.1 28.2 + - + +
378D GLY* 4.4 8.8 - - - +
379D ARG 3.2 0.4 - - - -
380D LEU* 1.3 76.7 - - - +
382D SER* 1.3 58.0 + - - +
383D LEU 3.4 4.7 + - - +
516D ILE* 4.3 16.3 + - + +
----------------------------------------------------------
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