Contacts of the helix formed by residues 415 - 424 (chain A) in PDB entry 3GZN
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 ASN 415 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG* 2.7 41.8 + - - +
413A THR 3.5 3.7 + - - +
414A ILE* 1.3 74.0 - - - +
416A LYS* 1.3 66.8 + - - +
417A ASP* 3.2 4.3 - - + +
418A GLU* 2.9 23.9 + - + +
419A ILE* 3.1 14.3 + - + +
540A GLN* 2.8 27.2 + - - +
541A LEU* 3.7 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU 4.6 7.6 + - - -
414A ILE* 3.1 29.2 + - + +
415A ASN* 1.3 69.9 - - - +
417A ASP* 1.3 68.4 + - - +
419A ILE* 2.9 4.5 + - - +
420A ILE* 2.7 44.8 + - + +
475A TYR 3.0 27.8 + - - +
476A GLY* 3.7 19.4 + - - +
477A LEU* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 3.2 1.9 - - + -
416A LYS* 1.3 79.3 - - - +
418A GLU* 1.3 55.5 + - - +
420A ILE* 4.4 6.9 - - - +
421A SER* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 2.9 23.8 + - + +
417A ASP* 1.3 76.0 - - - +
419A ILE* 1.3 61.6 + - - +
421A SER* 3.8 5.2 + - - -
422A SER* 2.7 41.1 + - - -
539A PHE* 4.2 18.0 - - + -
540A GLN* 3.3 32.6 + - - +
541A LEU* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 3.7 36.3 - - + -
415A ASN 3.1 9.5 + - - +
416A LYS 2.9 5.5 + - - +
418A GLU* 1.3 75.0 - - - +
420A ILE* 1.3 65.6 + - - +
422A SER* 3.0 5.9 + - - -
423A MET* 2.9 26.0 + - + +
430A ILE* 4.3 19.6 - - + +
433A TYR* 4.9 11.9 - - + -
434A LEU* 4.0 29.6 - - + -
471A PHE* 5.9 0.7 - - + -
477A LEU* 4.2 21.5 - - + -
479A VAL* 4.7 4.5 - - + -
541A LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS* 2.7 42.7 + - + +
417A ASP* 4.4 6.1 - - - +
419A ILE* 1.3 70.5 - - - +
421A SER* 1.3 65.2 + - - +
423A MET* 3.1 12.6 + - - +
424A ASP* 3.5 10.2 + - - +
476A GLY 5.3 4.0 - - - +
477A LEU* 4.1 13.0 - - + -
478A SER* 4.9 14.1 - - - +
479A VAL* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASP 2.9 22.6 + - - -
418A GLU* 3.8 7.6 + - - -
420A ILE* 1.3 77.3 - - - +
422A SER* 1.3 62.8 + - - +
424A ASP* 3.3 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 2.7 28.8 + - - -
419A ILE 3.0 5.3 + - - -
421A SER* 1.3 73.4 + - - +
423A MET* 1.3 60.8 + - - +
424A ASP* 3.1 7.1 + - - +
425A ASN* 3.5 5.4 + - - +
428A ASN* 3.2 44.3 + - - +
430A ILE* 3.7 8.5 - - - -
539A PHE* 3.4 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ILE* 2.9 15.9 + - + +
420A ILE 3.1 9.1 + - - +
422A SER* 1.3 72.7 - - - +
424A ASP* 1.3 65.9 + - - +
425A ASN 3.2 14.0 - - - +
426A PRO* 3.6 25.7 - - + +
428A ASN 4.9 0.2 - - - +
430A ILE* 3.5 22.2 - - + -
431A VAL* 3.9 20.9 - - + -
434A LEU* 3.8 19.3 - - + -
479A VAL* 3.7 29.4 - - + -
480A MET 3.3 29.2 - - - +
481A VAL* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE 3.5 6.2 + - - +
421A SER* 3.3 23.8 + - - +
422A SER 3.1 0.6 - - - +
423A MET* 1.3 77.1 - - - +
425A ASN* 1.3 57.5 + - - +
426A PRO* 3.6 8.0 - - - +
----------------------------------------------------------
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