Contacts of the strand formed by residues 453 - 457 (chain A) in PDB entry 1ZM9
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 ILE 453 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 4.3 8.1 - - - +
21A ASN* 3.5 33.1 + - - +
74A ALA* 4.4 7.4 - - + -
101A ASN* 3.6 25.9 + - + +
103A ILE* 3.7 22.2 - - + -
121A VAL* 3.9 8.7 - - + +
397A PHE* 3.3 35.9 - - + -
398A GLY 3.3 9.9 - - - +
399A ARG* 3.9 20.2 - - + -
436A LEU* 5.2 1.2 - - - +
437A MET* 5.3 5.7 + - + -
452A ASN* 1.3 78.7 - - - +
454A ILE* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 4.6 5.6 - - + -
397A PHE* 3.9 4.5 - - - -
398A GLY 3.1 30.7 + - - +
400A VAL* 3.9 25.4 - - + -
405A VAL* 4.3 10.1 - - + -
434A VAL* 3.5 25.4 - - + -
435A VAL 3.1 20.2 - - - +
436A LEU* 3.4 32.1 - - + -
437A MET* 4.3 7.6 - - - +
445A ILE* 4.1 2.7 - - + -
448A CYS* 3.8 20.4 - - - -
452A ASN 3.6 0.8 + - - +
453A ILE* 1.3 76.1 - - - +
455A GLY* 1.3 63.4 + - - +
456A LEU* 4.3 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TYR* 5.6 0.4 - - - -
396A ALA 3.2 9.6 - - - -
434A VAL* 3.5 4.3 - - - -
435A VAL* 2.8 44.8 + - - -
437A MET* 3.8 17.6 - - - +
454A ILE* 1.3 77.7 - - - +
456A LEU* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.7 25.4 - - + -
382A VAL* 4.9 0.2 - - + -
395A TYR* 3.4 9.4 - - - +
396A ALA* 2.9 38.6 + - + +
405A VAL* 3.8 24.2 - - + -
431A ILE* 4.0 11.0 - - + -
433A ARG 3.5 2.7 - - - +
434A VAL* 4.3 11.7 - - + -
454A ILE* 4.3 10.1 - - + +
455A GLY* 1.3 81.2 - - - +
457A VAL* 1.3 62.6 + - - +
458A GLY 4.3 0.5 + - - -
459A ILE* 3.4 20.1 + - + -
469A LEU* 3.2 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 5.7 1.1 - - - +
393A ARG* 5.9 2.5 - - - +
395A TYR* 3.4 44.2 - - + +
431A ILE* 4.1 2.2 - - - +
432A GLN* 3.0 34.4 + - + +
433A ARG* 2.6 54.1 + - + +
435A VAL* 3.9 23.1 - - + -
456A LEU* 1.3 79.3 - - - +
458A GLY* 1.3 63.4 + - - +
459A ILE* 5.3 0.6 - - - +
460A ASP* 6.0 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