Contacts of the strand formed by residues 515 - 520 (chain A) in PDB entry 3ZW3
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 SER 515 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 3.3 7.3 - - - +
369A ASP* 2.8 51.5 + - - +
481A VAL* 4.2 15.6 - - - +
482A LEU 3.3 9.0 - - - -
483A HIS* 3.7 30.0 - - - -
484A MET* 4.5 0.7 - - - -
513A SER 3.7 0.4 + - - -
514A MET* 1.3 78.5 - - - +
516A ILE* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 4.4 8.1 - - + -
367A GLY 3.6 11.2 - - - +
368A ILE* 3.8 14.4 - - + -
383A VAL* 3.8 29.8 - - + -
431A LEU* 4.0 26.0 - - + -
433A ILE* 5.3 0.7 - - + -
464A VAL* 3.9 17.5 - - + -
480A TYR 3.7 1.6 - - - +
481A VAL* 3.5 2.3 - - - -
482A LEU* 2.9 47.2 + - + +
484A MET* 3.9 22.2 - - + -
515A SER* 1.3 75.9 - - - +
517A SER* 1.3 62.9 + - - +
518A ILE* 4.1 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.9 0.5 - - - -
366A ARG* 3.0 48.2 + - - +
367A GLY 3.0 16.8 + - - +
369A ASP* 5.6 4.5 - - - -
479A GLU* 5.1 1.9 + - - -
480A TYR 3.4 8.0 + - - -
481A VAL* 4.2 17.2 - - - +
516A ILE* 1.3 73.4 - - - +
518A ILE* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.0 7.4 - - + -
364A LYS 3.2 13.0 - - - +
365A ILE* 3.9 22.0 - - + -
366A ARG* 4.4 4.0 - - - -
429A LEU* 4.3 7.6 - - + -
431A LEU* 4.0 16.8 - - + -
466A LEU* 3.9 23.8 - - + -
479A GLU* 3.4 9.8 - - - +
480A TYR* 2.9 50.8 + - + +
482A LEU* 4.4 9.6 - - + -
516A ILE* 4.2 9.2 - - + -
517A SER* 1.3 79.5 + - - +
519A LEU* 1.3 61.5 - - - +
520A LEU* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 2.8 50.5 + - + +
366A ARG* 4.1 22.4 - - - +
413A TRP* 3.7 28.6 - - + -
478A GLY* 3.7 9.6 - - - -
479A GLU* 3.5 31.0 - - + +
518A ILE* 1.3 74.7 - - - +
520A LEU* 1.3 84.2 + - - +
521A ASP* 4.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 4.6 13.9 - - + -
362A ARG 4.7 4.5 - - - +
363A VAL* 3.4 36.8 - - + -
429A LEU* 4.7 3.4 - - + -
466A LEU* 4.1 13.7 - - + -
468A LEU* 4.7 8.1 - - + -
476A ARG* 3.6 48.7 - - + +
477A ARG* 4.8 2.1 + - - -
478A GLY* 2.9 34.4 + - - +
480A TYR* 4.1 7.6 - - + -
518A ILE* 3.9 11.2 - - + -
519A LEU* 1.3 82.3 - - - +
521A ASP* 1.3 63.1 + - - +
522A ASN* 4.6 2.7 - - - +
----------------------------------------------------------
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