Contacts of the strand formed by residues 2 - 9 (chain Z) in PDB entry 5WTI
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 ALA 2 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Z MET* 1.3 74.1 - - - +
3Z THR* 1.3 62.4 + - - +
4Z ARG* 3.6 6.8 + - - +
514Z VAL 3.5 1.9 - - - +
515Z ASN* 3.5 1.5 - - - -
516Z ILE* 2.9 46.1 + - + +
518Z PRO* 4.0 17.5 - - + -
864Z GLU* 4.1 22.2 - - - +
865Z ILE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 3 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B C 3.0 26.0 - - - +
19E G 3.4 37.8 + - + +
1Z MET 3.8 6.2 + - - -
2Z ALA* 1.3 69.8 - - - +
4Z ARG* 1.3 81.2 + - - +
513Z THR* 3.5 25.8 - - + -
514Z VAL 3.4 4.9 - - - +
515Z ASN* 3.3 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 4 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B C 3.5 50.7 + - - +
19E G 4.4 1.8 - - - -
2Z ALA* 3.6 8.0 + - - +
3Z THR* 1.3 109.2 + - - +
5Z SER* 1.3 59.8 + - - +
6Z PHE* 4.4 5.2 - - + -
513Z THR* 3.5 2.1 - - - +
514Z VAL* 2.6 57.4 + - + +
516Z ILE* 4.1 19.7 - - + -
861Z LEU* 2.8 42.8 + - - +
864Z GLU* 2.6 34.1 + - - +
865Z ILE* 4.2 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 5 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B C 3.1 28.8 + - - +
104B G 3.8 19.5 + - - -
19E G 3.3 24.7 - - - +
4Z ARG* 1.3 74.6 - - - +
6Z PHE* 1.3 70.7 + - - +
7Z ILE* 4.1 4.9 - - - +
449Z GLN* 5.0 1.2 + - - +
511Z ASN* 2.6 31.5 + - - -
512Z MET 3.5 4.9 - - - -
513Z THR* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 6 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B C 4.8 8.1 - - - -
4Z ARG* 4.4 8.5 - - + -
5Z SER* 1.3 79.4 + - - +
7Z ILE* 1.3 62.9 + - - +
8Z LEU* 3.9 5.2 + - + +
449Z GLN* 3.5 57.0 - - - +
450Z PHE* 4.0 20.6 - - + -
453Z GLN* 4.2 4.5 - - - -
454Z ILE* 3.6 24.7 - - + -
468Z TYR* 4.2 20.0 - + - -
510Z PHE 3.6 2.8 - - - +
512Z MET* 3.0 36.2 + - + +
514Z VAL* 3.5 33.4 - - + -
516Z ILE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B G 4.3 14.2 + - - +
43B U 6.0 1.6 - - - +
104B G 4.2 26.5 - - - +
5Z SER* 4.1 3.4 - - - +
6Z PHE* 1.3 71.8 - - - +
8Z LEU* 1.3 65.0 + - - +
447Z SER* 4.2 11.4 + - - -
449Z GLN* 5.0 5.8 + - - +
487Z GLN* 5.1 6.3 - - - +
509Z TYR* 3.6 39.9 - - + -
510Z PHE 3.6 4.5 - - - +
511Z ASN* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B G 4.9 0.2 - - - -
6Z PHE* 4.0 8.3 - - + +
7Z ILE* 1.3 76.4 - - - +
9Z LYS* 1.3 59.9 + - - +
418Z LEU* 4.6 8.7 - - + -
444Z LEU* 4.1 28.3 - - + -
445Z LEU 3.5 20.9 - - - +
446Z PRO* 4.9 1.1 - - + -
447Z SER* 3.9 24.0 - - - +
450Z PHE* 4.0 33.4 - - + -
509Z TYR* 3.4 3.8 - - - -
510Z PHE* 2.7 42.3 + - - +
512Z MET* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B A 3.3 21.1 + - - +
42B G 3.0 54.5 + - - +
43B U 2.7 24.6 + - - +
8Z LEU* 1.3 73.4 - - - +
10Z ILE* 1.3 72.4 + - - +
12Z PRO* 6.3 0.7 - - + -
444Z LEU* 3.7 1.6 - - - -
445Z LEU* 2.8 45.8 + - + +
507Z ARG* 3.8 27.3 - - + +
508Z ILE 3.5 14.1 - - - +
509Z TYR* 3.7 15.7 - - + -
----------------------------------------------------------
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