Contacts of the strand formed by residues 91 - 96 (chain F) in PDB entry 1Z6Z
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 ARG 91 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET 5.6 0.2 + - - -
2F LEU* 3.7 53.2 + - + +
4F ARG 3.2 3.2 + - - +
5F ALA* 3.1 24.4 - - + +
6F VAL 3.0 24.3 + - - -
89F LEU* 3.5 4.5 - - - +
90F GLN* 1.3 81.1 + - - +
92F LEU* 1.3 69.5 + - - +
93F LEU* 4.4 13.9 - - + +
145F LEU* 3.5 5.8 - - - +
146F ASN* 3.3 35.6 + - - +
148F THR* 3.9 19.5 + - - -
242F LEU* 3.8 30.9 + - - +
243F GLU* 4.8 5.3 + - - +
245F ASP* 5.2 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F VAL* 3.4 27.4 - - + +
8F LEU* 5.2 3.4 - - + -
89F LEU* 4.6 3.4 - - + -
91F ARG* 1.3 73.9 - - - +
93F LEU* 1.3 65.7 + - - +
94F LEU* 5.2 0.9 - - + +
135F VAL* 3.9 25.6 - - + +
136F LEU* 4.3 9.2 - - + -
139F PHE* 3.7 47.3 - - + +
145F LEU* 3.7 11.1 - - + +
146F ASN 2.9 10.8 + - - +
147F ARG* 4.1 23.8 - - + -
148F THR* 2.9 31.7 + - - +
149F VAL* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 4.0 16.4 - - + -
5F ALA* 5.7 0.7 - - + -
6F VAL 2.9 10.7 + - - +
7F CYS* 3.3 15.7 - - + -
8F LEU* 2.8 33.4 + - - +
24F LEU* 3.9 28.0 - - + -
28F LEU* 5.6 0.7 - - + -
91F ARG* 4.1 16.6 - - + +
92F LEU* 1.3 76.2 - - - +
94F LEU* 1.3 56.6 + - - +
95F ILE* 4.1 16.6 - - + -
148F THR* 3.4 30.1 - - + +
150F VAL* 4.2 4.5 - - + -
242F LEU* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 3.6 25.1 - - + +
10F THR* 5.5 1.3 - - + -
92F LEU* 4.2 1.2 - - + +
93F LEU* 1.3 73.0 - - - +
95F ILE* 1.3 62.7 + - - +
96F ASN* 3.5 22.2 - - - +
131F LEU* 4.1 20.9 - - + +
132F THR* 3.4 48.2 - - + +
135F VAL* 4.5 18.2 - - + -
148F THR 3.0 8.1 + - - +
149F VAL* 3.5 14.7 - - + -
150F VAL* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F CYS* 5.0 0.9 - - - -
8F LEU 2.8 15.9 + - - +
9F LEU* 3.8 16.4 - - + +
10F THR* 3.4 20.4 + - - -
20F LEU* 3.8 25.4 - - + -
24F LEU* 3.9 24.5 - - + -
93F LEU* 4.1 24.0 - - + +
94F LEU* 1.3 79.9 - - - +
96F ASN* 1.3 59.4 + - - +
97F ASN* 3.1 8.6 + - + -
150F VAL* 3.7 15.9 - - + -
152F ILE* 4.0 29.8 - - + -
238F LEU* 4.8 6.5 - - + -
239F LEU* 5.8 0.2 - - + -
242F LEU* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR* 3.8 5.0 + - - -
94F LEU* 3.5 16.7 + - - +
95F ILE* 1.3 68.7 - - - +
97F ASN* 1.3 59.0 + - - +
98F ALA 3.8 0.7 - - - -
128F MET* 3.7 42.4 - - + +
131F LEU* 3.9 18.4 - - - +
132F THR* 3.1 23.2 + - - -
150F VAL 2.8 24.9 + - - +
151F ASN* 4.3 0.4 - - - -
152F ILE* 3.1 25.2 + - - +
174F ARG* 3.2 10.5 + - - +
178F PHE* 3.4 13.5 - - - -
----------------------------------------------------------
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