Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 5ZCJ
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 TYR 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE 4.5 0.5 + - - -
13B SER* 4.5 0.9 - - - -
14B ARG* 3.4 62.3 + - + +
93B GLU 3.1 17.7 + - - +
94B ALA 3.3 4.4 - - - +
95B ASP* 1.3 79.0 - - - +
97B LEU* 1.3 68.3 + - - +
98B SER* 3.2 35.3 - - - -
99B SER* 2.5 28.2 + - - -
111B HIS* 4.4 7.9 - - + -
112B LEU 4.0 4.7 - - - -
113B TYR* 3.6 24.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 5.2 1.4 + - - -
95B ASP 4.4 2.9 - - - +
96B TYR* 1.3 87.9 - - - +
98B SER* 1.3 61.0 + - - +
112B LEU* 2.8 42.6 + - + +
113B TYR* 4.4 1.1 - - - -
114B ALA* 3.9 20.9 - - + -
175B PHE* 4.2 8.7 - - + -
176B ALA* 4.1 11.4 - - + -
179B VAL* 4.0 25.4 - - + -
180B LEU* 4.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 4.0 13.5 - - - +
96B TYR* 3.2 17.6 - - - -
97B LEU* 1.3 80.6 - - - +
99B SER* 1.3 62.2 + - - +
100B HIS* 3.0 29.2 + - - -
112B LEU* 2.8 40.2 + - - +
175B PHE* 3.5 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.5 8.3 - - - +
12B ILE* 2.9 52.7 + - - +
13B SER 4.5 2.5 - - - -
14B ARG* 4.5 2.9 - - - -
96B TYR* 2.5 24.4 + - - -
98B SER* 1.3 72.4 + - - +
100B HIS* 1.3 62.5 + - - +
109B VAL* 4.1 0.9 - - - -
110B ALA 3.3 6.5 - - - -
111B HIS* 2.7 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.6 50.7 - - + -
10B LYS 3.6 3.4 - - - +
11B GLN* 3.9 19.1 - - + +
12B ILE* 4.6 0.4 - - - +
98B SER* 3.0 33.2 + - - -
99B SER* 1.3 77.1 - - - +
101B LEU* 1.3 65.5 + - - +
102B THR 3.8 0.3 + - - -
109B VAL* 3.3 2.9 - - - -
110B ALA* 2.7 45.9 + - + +
171B CYS* 6.3 1.6 - - + -
172B GLN* 4.8 14.9 + - + +
175B PHE* 4.0 32.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.7 18.2 - - - +
10B LYS* 3.1 35.5 + - + +
12B ILE* 3.7 42.8 - - + -
20B LEU* 4.4 7.6 - - + -
24B TRP* 3.7 36.1 - - + -
100B HIS* 1.3 72.3 - - - +
102B THR* 1.3 67.9 + - - +
108B VAL 3.7 2.9 - - - +
109B VAL* 4.0 15.5 - - + -
----------------------------------------------------------
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