Contacts of the strand formed by residues 88 - 93 (chain J) in PDB entry 1ZGL
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 GLU 88 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J PRO 4.0 2.9 + - - +
87J PRO* 1.3 73.2 - - - +
89J VAL* 1.3 61.3 + - - +
90J THR* 5.3 4.3 - - + +
108J PHE 3.5 4.7 - - - +
109J ILE* 3.5 1.9 - - - -
110J ASP* 3.0 41.0 + - - +
111J LYS* 4.3 16.1 - - + +
174J LEU* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J PRO 4.0 3.1 + - - +
88J GLU* 1.3 77.9 - - - +
90J THR* 1.3 76.7 + - - +
107J CYS* 3.4 32.3 - - - -
108J PHE 3.7 2.2 - - - +
109J ILE* 3.9 16.6 - - + -
163J CYS* 4.5 0.7 - - - -
165J VAL* 3.7 27.1 - - + -
174J LEU* 3.7 30.2 - - + +
176J LYS* 3.4 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J GLU* 5.3 4.5 - - + +
89J VAL* 1.3 90.3 - - - +
91J VAL* 1.3 65.7 + - - +
92J LEU* 3.4 8.3 - - - +
107J CYS* 3.8 0.2 - - - -
108J PHE* 3.0 42.3 + - - +
110J ASP* 5.8 1.6 - - - -
176J LYS* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J THR* 1.3 79.1 - - - +
92J LEU* 1.3 73.3 + - - +
105J LEU* 4.7 7.0 - - + -
106J ILE 3.4 13.7 - - - +
107J CYS* 4.6 2.5 - - - -
121J TRP* 4.5 14.8 - - + -
161J TYR* 6.4 1.3 - - + -
163J CYS* 4.1 17.3 - - + +
176J LYS* 3.7 37.9 - - + +
177J HIS 4.9 3.4 - - - +
178J TRP* 4.2 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J THR* 3.4 14.8 - - - +
91J VAL* 1.3 84.8 - - - +
93J THR* 1.3 63.1 + - - +
105J LEU* 3.6 3.0 - - - -
106J ILE* 2.6 77.4 + - + +
108J PHE* 4.4 9.6 - - + +
178J TRP* 5.2 7.2 - - - +
148K ILE* 4.0 33.0 - - + -
149K GLN 5.9 0.7 - - - +
150K ASN* 4.6 4.9 - - - +
156K GLN* 4.1 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J LEU* 1.3 77.5 - - - +
94J ASN* 1.3 67.5 + - - +
95J SER* 3.7 16.7 + - - -
96J PRO* 5.2 0.9 - - - +
97J VAL* 3.4 29.4 + - + +
103J ASN* 4.0 9.2 - - - +
104J VAL 3.7 3.8 - - - +
105J LEU* 4.8 2.7 - - + -
106J ILE* 4.8 2.2 - - - -
153J PHE* 4.2 12.6 - - + -
178J TRP* 3.6 25.3 + - + +
156K GLN* 3.0 18.9 + - - +
----------------------------------------------------------
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