Contacts of the strand formed by residues 114 - 118 (chain B) in PDB entry 1ZHH
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 PHE 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 3.3 5.2 - - - +
113B GLU* 1.3 80.4 - - - +
115B ARG* 1.3 66.9 + - - +
116B PHE* 4.3 13.9 - + - -
126B ASP* 6.2 0.9 - - + -
127B ASP* 3.5 18.8 - - - +
129B ASN* 3.8 7.9 - - + -
130B ALA* 3.9 22.2 - - + +
133B TYR* 4.4 4.3 - + - -
135B VAL* 4.1 15.7 - - + -
140B LEU* 3.6 23.3 - - + -
143B LEU* 4.0 12.6 - - + -
167B MET* 3.9 17.3 - - - -
189B ALA* 2.9 55.5 + - + +
191B VAL* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 6.1 0.8 - - - +
78B ASN* 4.0 16.4 - - - +
100B PHE* 3.3 58.9 - - - +
103B ILE* 5.3 0.8 - - - +
104B ASP* 3.1 37.6 + - - -
111B THR* 5.0 0.6 - - - +
112B PRO* 3.5 32.7 + - + +
114B PHE* 1.3 80.0 - - - +
116B PHE* 1.3 67.6 + - - +
125B TRP* 3.9 7.1 - - + -
126B ASP* 3.5 1.9 - - - +
127B ASP* 3.1 46.0 + - - +
186B SER* 5.6 2.9 - - - +
187B PHE 3.2 16.6 - - - +
188B ASN* 3.8 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 4.3 13.0 - + - -
115B ARG* 1.3 80.7 - - - +
117B LEU* 1.3 65.4 - - - +
118B THR* 3.8 9.2 - - + -
123B ILE* 3.7 31.2 - - + -
125B TRP* 3.2 18.4 - - - +
126B ASP* 3.5 12.8 - - + +
140B LEU* 3.8 39.0 - - + -
143B LEU* 4.5 9.0 - - + -
144B ALA* 3.9 8.1 - - + -
169B VAL* 5.3 3.1 - - + -
186B SER* 3.7 2.3 + - - -
187B PHE* 2.9 79.6 + + + +
189B ALA* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 4.2 27.8 - - + -
87B PHE* 4.1 17.0 - - + -
88B TYR* 3.9 14.8 - - + +
96B LEU* 3.8 30.7 - - + -
100B PHE* 5.3 3.8 - - + -
116B PHE* 1.3 75.9 - - - +
118B THR* 1.3 63.1 + - - +
123B ILE* 3.5 4.9 - - - +
124B ILE* 3.0 31.6 + - + +
125B TRP* 2.9 24.5 + - + +
185B PHE 3.3 3.1 - - - +
186B SER* 3.5 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 2.7 24.0 + - - -
116B PHE* 3.8 14.8 - - + -
117B LEU* 1.3 79.0 - - - +
119B ASP* 1.3 71.8 + - - +
122B GLY* 3.3 13.0 - - - -
123B ILE* 3.9 12.1 - - + -
124B ILE* 4.2 2.9 - - - +
144B ALA* 4.4 6.7 - - + -
184B GLY* 3.2 0.9 - - - -
185B PHE* 2.8 37.9 + - - +
187B PHE* 3.5 24.6 - - + -
----------------------------------------------------------
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