Contacts of the strand formed by residues 129 - 134 (chain B) in PDB entry 3ORH
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 129 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.6 20.6 - - + +
65B LEU* 3.7 25.1 - - + -
87B TRP* 3.5 57.9 - + + -
124B LEU* 4.2 15.9 - - + -
125B PRO* 4.2 1.8 - - + -
127B GLY 3.7 0.6 - - - -
128B HIS* 1.3 97.5 - + + +
130B ASP* 1.3 61.7 + - - +
131B GLY 3.3 11.2 - - - +
132B ILE* 4.3 9.6 - - + -
159B LEU* 3.1 39.4 + - + +
160B LEU* 3.4 6.8 - - - +
161B LYS* 2.9 29.0 + - - -
164B GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 4.8 0.7 - - - -
60B LYS* 3.9 21.7 - - + +
61B GLY 3.4 19.1 - - - +
62B GLY* 3.5 9.3 - - - -
63B ARG* 2.8 31.0 + - - +
129B PHE* 1.3 72.8 - - - +
131B GLY* 1.3 57.1 + - - +
160B LEU* 4.3 0.2 - - - -
161B LYS* 3.3 39.5 + - - +
164B GLY* 3.2 8.8 - - - -
165B VAL* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 3.3 22.4 + - - -
63B ARG 3.3 4.4 + - - +
64B VAL* 3.3 6.6 - - - +
65B LEU 2.9 23.8 + - - -
129B PHE* 3.3 2.9 - - - +
130B ASP* 1.3 80.6 - - - +
132B ILE* 1.3 66.8 + - - +
160B LEU* 4.2 0.9 - - - -
165B VAL* 3.2 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 3.9 5.3 - - - +
65B LEU* 3.2 27.1 - - + +
67B VAL* 4.8 0.9 - - + -
129B PHE* 4.3 4.0 - - + -
131B GLY* 1.3 79.3 - - - +
133B LEU* 1.3 68.3 + - - +
151B PHE* 3.9 26.9 - - + -
156B ALA* 3.8 35.4 - - + +
159B LEU* 3.9 19.3 - - + -
160B LEU* 3.8 16.8 - - + +
165B VAL 2.9 8.6 + - - +
166B LEU* 3.6 13.6 - - + -
167B THR* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.8 15.3 - - + +
54B ALA* 3.7 33.0 - - - +
57B ALA* 3.8 11.1 - - + +
64B VAL* 5.4 1.1 - - + -
65B LEU 2.8 13.0 + - - +
66B GLU* 3.4 16.9 - - + +
67B VAL* 2.8 31.5 + - - +
74B ALA* 3.8 25.4 - - + -
78B VAL* 4.4 8.1 - - + -
132B ILE* 1.3 72.9 - - - +
134B TYR* 1.3 58.9 + - - +
135B ASP* 3.9 24.0 - - + +
167B THR* 3.5 15.7 - - + +
168B TYR* 5.5 0.2 - - - -
4001B SAH 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.9 15.3 - - + -
117B TRP* 2.8 41.7 + + - -
132B ILE 4.1 0.6 - - - -
133B LEU* 1.3 71.4 - - - +
135B ASP* 1.3 60.9 + - - +
136B THR* 2.8 23.0 + - + -
147B HIS* 2.7 36.4 + + - -
148B GLN* 3.6 27.8 - - + -
151B PHE* 3.4 45.5 - + + -
152B ILE* 5.8 0.9 - - + -
166B LEU* 4.8 2.7 - - + -
167B THR 3.0 8.8 + - - +
168B TYR* 3.1 34.5 - - + +
169B CYS 3.2 9.8 + - - +
----------------------------------------------------------
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