Contacts of the strand formed by residues 146 - 151 (chain B) in PDB entry 1LU9
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 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 4.4 19.8 - - - +
121B LYS 2.8 17.4 + - - +
122B LYS* 3.4 20.1 - - + +
123B ALA 2.9 23.3 + - - +
144B GLY 4.8 2.7 - - - +
145B ALA* 1.3 70.6 - - - +
147B VAL* 1.3 60.1 + - - +
148B VAL* 4.8 2.3 - - + +
173B THR* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.3 8.7 - - + +
125B VAL* 4.4 8.3 - - + -
137B ALA* 3.9 31.9 - - + +
140B LEU* 3.5 31.2 - - + -
141B ALA* 3.6 16.4 - - + +
145B ALA* 3.4 12.0 + - + +
146B GLU* 1.3 75.4 - - - +
148B VAL* 1.3 73.0 + - - +
171B ASN 4.7 3.7 + - - +
172B VAL* 3.8 13.2 - - + +
173B THR* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 3.8 28.9 - - + +
123B ALA 2.9 12.0 + - - +
124B VAL* 3.5 10.6 - - + +
125B VAL* 2.9 27.7 + - - +
146B GLU 4.8 3.1 - - - +
147B VAL* 1.3 77.3 - - - +
149B LEU* 1.3 61.6 + - - +
150B CYS* 3.9 8.6 + - - -
173B THR* 3.3 26.7 - - + +
175B ALA* 3.8 30.3 - - + -
186B ALA* 6.0 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.9 10.5 - - + +
128B GLY* 2.9 50.5 - - - +
129B THR* 4.0 2.0 - - + +
133B GLY 4.9 0.7 - - - +
134B MET* 4.5 6.7 - - - -
137B ALA* 3.9 20.9 - - + -
147B VAL 4.1 0.6 - - - -
148B VAL* 1.3 71.2 - - - +
150B CYS* 1.3 64.6 + - - +
157B ALA* 4.0 4.9 - - - +
160B ALA* 3.9 25.6 - - + +
161B ALA* 4.3 9.6 - - + +
164B VAL* 4.7 2.2 - - + -
172B VAL* 3.8 13.5 - - + -
173B THR 2.8 14.6 + - - +
174B ALA* 3.2 9.1 - - - +
175B ALA 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 3.8 28.3 - - - -
125B VAL 3.0 13.9 + - - +
126B LEU* 4.0 12.3 - - + -
127B ALA 3.2 5.0 + - - +
128B GLY* 2.9 27.0 + - - -
129B THR* 4.2 1.5 + - - -
148B VAL* 4.2 14.4 - - - -
149B LEU* 1.3 77.0 - - - +
151B GLY* 1.3 58.5 + - - +
157B ALA* 4.6 1.1 - - - -
175B ALA* 3.3 8.7 - - - -
177B THR* 3.8 33.7 - - + +
186B ALA* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 4.9 5.4 - - - -
129B THR* 3.9 20.9 - - - -
150B CYS* 1.3 75.4 - - - +
152B ARG* 1.3 64.0 + - - -
153B LYS* 3.1 5.2 + - - -
156B LYS* 4.4 1.3 - - - -
157B ALA* 3.9 6.6 - - - +
175B ALA 3.2 6.3 + - - -
176B GLU* 3.5 4.2 - - - -
177B THR* 2.9 27.5 + - - -
----------------------------------------------------------
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