Contacts of the strand formed by residues 183 - 187 (chain B) in PDB entry 2CNW
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 LEU 183 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.4 7.9 - - + -
99B ASN* 3.5 25.6 - - + +
101B TRP* 3.9 28.3 - - + -
122B TYR* 3.5 44.9 - - + -
127B ARG* 4.4 7.9 - - + -
128B ARG 3.6 1.6 + - - -
129B PRO* 3.0 13.6 - - + +
130B LEU 2.7 32.9 + - - +
181B ARG 3.6 0.4 - - - -
182B ASP* 1.3 85.4 + - - +
184B ILE* 1.3 58.6 + - - +
185B LEU* 3.9 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 3.6 36.3 - - - +
99B ASN 2.8 15.3 + - - +
100B LEU* 3.4 21.7 - - + -
101B TRP* 2.8 31.5 + - - +
130B LEU* 3.4 15.9 - - + +
132B VAL* 3.9 24.0 - - + -
172B VAL* 3.6 22.7 - - + -
176B ALA* 3.7 16.8 - - + -
181B ARG 4.7 2.9 - - - +
182B ASP 5.1 0.7 - - - -
183B LEU* 1.3 79.0 - - - +
185B LEU* 1.3 63.5 + - - +
186B VAL* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.7 37.0 - - + -
103B LEU* 4.3 10.3 - - + -
115B ALA* 3.8 10.3 - - + +
118B LEU* 4.0 20.9 - - + -
119B ALA* 3.7 35.0 - - + +
129B PRO* 4.2 14.6 - - + -
130B LEU 2.9 10.6 + - - +
131B LEU* 3.7 13.7 - - + +
132B VAL* 2.9 24.3 + - - -
183B LEU* 4.1 16.4 - - + +
184B ILE* 1.3 74.0 - - - +
186B VAL* 1.3 62.1 + - - +
187B ASP* 3.6 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.8 21.3 - - + -
101B TRP 2.8 19.8 + - - +
102B PHE* 3.6 15.6 - - + -
103B LEU* 3.0 30.8 + - - +
132B VAL* 3.9 21.8 - - + -
134B ALA* 4.0 18.4 - - + -
168B ILE* 6.3 0.4 - - + -
172B VAL* 6.0 1.1 - - + -
184B ILE* 4.1 9.9 - - + -
185B LEU* 1.3 72.3 - - - +
187B ASP* 1.3 61.9 + - - +
188B THR* 3.5 18.8 + - + +
205B LEU* 4.8 2.7 - - + -
209B LEU* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.3 6.5 - - - +
111B LYS* 3.7 6.8 - - - +
112B THR* 2.7 51.2 + - - +
115B ALA* 4.4 11.9 - - + -
132B VAL 3.0 15.3 + - - +
133B ALA* 4.9 3.3 - - - +
134B ALA* 3.1 27.4 + - - +
135B ASP* 3.8 8.6 + - - +
141B ALA* 5.2 2.4 - - - +
145B LEU* 4.0 18.2 - - + +
185B LEU 3.6 1.8 + - - +
186B VAL* 1.3 70.9 - - - +
188B THR* 1.3 69.7 + - - +
1002B MG 4.1 2.2 - - - -
----------------------------------------------------------
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