Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 4N6N
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 LYS 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP 3.4 2.6 + - - +
140A HIS* 3.4 21.8 - - + +
141A VAL 3.0 22.3 + - - -
179A TYR* 3.6 6.5 - - - +
180A ARG* 1.3 112.3 - - + +
182A MET* 1.3 60.9 + - - +
203A ASN* 3.5 15.7 - - + +
275A ILE* 4.1 23.3 - - + -
278A MET* 3.6 25.9 - - - +
283A PHE* 3.6 20.9 - - + -
1C NAG 3.6 23.3 + - - -
2C NAG 5.9 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.2 21.1 - - + +
143A ILE* 3.7 20.6 - - + -
170A ILE* 3.9 26.0 - - + -
173A MET* 3.6 32.1 - - - +
179A TYR* 3.7 35.4 - - + -
181A LYS* 1.3 76.0 - - - +
183A VAL* 1.3 67.4 + - - +
184A PHE* 3.9 22.4 - - + -
203A ASN 3.0 7.6 + - - +
204A VAL* 3.3 8.1 - - + +
205A TYR* 2.9 25.1 + - - +
275A ILE* 4.5 1.0 - - - +
283A PHE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL 2.8 9.8 + - - +
142A PHE* 3.4 12.2 - - + -
143A ILE* 2.8 32.7 + - - +
182A MET* 1.3 79.3 - - - +
184A PHE* 1.3 61.5 + - - +
185A TYR* 3.8 30.5 - - + -
205A TYR* 3.2 18.6 - - + +
251A LEU* 4.1 11.9 - - + -
275A ILE* 3.9 15.5 - - + -
283A PHE* 3.6 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 5.1 1.6 - + - -
117A LEU* 4.8 2.5 - - + -
143A ILE* 3.3 49.4 - - + -
145A PHE* 6.5 0.2 - - + -
166A LEU* 4.4 14.8 - - + -
170A ILE* 3.9 34.3 - - + -
182A MET* 3.9 20.0 - - + -
183A VAL* 1.3 75.7 - - - +
185A TYR* 1.3 66.6 + - - +
186A ILE* 4.2 16.2 - - + -
195A MET* 3.7 21.3 - - + -
204A VAL* 3.8 20.2 - - + -
205A TYR 3.0 6.8 + - - -
206A ALA* 3.2 13.6 - - + -
207A THR 2.9 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.7 20.0 - + + -
143A ILE 2.9 7.7 + - - +
144A TYR* 3.3 18.4 - - + -
145A PHE 3.1 23.7 + - - -
183A VAL* 3.8 18.1 + - + -
184A PHE* 1.3 77.3 - - - +
186A ILE* 1.3 63.1 + - - +
205A TYR* 5.4 1.8 - + - -
207A THR* 3.3 25.6 - - + -
233A TYR* 3.3 13.0 - - + +
237A TRP* 3.5 41.3 - + + -
251A LEU* 3.5 22.7 + - + +
254A GLN* 2.6 36.0 + - + +
255A TYR* 5.4 0.7 + - - -
284A GLN* 3.7 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.6 13.2 - - + -
154A LEU* 3.8 33.2 - - + -
166A LEU* 5.3 0.7 - - + -
184A PHE* 4.2 16.6 - - + -
185A TYR* 1.3 77.6 - - - +
187A GLU* 1.3 61.7 + - - +
191A SER* 3.6 21.4 + - - +
194A MET* 4.2 11.0 - - + -
195A MET* 3.6 43.3 - - + -
207A THR 3.1 11.6 + - - +
208A THR* 3.4 9.2 - - + -
209A ALA 2.9 27.5 + - - -
233A TYR* 3.4 6.9 + - - -
----------------------------------------------------------
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