Contacts of the strand formed by residues 183 - 189 (chain A) in PDB entry 2NTC
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 183 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 3.1 6.2 - - - +
182A THR* 1.3 83.1 + - - +
184A ILE* 1.3 66.5 + - - +
185A SER* 3.2 29.4 - - - -
196A PHE* 3.9 13.5 - + - -
197A PHE* 3.2 5.9 - - - +
198A LEU* 3.0 33.5 + - + +
233A TYR* 3.8 4.7 - + - -
246A GLU* 3.5 21.5 - - + -
247A SER* 3.6 12.6 - - - -
248A LEU* 3.4 32.5 - - + -
251A GLY* 3.7 13.7 - - - -
252A LEU* 3.7 24.0 - - + -
257A PHE* 3.8 28.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.5 61.9 - - + +
175A ILE* 3.7 25.4 - - + -
176A MET* 4.5 6.1 - - + +
181A VAL* 4.0 13.5 - - + -
183A PHE* 1.3 80.8 - - - +
185A SER* 1.3 67.8 + - - +
195A LEU* 4.9 5.8 - - + -
196A PHE 3.3 13.5 - - - +
197A PHE* 3.7 12.6 - - + -
246A GLU* 3.4 1.6 - - - +
247A SER* 2.8 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 4.2 4.5 - - - -
183A PHE* 3.2 20.1 - - - -
184A ILE* 1.3 76.1 - - - +
186A ARG* 1.3 59.9 + - - +
187A HIS* 2.8 31.7 + - - -
195A LEU* 3.4 5.4 - - - +
196A PHE* 2.9 38.5 + - - +
233A TYR* 3.8 1.4 - - - -
243A VAL* 5.3 0.2 - - - -
245A GLU 3.5 5.2 - - - -
246A GLU* 3.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 3.5 17.8 + - - +
168A ALA* 3.5 20.2 - - + +
169A ALA* 3.5 29.3 - - - +
172A TYR* 3.9 17.7 - - + +
185A SER* 1.3 73.6 - - - +
187A HIS* 1.3 68.4 + - - +
193A ASN* 3.1 27.6 + - - +
194A ILE 3.5 3.6 - - - +
195A LEU* 3.7 12.1 - - + -
243A VAL* 3.7 2.3 - - - +
244A ILE* 3.0 55.1 + - + +
245A GLU* 2.8 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 2.8 41.2 + - - -
186A ARG* 1.3 79.3 + - - +
188A ASN* 1.3 65.0 + - - +
193A ASN* 3.1 15.2 + - - +
194A ILE* 2.7 51.3 + - + +
196A PHE* 4.0 8.6 - - + +
233A TYR* 4.1 10.8 - + - -
236A LEU* 3.4 50.4 + - + +
242A SER 3.1 10.7 + - - +
243A VAL* 4.0 17.7 - - + +
244A ILE* 3.8 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 4.4 11.6 - - - -
187A HIS* 1.3 72.4 - - - +
189A SER* 1.3 60.0 + - - +
190A TYR 4.4 0.4 - - - +
191A ASN 5.6 1.4 + - - -
192A HIS 3.9 3.3 - - - +
193A ASN* 3.5 13.7 + - - -
240A PRO 4.8 3.6 - - - +
241A PHE* 3.1 32.2 - - - +
242A SER* 2.7 34.7 + - - +
244A ILE* 3.8 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 3.5 9.5 - - - +
162A TYR* 3.7 14.1 + - - -
187A HIS 3.7 0.4 + - - -
188A ASN* 1.3 73.9 - - - +
190A TYR* 1.3 71.4 + - - +
191A ASN 3.2 2.0 - - - -
192A HIS* 2.6 30.7 + - - +
194A ILE* 3.1 27.1 - - - +
240A PRO 5.1 0.7 - - - -
241A PHE* 2.9 29.5 - - - -
----------------------------------------------------------
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