Contacts of the strand formed by residues 178 - 184 (chain D) in PDB entry 3NDR
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 THR 178 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MSE 3.7 29.4 - - + -
134D GLY 3.3 4.8 + - - -
135D ARG* 3.6 40.7 - - - +
136D VAL* 2.7 30.5 + - - +
176D ASN 5.2 1.1 - - - +
177D ILE* 1.3 80.6 - - - +
179D ALA* 1.3 56.1 + - - +
180D ASN* 4.4 5.2 + - - -
231D ALA 5.0 1.2 + - - +
232D ARG 4.1 7.9 - - - +
234D ILE 3.6 24.5 + - - +
235D THR* 3.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D VAL* 3.4 13.7 - - + -
165D THR* 3.5 15.3 - - + +
168D LEU* 4.0 23.6 - - + -
169D ALA* 3.8 23.4 - - - +
172D LEU* 5.4 2.2 - - + -
177D ILE 4.1 0.9 + - - +
178D THR* 1.3 73.6 - - - +
180D ASN* 1.3 62.1 + - - +
235D THR* 3.1 7.9 + - - -
236D GLY* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ARG* 6.3 0.2 - - - +
136D VAL* 2.8 12.4 + - - +
137D ILE* 3.5 5.0 - - + +
138D SER* 3.0 23.8 + - - -
165D THR* 3.7 9.8 + - - +
178D THR* 4.4 6.5 + - - -
179D ALA* 1.3 74.4 - - - +
181D ALA* 1.3 63.3 + - - +
226D LEU* 4.2 29.5 + - + +
231D ALA* 4.9 1.2 + - - +
234D ILE* 2.8 40.8 + - - +
235D THR* 3.2 3.0 - - - +
236D GLY 3.0 10.2 + - - -
237D GLN 3.0 29.4 + - - +
239D LEU* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D SER* 3.1 15.5 - - - +
140D ALA* 4.9 3.4 - - + -
161D VAL* 5.2 1.1 - - + -
162D ILE* 4.7 11.9 - - + -
165D THR* 3.9 18.2 - - + +
180D ASN* 1.3 80.4 - - - +
182D VAL* 1.3 61.8 + - - +
226D LEU* 4.7 0.5 - - - +
237D GLN 3.0 5.3 + - - +
238D THR* 3.1 22.8 - - + +
239D LEU* 2.7 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ILE* 4.1 11.7 - - + -
138D SER 3.0 7.7 + - - +
139D ILE* 3.6 9.9 - - + -
140D ALA* 2.7 31.4 + - - -
181D ALA* 1.3 78.8 - - - +
183D THR* 1.3 67.3 + - - +
184D PRO* 3.2 11.0 - - + +
219D ILE* 4.9 11.0 - - + -
222D VAL* 5.0 5.8 - - + -
223D VAL* 4.7 10.5 - - + -
226D LEU* 3.5 27.8 - - + -
239D LEU* 3.1 14.1 - - + +
241D VAL* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 3.8 7.4 - - + -
141D SER 3.2 34.1 - - - +
142D ASN* 3.6 2.0 - - - -
145D PHE* 3.4 13.9 - - + -
162D ILE* 4.3 5.2 - - + -
182D VAL* 1.3 73.4 - - - +
184D PRO* 1.3 63.9 - - - +
238D THR* 3.4 21.7 - - + +
239D LEU 2.7 10.0 + - - -
240D ASN* 2.7 36.8 + - - +
241D VAL 2.9 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 4.8 3.6 - - + -
139D ILE* 3.9 12.8 - - + -
140D ALA 3.6 8.3 - - - +
141D SER* 3.7 0.4 - - - -
142D ASN* 3.0 20.7 + - - -
182D VAL* 3.2 14.6 - - + +
183D THR* 1.3 84.0 - - - +
185D GLY* 1.3 63.7 + - - +
187D ILE* 4.2 3.6 - - + -
219D ILE* 3.7 32.3 - - + -
241D VAL* 3.5 9.0 - - + +
251D NAD 3.1 41.0 - - + +
----------------------------------------------------------
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