Contacts of the strand formed by residues 176 - 184 (chain B) in PDB entry 4MDH
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 ASP 176 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.3 20.9 - - + +
173B THR* 2.6 44.2 + - - +
175B ASP* 1.3 76.0 - - - +
177B VAL* 1.3 59.0 + - - +
178B LYS* 4.0 5.6 + - - +
198B LYS 3.9 0.3 - - - +
199B VAL* 3.2 5.8 + - + -
200B LYS* 2.9 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 2.9 48.2 + - + +
166B ILE* 4.2 27.8 - - + -
167B ALA* 4.4 5.4 - - - +
172B VAL* 4.7 0.4 - - + -
173B THR 3.6 15.0 - - - +
174B SER 3.6 7.9 - - - +
175B ASP 3.2 3.2 - - - -
176B ASP* 1.3 81.6 - - + +
178B LYS* 1.3 61.4 + - - +
180B VAL* 4.0 24.5 - - + -
198B LYS 3.5 11.2 - - - +
199B VAL* 4.6 8.1 - - + -
208B VAL* 4.8 3.4 - - + -
264B GLU* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASP 6.0 0.9 - - - +
176B ASP 4.0 4.7 + - - +
177B VAL* 1.3 76.3 - - - +
179B ASN* 1.3 81.8 + - - +
180B VAL 3.1 3.2 + - - -
197B ALA* 3.1 21.1 - - - +
198B LYS* 3.2 23.5 + - + -
200B LYS* 6.6 0.4 - - - +
205B GLU* 3.9 24.9 + - - +
262B GLU 4.8 10.3 + - - -
263B GLY* 4.6 12.7 + - - +
264B GLU* 4.1 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B HIS* 5.9 0.2 - - - -
178B LYS* 1.3 80.2 - - - +
180B VAL* 1.3 65.6 + - - +
181B ILE* 3.6 4.5 + - - +
193B ASP 4.2 1.2 - - - +
196B HIS 3.3 29.0 + - - +
197B ALA* 3.8 2.0 - - - +
198B LYS* 4.7 8.9 - - - +
263B GLY 3.4 15.8 + - - -
264B GLU* 3.2 12.8 + - - +
265B PHE* 3.0 70.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B HIS* 3.3 30.0 + - + +
162B ALA* 3.6 27.8 - - + +
163B LYS* 4.0 21.8 - - + +
166B ILE* 5.2 2.0 - - + -
177B VAL* 4.0 26.5 - - + -
178B LYS 3.1 4.2 + - - -
179B ASN* 1.3 80.8 - - - +
181B ILE* 1.3 66.8 + - - +
182B ILE* 4.0 13.9 - - + -
192B PRO* 5.5 0.2 - - + -
193B ASP 3.9 10.5 - - - +
194B VAL* 4.6 12.3 - - + -
197B ALA* 4.2 9.6 - - + -
265B PHE* 4.4 4.3 - - - +
266B VAL 5.3 0.2 - - - -
267B SER* 3.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASN 3.9 2.7 - - - +
180B VAL* 1.3 82.4 - - - +
182B ILE* 1.3 73.9 + - - +
183B TRP* 3.5 33.0 - - + +
191B TYR 2.9 3.3 - - - +
192B PRO* 3.5 1.2 - - - +
193B ASP* 2.5 46.4 + - + +
196B HIS* 3.7 32.8 - - + -
265B PHE* 3.8 19.5 - - + -
267B SER* 4.0 1.8 - - - +
287B PHE 4.7 0.2 - - - -
288B PRO* 3.9 23.3 - - + -
302B LEU* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 4.0 27.6 - - + -
158B ASP* 3.2 20.2 - - + +
159B HIS* 3.0 39.9 - - + +
162B ALA* 4.0 4.9 - - + -
180B VAL* 4.0 15.0 - - + -
181B ILE* 1.3 81.9 - - - +
183B TRP* 1.3 64.9 - - - +
185B ASN 5.4 0.7 - - - +
190B GLN* 4.3 19.1 - - + +
191B TYR 3.6 0.4 - - - -
192B PRO* 4.1 14.8 - - + -
267B SER* 3.2 19.8 + - - +
286B SER* 2.7 28.8 + - - +
287B PHE* 4.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.5 20.0 - - + +
182B ILE* 1.3 74.7 - - - +
184B GLY* 1.3 61.8 + - - +
190B GLN* 3.5 8.0 - - - +
191B TYR* 2.9 69.5 + + + +
193B ASP* 3.2 27.0 + - + +
196B HIS* 5.5 0.2 - + - -
277B TYR* 4.0 24.9 - + + -
285B TYR* 4.0 16.8 - + - +
286B SER* 3.5 18.8 - - - -
287B PHE* 3.9 16.6 - + - -
288B PRO* 3.7 32.1 - - + -
302B LEU* 4.9 3.1 - - + -
304B ILE* 3.8 24.7 - - + +
312B MET* 3.7 22.8 - - + -
315B THR* 4.1 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 3.1 7.6 + - - -
183B TRP* 1.3 73.0 - - - +
185B ASN* 1.3 63.2 + - - -
285B TYR* 3.5 26.6 - - - -
286B SER* 2.9 40.4 + - - -
315B THR* 3.5 9.6 - - - -
319B LEU* 3.7 4.5 - - - -
----------------------------------------------------------
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