Contacts of the strand formed by residues 161 - 166 (chain B) in PDB entry 3DYD
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 ASN 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN* 1.3 75.2 - - - +
162B ILE* 1.3 65.6 + - - +
163B LEU* 3.5 13.7 - - - +
181B ILE* 4.3 0.4 - - - -
182B GLU* 3.2 26.4 + - + +
184B LYS* 4.1 20.7 - - + +
206B ASP* 3.1 35.5 + - - -
208B LYS* 3.0 23.0 + - - +
209B THR* 2.8 22.1 + - - -
210B ALA* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.7 26.0 - - + -
156B ALA* 4.5 7.2 - - + -
161B ASN* 1.3 77.3 - - - +
163B LEU* 1.3 65.6 + - - +
164B VAL* 3.8 13.9 + - + -
172B TYR 4.2 4.0 - - - +
176B ALA* 3.6 28.5 - - + -
181B ILE* 4.1 11.2 - - + -
182B GLU 2.9 15.9 + - - +
183B VAL* 3.6 3.7 - - + -
184B LYS 2.9 26.0 + - - +
211B CYS* 3.4 30.7 - - + +
213B ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASN* 3.5 22.7 - - - +
162B ILE* 1.3 73.9 - - - +
164B VAL* 1.3 60.5 + - - +
184B LYS* 3.3 21.5 - - + +
186B TYR* 3.8 7.9 - - + -
201B LEU* 3.6 27.4 - - + +
204B LEU* 3.9 15.7 - - + +
205B ILE* 3.4 30.3 - - + -
209B THR* 4.0 14.6 - - + +
211B CYS 3.1 9.0 + - - +
212B LEU* 3.7 17.0 - - + -
213B ILE* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.8 20.6 - - + -
163B LEU* 1.3 77.9 - - - +
165B PRO* 1.3 84.9 - - + +
168B GLY* 5.3 1.3 - - - -
169B PHE 5.1 3.4 - - - +
172B TYR* 3.7 35.7 - - + -
173B LYS* 5.1 5.4 - - + +
183B VAL* 3.9 14.6 - - + -
184B LYS 2.8 6.1 + - - -
185B LEU* 3.3 23.5 - - + -
186B TYR* 2.9 28.1 + - - -
213B ILE* 4.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 1.3 103.3 - - + +
166B ARG* 1.3 59.4 + - - +
167B PRO 3.7 9.4 - - - +
168B GLY* 3.4 22.9 + - - -
172B TYR* 4.3 11.4 - - + -
185B LEU* 4.3 2.9 - - - +
186B TYR* 3.4 35.0 - - + +
188B LEU* 4.3 11.2 - - + -
213B ILE* 3.8 17.9 - - + +
215B ASN* 4.9 13.0 - - + +
410B PHE 5.0 0.3 - - - +
411B GLU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO* 1.3 75.5 - - - +
167B PRO* 1.4 62.4 - - - +
185B LEU* 4.0 28.7 - - + +
186B TYR 2.8 19.1 + - - +
187B ASN* 2.8 41.1 + - - +
188B LEU* 2.8 28.5 + - - +
410B PHE 4.7 0.4 - - - -
411B GLU* 2.7 39.4 + - + +
412B TYR* 3.6 29.4 - - - -
413B PRO* 4.0 14.6 - - - +
----------------------------------------------------------
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