Contacts of the strand formed by residues 205 - 209 (chain D) in PDB entry 3COG
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 ILE 205 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 4.1 27.8 - - + -
100D LEU* 4.4 4.0 - - + -
183D ILE* 4.0 13.5 - - + -
184D LEU 3.2 3.2 + - - +
185D VAL* 3.6 28.2 - - + -
186D VAL* 2.9 26.9 + - - -
199D LEU* 4.1 3.1 - - - -
203D ALA* 3.4 6.1 - - - +
204D ASP* 1.3 86.7 - - - +
206D SER* 1.3 69.0 + - - +
207D MET* 4.2 0.9 - - + +
225D VAL* 3.5 23.8 - - + -
226D SER 3.4 4.7 - - - +
227D VAL* 4.3 5.8 - - + -
232D LEU* 4.0 13.2 - - + -
236D LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASP* 3.0 30.9 + - - -
186D VAL 3.5 4.3 - - - -
188D ASN* 3.9 1.6 - - - +
198D PRO* 3.6 25.0 - - - +
199D LEU* 4.0 16.9 - - - +
205D ILE* 1.3 72.7 - - - +
207D MET* 1.3 60.1 + - - +
208D TYR* 3.2 14.9 + - - -
224D LEU 4.0 0.3 - - - +
225D VAL* 3.6 0.9 - - - -
226D SER* 2.8 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLY* 3.3 33.0 - - - +
93D ALA* 4.2 10.3 - - + -
94D THR* 3.8 8.1 - - - +
97D ILE* 4.3 5.8 - - + -
155D TRP* 3.9 15.3 - - + -
185D VAL* 4.1 14.8 - - + -
186D VAL 2.8 11.9 + - - +
187D ASP* 3.4 35.1 - - - +
188D ASN* 2.7 31.9 + - - -
205D ILE* 4.2 7.2 - - + -
206D SER* 1.3 71.9 - - - +
208D TYR* 1.3 88.5 - - - +
209D SER 3.8 1.6 - - - +
224D LEU 3.3 10.1 - - - +
225D VAL* 4.4 0.7 - - + -
500D PLP 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 4.9 0.4 - - + -
79D ASP* 2.5 42.6 + - - -
188D ASN* 2.8 53.6 + - + -
189D THR* 3.6 7.9 - - - -
192D SER* 3.9 1.8 - - - -
193D PRO* 3.4 25.6 - - + +
206D SER* 3.2 13.5 + - - -
207D MET* 1.3 87.4 - - - +
209D SER* 1.3 68.4 + - - +
210D ALA 3.9 2.5 - - - +
214D MET* 3.7 26.9 - - + -
223D GLY* 3.2 5.7 - - - -
224D LEU* 2.8 52.7 + - + +
226D SER* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLY* 4.0 3.8 - - - -
189D THR* 2.8 27.5 + - - +
207D MET* 3.8 1.8 - - - +
208D TYR* 1.3 73.2 - - - +
210D ALA* 1.3 59.8 + - - +
211D THR* 3.1 10.5 + - - -
212D LYS* 3.4 9.9 + - - +
213D TYR 4.5 1.9 + - - -
214D MET* 4.6 2.4 - - - +
222D MET 3.7 4.5 - - - -
500D PLP 2.9 66.1 + - - +
----------------------------------------------------------
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