Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 3GBA
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 110 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLY* 1.3 72.0 - - - -
111D SER* 1.3 72.4 + - - +
142D THR* 3.7 34.5 - - + +
145D PHE* 3.6 37.5 - - + -
146D PHE* 4.4 1.3 - - + -
188D LEU* 4.0 12.1 - - + -
189D MET 3.8 5.8 - - - +
190D GLU* 4.5 3.6 - - + +
210D LEU* 3.4 1.6 - - - -
211D ILE* 2.8 51.4 + - + +
212D ASP* 2.8 16.7 + - - +
214D LYS* 3.4 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLY 3.6 1.1 + - - -
110D ILE* 1.3 77.5 - - - +
112D ILE* 1.3 70.2 + - - +
188D LEU* 3.4 9.8 - - - +
189D MET 2.9 33.6 + - - -
191D SER* 5.2 0.4 - - - -
194D ILE* 3.7 13.9 - - - -
206D GLN* 3.1 27.6 - - - +
207D ILE 3.4 5.5 + - - -
209D GLY 2.9 23.3 + - - -
210D LEU* 4.3 5.2 - - - -
211D ILE* 5.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SER* 1.3 87.5 + - - +
113D LEU* 1.3 69.8 + - - +
114D TYR* 4.3 0.2 - - + -
120D ILE* 6.1 0.2 - - + -
122D SER 3.9 4.0 - - - +
123D ALA* 3.7 34.1 - - + +
126D LEU* 3.8 21.8 - - + -
186D ALA* 4.0 18.4 - - + -
187D LEU 3.6 4.9 - - - +
188D LEU* 3.7 18.6 - - + -
194D ILE* 3.8 3.3 - - - +
206D GLN* 3.2 8.7 - - - +
207D ILE* 2.8 62.2 + - + +
211D ILE* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 1.3 70.1 - - - +
114D TYR* 1.3 65.0 + - - +
177D ILE* 4.5 10.5 - - + -
180D VAL* 4.0 24.8 - - + +
186D ALA* 3.3 3.3 - - - +
187D LEU* 2.8 44.2 + - + +
189D MET* 3.9 27.4 - - + -
194D ILE* 4.1 11.6 - - + +
197D VAL* 4.0 21.1 - - + -
198D THR* 3.6 30.3 - - + -
204D LEU* 4.0 18.6 - - + -
205D THR 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 4.0 1.3 + - + -
113D LEU* 1.3 76.0 - - - +
115D ARG* 1.3 96.0 + - + +
118D THR* 3.5 34.5 - - + +
120D ILE* 4.3 8.5 - - + -
126D LEU* 5.9 0.2 - - + -
132D ILE* 3.2 37.3 - - + +
180D VAL* 4.1 4.7 - - + -
184D ASP* 2.6 29.8 + - - -
185D TYR 3.4 21.5 - - - -
186D ALA* 3.7 15.3 - - + -
204D LEU* 3.3 10.2 - - - +
205D THR* 2.8 33.4 + - - +
207D ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR* 1.3 113.2 - - + +
116D LYS* 1.3 66.5 + - - +
117D GLY 4.1 0.2 + - - -
118D THR* 3.7 16.2 + - + +
180D VAL* 4.5 8.0 + - - +
181D LEU 5.7 1.6 + - - -
182D THR 5.5 0.8 - - - -
183D THR 3.2 29.1 + - - +
184D ASP* 3.4 29.6 + - - +
203D ASN* 3.5 11.7 - - + +
204D LEU* 4.0 9.7 - - + +
205D THR* 3.8 7.9 - - - +
207D ILE* 4.3 2.9 - - - +
----------------------------------------------------------
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