Contacts of the strand formed by residues 110 - 115 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.6 0.2 - - - +
109B GLY* 1.3 72.3 - - - -
111B SER* 1.3 72.5 + - - +
142B THR* 3.7 34.3 - - + +
145B PHE* 3.6 36.8 - - + -
146B PHE* 4.4 0.9 - - + -
188B LEU* 4.1 11.2 - - + -
189B MET 3.4 8.1 - - - +
190B GLU* 4.4 2.2 - - + +
210B LEU* 3.3 2.4 - - - -
211B ILE* 2.8 52.5 + - + +
212B ASP* 2.8 19.3 + - - +
214B LYS* 3.5 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY 3.6 1.5 + - - -
110B ILE* 1.3 76.4 - - - +
112B ILE* 1.3 71.6 + - - +
188B LEU* 3.4 9.3 - - - +
189B MET 2.7 32.2 + - - -
191B SER* 5.2 0.4 - - - -
194B ILE* 3.8 8.5 - - - -
206B GLN* 3.1 34.5 - - - +
207B ILE 3.4 5.5 + - - -
209B GLY 2.9 22.7 + - - -
210B LEU* 4.3 5.2 - - - -
211B ILE* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 1.3 86.2 + - - +
113B LEU* 1.3 68.1 + - - +
114B TYR* 4.4 0.2 - - + -
120B ILE* 5.9 0.2 - - + -
122B SER 4.0 3.4 - - - -
123B ALA* 3.6 41.1 - - + +
126B LEU* 3.9 25.6 - - + -
157B MET* 5.2 0.2 - - + -
186B ALA* 4.0 8.5 - - + -
187B LEU 3.6 4.3 - - - +
188B LEU* 3.7 20.6 - - + -
194B ILE* 3.9 3.6 - - - -
206B GLN* 3.2 8.5 - - - +
207B ILE* 2.8 61.3 + - + +
211B ILE* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 1.3 70.8 - - - +
114B TYR* 1.3 61.0 + - - +
177B ILE* 4.4 11.0 - - + -
180B VAL* 4.0 21.2 - - + +
186B ALA* 3.3 6.2 - - - +
187B LEU* 2.8 36.3 + - + +
189B MET* 3.6 32.8 - - + -
194B ILE* 4.1 11.3 - - + +
197B VAL* 4.0 22.7 - - + -
198B THR* 3.6 30.1 - - + -
204B LEU* 4.0 23.3 - - + -
205B THR 3.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.0 0.6 + - + -
113B LEU* 1.3 75.7 - - - +
115B ARG* 1.3 104.7 + - - +
118B THR* 3.4 30.6 - - + +
120B ILE* 3.8 22.4 - - + -
126B LEU* 5.5 0.4 - - + -
132B ILE* 3.4 30.0 - - + +
180B VAL* 4.1 4.7 - - + -
184B ASP* 2.7 23.0 + - - -
185B TYR 3.4 22.4 - - - -
186B ALA* 3.7 14.1 - - + -
204B LEU* 3.4 9.2 - - - +
205B THR* 2.8 32.0 + - - +
207B ILE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 1.3 114.8 + - + +
116B LYS* 1.3 66.2 + - - +
118B THR* 3.8 23.6 + - + +
180B VAL* 4.4 8.0 + - - +
183B THR 4.3 5.5 + - - -
184B ASP* 2.8 47.6 + - - +
185B TYR 5.2 0.2 + - - -
203B ASN* 3.5 13.0 - - + +
204B LEU* 3.9 12.0 - - + +
205B THR* 4.0 6.3 - - - +
207B ILE* 4.4 2.8 - - - +
----------------------------------------------------------
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