Contacts of the strand formed by residues 145 - 148 (chain D) in PDB entry 2G4C
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 PHE 145 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.5 10.8 - - + -
148B VAL 3.8 3.1 - - - -
149B SER* 3.5 38.4 - - - -
144D ALA* 1.3 77.1 - - - +
146D ARG* 1.3 63.6 + - - +
147D LEU 3.8 0.7 + - - -
180D LYS* 3.1 6.4 - - - -
181D LEU* 3.0 49.4 + - + +
215D PHE* 4.3 19.7 + - + -
216D HIS 4.1 1.6 - - - -
217D PRO* 3.6 43.1 - - + -
229D LYS* 5.2 5.2 - - + -
230D SER 4.4 2.2 - - - -
231D ILE* 3.5 48.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG 3.6 0.2 - - - +
147B LEU* 4.0 0.6 - - - -
148B VAL 3.0 32.7 + - - +
150B ALA* 3.0 31.5 - - + +
153B LEU* 4.4 5.8 - - + -
138D LEU* 4.7 8.9 - - - +
139D LEU 3.6 22.4 + - - -
141D GLY 3.6 15.4 + - - +
144D ALA* 4.1 16.2 - - - +
145D PHE* 1.3 71.3 - - - +
147D LEU* 1.3 60.3 + - - +
148D VAL* 3.0 17.5 + - + +
175D LEU* 3.6 42.2 + - + +
178D SER* 2.9 33.8 + - - +
179D GLY 3.0 15.9 - - - -
180D LYS* 4.8 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 4.6 14.0 - - + +
146B ARG 3.7 4.0 - - - +
147B LEU* 3.0 36.3 - - + -
181B LEU* 3.7 17.0 - - + -
231B ILE* 4.1 17.9 - - + -
133D HIS* 3.7 38.6 - - + -
145D PHE 3.8 0.2 + - - -
146D ARG* 1.3 69.8 - - - +
148D VAL* 1.3 61.3 + - - +
149D SER* 3.9 3.3 + - - -
178D SER* 3.3 11.6 + - - -
179D GLY* 2.9 27.3 + - - +
180D LYS 4.6 0.7 - - - +
181D LEU* 3.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.3 7.0 - - - +
146B ARG* 3.0 31.8 + - + +
148B VAL* 3.0 36.8 - - + -
153B LEU* 5.0 3.6 - - + -
146D ARG* 3.0 12.3 + - + +
147D LEU* 1.3 73.9 - - - +
149D SER* 1.3 74.3 + - - +
153D LEU* 3.4 28.0 - - + -
170D PHE* 5.2 2.0 - - + -
174D VAL* 4.3 29.6 - - + -
178D SER* 4.4 1.8 - - - +
----------------------------------------------------------
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