Contacts of the strand formed by residues 207 - 217 (chain A) 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 GLY 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN 3.1 7.1 + - - +
125A VAL* 3.3 5.0 - - - -
126A PHE 2.9 22.5 + - - -
206A TYR* 1.3 79.5 - - - +
208A LEU* 1.3 69.8 - - - +
239A LEU* 4.0 4.5 - - - -
240A VAL 3.1 12.1 - - - -
241A TRP* 3.2 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 3.3 24.9 - - + +
128A VAL* 4.4 17.5 - - + +
189A ALA* 3.7 32.3 - - + +
192A HIS* 3.8 17.5 - - + -
193A TYR 4.3 2.0 - - - +
196A CYS* 4.0 24.0 - - + -
206A TYR* 4.0 9.0 - - + -
207A GLY* 1.3 82.5 - - - +
209A ALA* 1.3 62.1 + - - +
210A GLN* 5.0 0.9 - - - +
238A SER 3.6 3.1 - - - +
239A LEU* 4.1 1.1 - - - +
240A VAL* 3.1 29.5 + - - +
242A PHE* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 3.9 11.0 - - + -
115A TRP* 3.8 11.8 - - + -
119A VAL* 3.2 35.2 - - + -
125A VAL* 3.6 10.5 - - + +
126A PHE 2.9 7.0 + - - +
127A PRO* 3.4 5.0 - - - +
128A VAL* 3.3 24.1 + - - +
208A LEU* 1.3 72.4 - - - +
210A GLN* 1.3 63.5 + - - +
238A SER 3.2 5.2 - - - -
239A LEU* 4.3 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 4.7 0.6 - - - -
115A TRP* 4.3 3.5 - - - -
128A VAL* 3.9 29.3 - - + +
129A ASP* 4.5 0.9 - - - +
130A ALA* 3.2 35.8 + - - +
182A ARG* 3.6 11.9 + - - +
185A LEU* 3.2 48.5 + - + +
189A ALA* 4.4 5.3 - - - +
208A LEU 5.0 0.9 - - - +
209A ALA* 1.3 77.0 - - - +
211A ILE* 1.3 65.6 + - - +
212A GLY* 5.7 0.2 - - - -
237A ALA* 3.5 0.7 - - - -
238A SER* 2.6 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 3.7 34.3 - - + +
114A TRP* 3.5 30.5 - - + -
115A TRP* 3.9 15.8 - - + -
185A LEU* 4.1 0.9 - - - -
210A GLN* 1.3 77.7 - - - +
212A GLY* 1.3 60.6 + - - +
235A THR* 4.1 8.5 - - + -
236A GLU 3.2 6.7 - - - +
237A ALA* 3.6 20.2 - - + -
342A LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A HIS* 5.9 0.9 - - - -
182A ARG* 4.0 11.0 - - - -
185A LEU* 3.6 7.9 - - - +
210A GLN* 5.7 0.2 - - - -
211A ILE* 1.3 78.6 - - - +
213A VAL* 1.3 63.7 + - - -
214A CYS* 3.8 2.6 + - - -
235A THR* 4.0 4.0 - - - -
236A GLU* 2.6 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 5.7 0.4 - - - +
132A HIS* 4.3 8.0 + - + +
182A ARG* 2.6 33.4 + - - +
212A GLY* 1.3 73.6 - - - -
214A CYS* 1.3 65.0 + - - +
215A PHE* 4.2 14.1 - - + -
233A GLU* 3.9 23.6 - - + +
234A LYS 3.0 10.3 - - - +
235A THR* 3.7 17.3 - - - +
132C HIS* 3.4 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 3.9 15.5 - - - +
183A GLU 3.9 3.4 - - - +
184A ASN* 3.9 18.4 - - - -
185A LEU* 4.0 16.4 - - - -
212A GLY 4.1 1.1 - - - -
213A VAL* 1.3 82.7 - - - +
215A PHE* 1.3 66.9 + - - +
216A HIS* 3.7 11.6 + - + +
232A GLY 3.5 3.3 - - - +
233A GLU* 3.5 0.5 - - - -
234A LYS* 2.6 37.1 + - - +
236A GLU* 3.3 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A HIS* 4.2 20.9 - + + -
181A LEU* 3.5 54.8 - - + +
182A ARG* 3.2 19.2 + - + +
183A GLU* 3.8 6.4 - - - +
213A VAL* 4.2 19.3 - - + -
214A CYS* 1.3 70.5 - - - +
216A HIS* 1.3 69.2 + - - +
217A PRO* 4.2 3.5 - - - +
231A ILE* 4.2 12.3 - - + -
232A GLY 3.2 7.0 - - - +
233A GLU* 3.5 41.3 - - + -
132C HIS* 3.6 27.8 - + + -
133C HIS* 5.0 4.9 - + - -
147C LEU* 6.2 0.2 - - + -
181C LEU* 5.4 2.2 - - + -
215C PHE* 5.1 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER 4.9 0.5 - - - +
183A GLU* 2.8 50.4 + - - +
214A CYS* 3.7 6.3 - - + +
215A PHE* 1.3 83.9 - - - +
217A PRO* 1.3 66.8 - - + +
218A VAL* 3.9 2.3 + - - +
231A ILE* 4.6 1.8 - - - -
232A GLY* 2.7 39.7 + - - +
234A LYS* 3.6 31.5 - - + +
236A GLU* 3.3 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER 5.5 6.7 - - - +
144A ALA* 5.6 10.5 - - + -
145A PHE* 4.4 13.9 - - + -
183A GLU* 4.7 5.8 - - - +
215A PHE 4.2 4.7 - - - +
216A HIS* 1.3 88.9 - - + +
218A VAL* 1.3 60.7 + - - +
229A LYS* 4.0 20.4 - - + -
230A SER 3.7 8.5 - - - +
231A ILE* 4.6 3.8 - - + -
151C GLU* 5.6 1.1 - - - +
----------------------------------------------------------
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