Contacts of the strand formed by residues 209 - 217 (chain X) in PDB entry 5GJQ
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 209 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X GLU* 3.7 17.0 - - + -
51X LYS 3.6 11.4 - - - +
52X LEU* 4.0 17.5 - - + -
53X VAL* 4.2 5.8 - - - +
197X ILE* 3.8 23.3 - - + -
198X TYR* 3.7 46.2 - + - -
201X HIS* 3.3 36.1 - + + -
208X ALA* 1.3 79.5 - - - +
210X GLU* 1.3 70.6 + - - +
211X LEU* 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X VAL 3.4 0.9 - - - +
51X LYS* 2.9 66.9 + - - +
53X VAL* 4.2 16.3 - - + +
59X GLU 4.4 3.8 - - - +
60X GLU* 3.3 34.7 - - + +
61X GLY* 3.3 14.4 + - - -
62X SER 5.4 0.2 - - - +
209X PHE* 1.3 79.3 - - - +
211X LEU* 1.3 67.2 + - - +
212X GLU* 5.6 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X VAL 3.6 14.4 - - - +
194X ALA* 3.7 31.9 - - + -
197X ILE* 3.8 34.8 - - + -
198X TYR* 4.5 9.2 - - + +
209X PHE* 4.3 9.6 - - + -
210X GLU* 1.3 79.7 - - - +
212X GLU* 1.3 69.4 + - - +
213X LEU* 4.0 19.3 - - + -
232X ARG* 3.9 20.1 - - - -
236X GLU* 4.0 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X GLY* 3.2 5.9 - - - -
49X VAL* 2.8 41.9 + - + +
51X LYS* 3.5 35.6 - - - +
64X LYS* 3.4 28.6 - - - +
65X ARG* 3.0 28.8 + - - +
66X LEU* 3.7 24.4 + - + +
210X GLU* 3.8 1.5 + - - +
211X LEU* 1.3 75.9 - - - +
213X LEU* 1.3 65.7 + - - +
226X ILE* 5.9 6.6 - - + +
232X ARG* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X VAL* 5.2 2.7 - - + -
47X PHE 3.2 11.0 - - - +
48X GLY* 4.0 0.9 - - - -
66X LEU* 3.8 2.2 - - - +
190X VAL* 4.0 21.8 - - + -
193X VAL* 3.9 24.7 - - + -
194X ALA* 4.7 2.0 - - + +
211X LEU* 4.0 30.0 + - + +
212X GLU* 1.3 87.2 - - - +
214X SER* 1.3 63.4 + - - +
226X ILE* 3.8 11.2 - - - +
227X VAL* 3.2 34.6 + - + +
232X ARG* 4.0 41.2 + - + +
235X ALA* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X VAL 3.8 0.3 - - - +
46X VAL* 3.3 11.7 - - - +
47X PHE* 2.9 43.1 + - - -
66X LEU* 3.2 25.9 - - - +
213X LEU* 1.3 73.3 + - - +
215X TRP* 1.3 58.8 + - - +
224X HIS* 3.3 34.7 + - - -
225X GLU 3.5 7.1 + - - -
226X ILE* 4.6 1.7 - - - +
227X VAL* 3.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X VAL 4.0 1.1 - - - -
46X VAL* 4.5 3.4 - - + -
186X CYS* 3.3 42.8 - - + -
187X ARG* 3.8 24.5 - - - -
190X VAL* 3.5 23.6 - - + -
214X SER* 1.3 73.9 - - - +
216X VAL* 1.3 67.5 + - - +
217X GLY 5.2 0.2 - - - +
219X LEU* 3.9 30.7 - - + -
220X THR* 3.9 23.1 - - + -
224X HIS* 3.1 7.6 - - - -
225X GLU* 2.9 32.5 + - - +
226X ILE 3.6 9.2 - - - -
227X VAL* 3.3 31.5 - - + +
228X PRO* 3.2 22.6 - - + +
231X ILE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X GLY* 3.2 2.4 - - - -
45X VAL* 2.8 57.9 + - + +
47X PHE* 5.0 2.2 - - + -
72X HIS 3.9 15.0 - - - +
138X GLY* 4.2 14.6 - - - -
139X SER* 4.0 1.3 - - - +
140X TYR* 3.7 24.2 - - + +
186X CYS* 5.3 2.0 - - - -
215X TRP* 1.3 79.6 - - - +
217X GLY* 1.3 60.7 + - - +
220X THR* 3.9 5.4 - - - -
222X GLY 4.1 9.4 - - - +
224X HIS* 3.7 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X ASP 3.5 12.1 - - - -
44X GLY* 3.8 0.4 - - - -
140X TYR* 3.5 20.2 - - - +
186X CYS* 5.0 2.2 - - - -
215X TRP* 5.2 0.2 - - - +
216X VAL* 1.3 78.8 - - - +
218X GLU* 1.3 60.4 + - - -
219X LEU* 3.1 4.7 - - - +
220X THR* 2.8 30.1 + - - +
222X GLY* 3.1 12.6 + - - -
----------------------------------------------------------
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