Contacts of the strand formed by residues 192 - 199 (chain f) 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 ALA 192 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26f ASP* 3.2 6.8 - - - -
27f THR* 3.2 42.0 + - + +
38f ARG 4.9 1.3 - - - +
190f GLY 2.8 7.7 + - - +
191f ASP* 1.3 78.6 - - - +
193f LEU* 1.3 62.1 + - - +
207f THR* 4.8 9.9 - - + -
208f VAL 3.6 11.9 - - - +
209f SER* 5.0 1.3 - - - -
210f LEU* 3.5 9.5 - - - +
212f LYS* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24f ALA* 4.1 6.1 - - + -
25f SER 3.4 22.0 - - - +
27f THR* 4.5 2.0 - - - -
175f VAL* 4.9 0.2 - - + -
176f LYS* 4.4 12.8 - - - +
179f PHE* 3.7 46.7 - - + -
180f ILE* 6.2 0.2 - - + -
192f ALA* 1.3 78.1 - - - +
194f ARG* 1.3 67.0 + - - +
195f ILE* 4.0 22.4 - - + -
206f GLU 3.7 0.9 - - - +
207f THR* 3.4 7.1 - - - +
208f VAL* 2.9 48.7 + - + +
210f LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23f VAL 4.1 0.9 - - - +
24f ALA* 3.2 3.5 - - - +
25f SER* 2.9 46.6 + - - +
27f THR* 4.3 14.3 - - + +
39f ASP* 4.4 14.3 + - - -
41f PRO* 3.9 32.8 - - + +
43f CYS* 4.6 2.9 - - + -
193f LEU* 1.3 73.5 - - - +
195f ILE* 1.3 64.4 + - - +
196f CYS* 4.1 15.7 - - - -
205f GLU* 4.0 32.7 + - + +
206f GLU 3.4 7.2 - - - +
207f THR* 3.5 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22f ILE* 3.6 27.1 - - + -
23f VAL 4.0 1.8 - - - -
24f ALA* 4.1 9.2 - - + -
172f MET* 3.9 35.9 - - + -
175f VAL* 3.9 17.5 - - + -
176f LYS* 4.1 24.2 - - + -
193f LEU* 4.0 19.1 - - + -
194f ARG* 1.3 79.4 - - - +
196f CYS* 1.3 64.5 + - - +
197f ILE* 4.1 5.9 - - + +
204f ARG 3.5 0.9 - - - +
205f GLU* 3.3 5.5 - - - +
206f GLU* 2.9 37.7 + - + +
208f VAL* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21f ALA 3.6 1.7 - - - +
22f ILE* 3.5 2.9 - - - -
23f VAL* 2.9 50.2 + - + +
43f CYS* 3.8 26.0 - - - -
51f VAL* 4.7 10.3 - - + -
194f ARG* 4.1 9.0 - - - -
195f ILE* 1.3 77.9 - - - +
197f ILE* 1.3 62.4 + - - +
198f VAL* 4.0 1.6 + - - +
203f ILE* 4.1 14.4 - - + -
204f ARG 3.2 7.0 - - - +
205f GLU* 3.9 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20f PHE* 4.4 10.3 - - + -
21f ALA 3.7 2.7 - - - +
22f ILE* 4.1 12.6 - - + +
168f LEU* 3.8 24.5 - - + -
172f MET* 3.7 31.6 - - + -
195f ILE* 4.1 13.2 - - + +
196f CYS* 1.3 77.7 - - - +
198f VAL* 1.3 63.9 - - - +
199f THR* 4.4 9.1 + - + -
202f GLY 3.4 2.3 - - - +
203f ILE* 3.2 7.1 - - - -
204f ARG* 2.9 81.7 + - + +
206f GLU* 4.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20f PHE* 3.1 8.7 - - - -
21f ALA* 2.9 39.6 + - + +
23f VAL* 5.0 2.5 - - + -
48f ASP 4.9 1.1 - - - +
49f LYS* 3.7 28.5 - - - +
51f VAL* 3.8 30.1 - - + +
111f GLY 4.4 7.2 - - - +
112f GLY* 4.0 6.5 - - - -
113f LEU* 3.9 18.6 - - + +
196f CYS 4.5 3.4 - - - +
197f ILE* 1.3 79.6 - - - +
199f THR* 1.3 64.5 + - - +
202f GLY 3.6 3.4 - - - +
203f ILE* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19f ASP* 3.5 26.0 - - - +
20f PHE* 3.6 13.2 - - + -
48f ASP 4.7 2.8 - - - +
49f LYS* 6.0 0.2 - - - +
113f LEU* 3.6 16.4 - - - +
168f LEU* 5.0 9.0 - - + -
197f ILE* 4.4 10.9 + - + -
198f VAL* 1.3 81.9 - - - +
200f LYS* 1.3 67.4 + - - +
201f GLU* 3.1 26.4 + - - +
202f GLY* 3.0 23.4 + - - +
204f ARG* 5.2 9.2 - - - +
----------------------------------------------------------
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