Contacts of the strand formed by residues 173 - 183 (chain C) in PDB entry 2JG8
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 GLN 173 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A CYS 3.7 5.4 - - - -
169A ASP* 3.4 16.8 + - - +
171A THR* 3.6 15.0 + - - +
177A GLN* 3.3 25.7 + - - +
178B PHE 5.5 0.3 - - - +
179B GLN* 5.6 5.1 - - - +
1224B CA 4.1 5.1 - - - -
145C SER* 3.5 4.0 - - - -
146C HIS* 3.1 49.0 + - + +
166C GLY* 5.8 0.5 - - - -
167C HIS 3.2 24.3 + - - +
168C THR* 3.4 16.3 - - - +
171C THR 3.9 0.4 + - - -
172C ASN* 1.3 80.2 + - - +
174C VAL* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 4.1 5.6 - - + -
168A CYS 3.6 29.1 + - - +
169A ASP* 4.7 2.4 + - - +
178A VAL 5.2 6.3 + - - +
179A VAL* 4.1 9.8 - - + +
180A SER* 3.5 41.6 + - - +
180B VAL* 4.3 11.6 - - - +
143C HIS* 3.8 23.1 - - + +
144C ALA 3.4 9.4 - - - +
145C SER* 4.2 11.2 - - - +
146C HIS* 4.1 2.7 - - - -
173C GLN* 1.3 76.5 - - - +
175C ASN* 1.3 64.5 + - - +
176C SER* 3.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.7 13.4 - - + +
142C TYR* 2.7 32.5 + - + -
143C HIS* 3.5 0.3 - - - -
144C ALA 2.7 40.4 + - - +
146C HIS* 3.7 19.3 - - + +
150C LEU* 3.2 27.5 + - + -
152C VAL* 4.1 7.0 - - - +
164C PHE* 2.9 28.0 + - - +
166C GLY 3.6 5.2 - - - +
174C VAL* 1.3 71.5 - - - +
176C SER* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 3.9 8.5 + - - -
146B HIS* 3.2 17.4 + - - -
180B VAL* 3.4 25.7 + - - +
181B THR 4.5 4.7 + - - -
182B THR* 3.3 16.4 - - - +
142C TYR* 3.4 12.9 + - - -
143C HIS* 3.7 28.3 - - - -
164C PHE* 3.8 2.1 - - - +
174C VAL* 3.8 3.5 + - - -
175C ASN* 1.3 82.4 + - - +
177C GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS* 3.4 14.0 - - - -
141C VAL* 3.3 4.5 - - - +
142C TYR* 3.0 51.7 + - - -
164C PHE* 3.7 12.6 - - - -
176C SER* 1.3 78.4 - - - +
178C GLY* 1.3 58.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS* 3.3 14.9 + - - -
214B ILE* 3.4 23.7 - - - +
216B SER* 4.7 2.3 + - - -
139C TYR* 4.6 5.2 - - - -
140C PHE 3.1 13.9 - - - -
141C VAL* 4.0 4.0 - - - -
142C TYR* 5.4 0.2 - - - -
154C LEU* 6.0 2.2 - - - -
162C VAL* 5.1 1.9 - - - +
164C PHE* 4.0 7.7 - - - -
177C GLY* 1.3 74.6 - - - -
179C VAL* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER* 4.0 9.4 - - - +
119B ILE* 4.1 14.8 - - + -
214B ILE* 3.9 19.7 - - + -
216B SER* 4.6 2.0 - - - -
138C TYR 4.0 0.3 - - - +
139C TYR* 3.7 6.5 - - - -
140C PHE* 3.0 31.0 + - + +
154C LEU* 4.1 23.8 - - + -
161C VAL* 4.2 3.6 - - + -
162C VAL* 4.2 13.5 - - + -
178C GLY* 1.3 76.8 - - - +
180C LEU* 1.3 76.2 + - - +
181C LEU* 4.1 28.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.8 13.0 - - + -
97B PHE 3.3 25.1 - - - +
98B SER* 2.9 15.1 + - - +
119B ILE* 4.3 0.3 - - - +
120B THR* 2.8 27.5 + - + -
216B SER* 4.1 5.4 - - - -
217B GLY 3.4 18.2 - - - +
218B PHE* 3.8 10.8 - - + -
137C LEU* 4.0 13.5 - - + -
138C TYR 3.2 7.0 - - - +
139C TYR* 3.5 38.6 - - + -
179C VAL* 1.3 76.5 - - - +
181C LEU* 1.3 65.7 + - - +
214C LEU* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.8 22.2 - - + -
120B THR* 4.0 2.9 - - - +
137C LEU* 3.9 4.7 - - - -
138C TYR* 2.8 36.4 + - - +
140C PHE* 4.0 25.6 - - + -
154C LEU* 4.1 23.3 - - + -
156C ARG* 4.2 35.4 - - + +
161C VAL* 4.2 9.0 - - + -
179C VAL* 4.1 12.8 - - + -
180C LEU* 1.3 83.4 - - - +
182C ARG* 1.3 60.9 + - - +
183C LEU* 3.6 15.7 + - + +
189C VAL* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 4.2 7.9 - - - +
120B THR* 4.5 5.6 + - + -
122B MET* 3.6 37.4 - - + +
136C GLY* 3.4 15.7 - - - +
137C LEU* 3.9 13.2 - - + +
156C ARG* 2.9 25.7 + - - +
181C LEU* 1.3 70.0 - - - +
183C LEU* 1.3 62.7 + - - +
184C GLN* 4.4 4.0 + - - -
217C ASP* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.7 29.8 - - + -
132C CYS* 4.2 13.5 - - + -
135C PRO* 3.4 5.7 - - - +
136C GLY* 2.8 37.1 + - - +
138C TYR* 3.8 11.7 - - + -
140C PHE* 3.7 21.1 - - + -
156C ARG* 3.5 39.9 - - + +
181C LEU* 4.1 14.1 - - + +
182C ARG* 1.3 76.1 - - - +
184C GLN* 1.3 63.0 + - - +
187C GLU* 3.4 12.8 - - + +
189C VAL* 3.9 8.1 - - + -
217C ASP* 5.1 0.2 - - - +
----------------------------------------------------------
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