Contacts of the helix formed by residues 163 - 173 (chain G) in PDB entry 3JSX
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 ASP 163 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E TRP* 5.0 1.6 + - - -
256E GLY 2.9 15.4 + - - +
258E HIS* 2.6 36.0 + - + +
155G TYR 3.9 5.4 - - - +
156G SER 3.9 2.5 + - - -
157G LEU* 3.2 25.2 - - + +
162G GLY* 1.3 70.7 - - - +
164G MET* 1.3 63.1 + - - +
165G ASN* 2.7 50.4 + - - +
166G VAL* 3.3 23.3 + - + +
167G ILE* 3.7 8.3 + - - +
263G ILE* 4.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 4.0 22.4 - - + -
146G ILE* 5.5 4.7 - - + -
148G THR* 5.0 3.8 - - - +
155G TYR* 3.1 37.9 + - + +
162G GLY 3.2 2.0 + - - -
163G ASP* 1.3 73.3 + - - +
165G ASN* 1.3 64.7 + - - +
166G VAL 3.2 0.2 - - - -
167G ILE* 3.2 27.4 + - - -
168G LEU* 3.1 38.3 + - + +
188G LEU* 4.5 11.2 - - + -
190G TYR* 3.4 41.3 - - + +
269G ILE* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G LEU* 4.9 3.4 - - - +
163G ASP* 2.7 33.6 + - - +
164G MET* 1.3 79.5 - - - +
166G VAL* 1.3 59.8 + - - +
168G LEU* 3.6 0.7 + - - -
169G TRP* 3.3 18.2 + - - +
255G VAL* 4.3 15.4 - - + +
263G ILE* 5.6 1.6 - - + -
266G ASP* 3.1 47.0 + - - +
267G ASN 4.4 0.4 - - - -
268G GLN* 3.3 32.9 + - + +
269G ILE* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E VAL* 4.3 9.5 - - + +
169E TRP* 3.0 44.9 - - + +
170E PRO* 4.4 1.0 - - + +
255E VAL* 3.8 31.0 - - + +
256E GLY* 5.1 0.7 - - - -
258E HIS* 4.5 0.2 - - + -
163G ASP* 3.3 19.9 + - + +
164G MET 3.2 0.4 - - - -
165G ASN* 1.3 77.7 - - + +
167G ILE* 1.3 65.3 + - - +
169G TRP* 3.4 3.8 + - - +
170G PRO* 3.1 19.8 - - - +
255G VAL* 4.0 21.5 - - + -
263G ILE* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E TRP* 4.7 11.9 - - - +
170E PRO* 4.2 14.1 - - + +
103G LEU* 4.6 8.3 - - + -
106G PHE* 3.3 62.2 - - + +
107G GLY* 5.2 0.2 - - - -
155G TYR* 3.7 26.0 - - + -
161G HIS 4.8 8.5 - - - +
163G ASP 4.1 12.6 - - - +
164G MET* 3.2 18.2 + - - +
166G VAL* 1.3 75.8 - - - +
168G LEU* 1.3 65.0 + - + +
170G PRO* 3.2 13.5 - - - +
171G ILE* 4.3 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G LEU* 3.8 28.5 - - + -
146G ILE* 4.0 18.2 - - + -
164G MET* 3.1 28.8 + - + +
165G ASN 3.7 7.4 - - - +
167G ILE* 1.3 77.2 - - + +
169G TRP* 1.3 54.1 + - - +
171G ILE* 2.7 33.0 + - + +
172G GLN* 2.9 29.0 + - - +
186G PRO* 4.0 11.4 - - + -
188G LEU* 4.2 6.7 - - + -
268G GLN* 3.9 11.9 - - + +
269G ILE* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E ILE 5.9 0.2 - - - -
161E HIS 4.1 20.5 + - - -
162E GLY* 5.1 0.6 - - - -
163E ASP 5.3 0.8 + - - -
166E VAL* 3.7 22.4 - - + +
167E ILE* 4.6 11.6 - - + +
165G ASN 3.3 11.5 + - - +
166G VAL 3.4 7.2 + - - +
168G LEU* 1.3 75.5 - - - +
170G PRO* 1.3 75.7 - - + +
173G SER* 2.9 56.0 + - - -
174G GLY 5.5 0.4 - - - +
222G PHE* 3.6 14.6 - + + -
254G SER* 3.4 26.5 - - - -
255G VAL* 3.9 13.5 - - + -
256G GLY* 3.3 36.2 - - - -
257G HIS* 4.5 12.3 - + - -
267G ASN* 4.2 0.4 - - - -
268G GLN* 3.4 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TRP 4.9 1.0 - - - +
106E PHE* 4.2 26.6 - - + +
166E VAL* 4.6 1.1 - - + +
167E ILE* 4.5 20.2 - - + +
170E PRO* 3.9 20.9 - - + -
166G VAL 3.1 18.6 - - - +
167G ILE 3.2 13.7 - - - +
169G TRP* 1.3 95.6 - - + +
171G ILE* 1.3 61.3 + - + +
174G GLY* 3.2 25.8 + - - +
175G ILE* 3.6 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G PHE* 5.0 4.7 - - + -
103G LEU* 5.4 2.9 - - + -
106G PHE 5.1 0.7 - - - +
107G GLY* 4.3 21.1 - - - -
108G VAL* 4.1 30.5 - - + +
116G PHE* 5.2 4.5 - - + -
144G LEU* 3.8 31.6 - - + -
146G ILE* 5.7 0.9 - - + -
167G ILE* 4.3 14.8 - - + +
168G LEU* 2.7 19.4 + - + +
170G PRO* 1.3 77.6 - - + +
172G GLN* 1.3 60.5 + - - +
173G SER 3.3 0.2 - - - -
175G ILE* 3.3 21.9 + - + +
176G LEU* 3.2 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G LEU* 3.6 27.5 - - + +
168G LEU* 2.9 19.9 + - - +
171G ILE* 1.3 76.6 - - - +
173G SER* 1.3 56.8 + - - +
176G LEU* 4.0 7.9 - - + -
177G HIS* 3.3 24.7 + - - +
183G VAL* 3.6 32.7 - - + +
184G LEU 4.0 2.0 + - - -
186G PRO* 3.3 32.9 - - - +
220G LEU* 3.5 3.9 - - - +
222G PHE* 3.3 9.9 - - + -
268G GLN* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E HIS 5.1 0.7 + - - -
132G TYR* 3.7 17.8 + - - -
169G TRP* 2.9 55.5 + - - -
172G GLN* 1.3 77.9 - - - +
174G GLY* 1.3 65.4 + - - -
175G ILE 3.3 1.9 + - - -
177G HIS* 3.6 4.1 + - - +
178G PHE* 3.0 25.3 + - - +
222G PHE* 3.7 15.8 - - - -
----------------------------------------------------------
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