Contacts of the helix formed by residues 163 - 179 (chain G) in PDB entry 1SMK
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 PRO 163 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG 6.2 0.7 - - - +
133G LEU* 5.0 5.4 - - + -
134G PHE* 4.1 36.6 - - + +
137G ASN* 4.9 2.5 - - + -
161G SER 3.4 1.8 - - - -
162G ASN* 1.3 94.6 - - - +
164G VAL* 1.3 63.3 + - - +
165G ASN* 3.2 7.0 - - + +
166G SER* 3.0 12.0 + - - +
167G THR* 2.8 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G LEU 4.2 1.8 - - - +
160G ILE* 3.3 31.0 - - + +
161G SER 3.3 2.1 + - - +
162G ASN* 3.6 2.4 - - - +
163G PRO* 1.3 71.6 - - - +
165G ASN* 1.3 59.0 + - - +
166G SER 2.8 6.8 + - - -
167G THR* 3.1 8.3 - - - +
168G VAL* 3.2 42.1 + - + +
188G GLY* 3.7 19.5 - - - -
189G VAL 4.0 8.7 - - - +
190G THR* 4.9 0.2 - - + -
220G HIS* 3.4 35.4 - - + +
297G PHE* 3.8 10.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
163G PRO* 3.2 5.1 - - + -
164G VAL* 1.3 77.0 - - - +
166G SER* 1.3 60.5 + - - +
169G PRO* 3.8 10.3 - - - +
219G GLY* 3.0 10.0 - - - -
220G HIS* 2.6 22.2 + - - +
221G ALA* 2.8 46.3 - - + +
224G THR* 3.2 10.1 + - - +
297G PHE* 3.9 16.9 - - - -
343G LEU* 3.5 13.3 - - + +
346G SER* 3.5 27.0 + - - +
347G ILE* 3.7 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 3.8 25.2 - - - -
163G PRO* 3.0 13.8 + - - +
164G VAL 2.8 1.6 + - - -
165G ASN* 1.3 78.3 - - - +
167G THR* 1.3 62.1 + - - +
169G PRO* 2.9 20.3 - - - +
170G ILE* 3.0 19.2 + - - +
346G SER* 2.9 37.4 + - - -
349G LYS* 4.3 6.6 - - - +
350G GLY* 3.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 5.8 0.4 - - + -
137G ASN* 5.0 4.0 - - + +
138G ALA* 5.6 0.2 - - - -
141G VAL* 3.8 27.5 - - + +
159G LEU* 3.7 13.6 - - - +
161G SER 2.9 27.7 + - - +
162G ASN 4.0 1.8 - - - +
163G PRO* 2.8 38.3 + - + +
164G VAL* 3.1 8.0 - - - -
166G SER* 1.3 71.1 - - - +
168G VAL* 1.3 59.8 + - - +
170G ILE* 3.1 18.5 + - + +
171G ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G LEU* 4.0 12.6 - - + -
164G VAL* 3.2 34.7 + - + +
167G THR* 1.3 82.3 + - - +
169G PRO* 1.3 70.2 - - + +
171G ALA* 3.1 5.8 + - - +
172G ALA* 3.0 18.2 + - - +
186G LEU* 3.7 20.3 - - + +
187G LEU 4.9 0.2 - - - -
188G GLY* 3.5 17.7 - - - -
297G PHE* 3.6 19.7 - - + +
298G VAL* 5.3 0.9 - - - -
307G PHE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G VAL 4.0 0.4 - - - +
165G ASN 3.8 13.9 - - - +
166G SER* 2.9 25.8 - - - +
168G VAL* 1.3 86.8 - - + +
170G ILE* 1.3 64.8 + - - +
172G ALA* 3.2 3.3 + - - +
173G GLU* 3.0 28.3 + - - +
297G PHE* 4.3 2.0 - - + -
307G PHE* 3.8 37.9 - - + -
347G ILE* 4.0 29.4 - - + +
351G VAL* 4.0 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 3.9 29.2 - - + -
138G ALA* 4.2 24.0 - - + +
141G VAL* 4.4 11.2 - - + -
142G LYS 4.7 1.6 - - - +
166G SER 3.0 21.0 + - - +
167G THR* 3.2 19.3 - - + +
169G PRO* 1.3 76.7 - - - +
171G ALA* 1.3 64.9 - - - +
173G GLU* 3.1 5.0 + - - +
174G VAL* 2.9 28.8 + - + +
350G GLY* 3.7 20.4 - - - +
353G PHE* 4.3 7.0 - - + -
354G ILE* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G CYS* 3.3 32.5 - - - -
159G LEU* 4.1 10.1 - - + -
167G THR 2.9 11.4 + - - +
168G VAL 3.3 9.2 - - - +
170G ILE* 1.3 76.6 - - - +
172G ALA* 1.3 64.3 + - - +
174G VAL* 2.8 16.8 + - - +
175G PHE* 2.9 21.8 + - + -
186G LEU* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G VAL 3.0 9.1 + - - +
169G PRO 3.5 5.2 - - - +
171G ALA* 1.3 75.7 - - - +
173G GLU* 1.3 58.5 + - - +
175G PHE* 3.3 4.8 + - - +
176G LYS* 3.0 37.1 + - - +
181G TYR* 3.5 31.4 - - + -
186G LEU* 4.0 4.4 - - + +
307G PHE* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G PRO 3.0 16.9 + - - +
170G ILE 3.4 5.6 - - - +
172G ALA* 1.3 73.8 - - - +
174G VAL* 1.3 66.0 + - - +
175G PHE 3.1 2.0 - - - -
176G LYS* 2.6 43.9 + - - +
177G LYS* 3.1 26.7 + - - +
307G PHE* 5.7 1.9 - - - -
351G VAL* 3.6 42.8 - - + +
354G ILE* 3.4 25.0 - - + +
355G ARG* 2.8 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G LYS* 4.3 9.9 - - + -
145G CYS* 3.8 28.9 - - + +
146G GLU* 3.9 28.5 - - + +
149G ALA* 5.5 0.4 - - + -
170G ILE* 2.9 22.4 + - + +
171G ALA* 2.8 11.0 + - - +
173G GLU* 1.3 75.9 - - - +
175G PHE* 1.3 57.0 + - - +
177G LYS* 4.3 4.0 - - - +
178G ALA* 3.1 25.9 + - + +
354G ILE* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G CYS* 3.1 44.2 - - + -
148G ILE* 3.9 18.6 - - + -
149G ALA* 3.5 25.4 - - + -
157G VAL* 4.6 10.8 - - + -
171G ALA* 2.9 26.4 + - + -
172G ALA* 3.6 3.4 - - - +
173G GLU 3.1 0.2 - - - -
174G VAL* 1.3 80.1 - - - +
176G LYS* 1.3 55.1 + - - +
178G ALA* 3.4 4.0 - - - -
179G GLY 2.6 26.9 + - - -
180G THR* 2.8 19.6 + - - +
181G TYR* 3.3 37.7 + + + +
182G ASP 5.3 0.9 - - - -
186G LEU* 4.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G ALA* 3.0 28.2 + - - +
173G GLU* 2.6 44.5 + - - +
175G PHE* 1.3 77.1 - - - +
177G LYS* 1.3 60.3 + - - +
179G GLY* 2.8 20.6 + - - -
181G TYR* 4.1 30.7 - - + -
307G PHE* 5.9 4.1 - - - -
355G ARG* 4.4 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G GLU 3.1 12.5 + - - +
174G VAL* 4.4 4.7 - - - +
176G LYS* 1.3 80.5 - - - +
178G ALA* 1.3 57.6 + - - +
354G ILE* 5.0 20.9 + - + +
355G ARG* 6.1 1.4 - - - +
356G SER 5.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ALA* 3.7 27.1 - - + -
174G VAL* 3.1 20.2 + - + +
175G PHE 3.7 4.0 - - - +
176G LYS 3.0 0.4 - - - -
177G LYS* 1.3 78.3 - - - +
179G GLY* 1.3 62.4 + - - +
180G THR* 3.3 9.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175G PHE 2.6 12.4 + - - -
176G LYS* 2.8 12.9 + - - -
177G LYS 3.7 0.2 + - - -
178G ALA* 1.3 76.5 - - - +
180G THR* 1.3 58.3 + - - +
181G TYR* 3.6 2.7 - - - -
----------------------------------------------------------
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