Contacts of the helix formed by residues 231 - 243 (chain G) in PDB entry 1SGF
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 LEU 231 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LEU* 3.9 16.8 - - + -
103G LEU* 3.6 33.7 - - + -
123G LEU* 5.2 5.8 - - + -
124G PRO* 4.3 12.8 - - + -
209G LEU* 3.8 27.1 - - + -
210G GLN 3.0 15.0 + - - +
211G GLY* 3.7 31.4 - - - +
212G ILE* 4.2 8.5 - - + -
229G THR* 3.0 9.5 + - + +
230G LYS* 1.3 68.1 - - - +
232G ASN* 1.3 65.9 + - - +
233G LYS 3.2 2.7 - - - -
234G PHE* 3.0 16.8 + - + +
235G THR* 3.3 15.7 + - + +
238G ILE* 5.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 232 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G PRO* 4.5 14.7 + - + +
125G THR* 4.4 8.2 + - - +
128G GLU 3.0 27.2 + - - +
129G GLU* 3.7 26.7 - - + +
130G PRO* 5.0 4.0 - - + -
210G GLN* 4.4 11.0 + - - +
230G LYS* 3.3 13.9 - - + +
231G LEU* 1.3 78.0 - - - +
233G LYS* 1.3 58.3 + - - +
234G PHE 3.0 2.0 + - - -
235G THR* 3.0 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASN* 6.0 1.1 - - - -
178G ASP* 3.0 57.3 + - - +
179G ALA* 4.4 10.3 - - + +
230G LYS* 3.7 22.3 + - + +
231G LEU 3.2 1.4 - - - -
232G ASN* 1.3 77.3 - - - +
234G PHE* 1.3 75.4 + - + +
235G THR 3.9 0.2 - - - -
236G SER 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G HIS* 3.5 32.8 - + - -
101G ASN* 3.2 37.7 - - + -
103G LEU* 3.6 26.0 - - + -
179G ALA* 3.7 26.9 - - + -
229G THR* 4.2 15.0 - - + -
230G LYS 3.2 27.4 - - - -
231G LEU* 3.0 9.4 + - + +
233G LYS* 1.3 94.3 - - + +
235G THR* 1.3 57.0 + - - +
236G SER 3.0 5.6 - - - -
237G TRP* 2.8 26.9 + - + +
238G ILE* 3.2 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G LEU* 4.0 19.1 - - + +
124G PRO* 3.5 46.3 + - + +
231G LEU* 3.3 9.2 + - + +
232G ASN* 3.0 21.4 + - - +
234G PHE* 1.3 74.1 - - - +
236G SER* 1.3 62.3 + - - +
238G ILE* 4.0 9.8 + - + +
239G LYS* 3.7 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233G LYS 5.6 0.4 - - - -
234G PHE 2.9 1.6 + - - -
235G THR* 1.3 80.4 + - - +
237G TRP* 1.3 64.7 + - - +
238G ILE 3.3 0.2 - - - -
239G LYS* 3.8 2.2 + - - +
240G ASP* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ILE* 3.3 41.7 - - + +
90G PRO 3.9 1.1 - - - -
91G HIS* 3.7 50.1 - + + +
92G PRO* 4.1 12.3 - - + +
103G LEU* 3.7 28.0 - - + -
105G LEU* 4.1 19.1 - - + -
234G PHE* 2.8 13.4 + - + +
236G SER* 1.3 77.4 - - - +
238G ILE* 1.3 77.9 + - + +
240G ASP* 3.5 4.6 + - + +
241G THR* 2.8 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G LEU* 4.1 10.8 - - + -
53G LEU* 4.6 16.6 - - + -
103G LEU* 4.0 13.9 - - + -
105G LEU* 4.1 12.3 - - + -
123G LEU* 3.8 28.7 - - + -
231G LEU* 5.0 4.3 - - + -
234G PHE* 3.2 19.0 + - + +
235G THR* 4.1 7.6 - - - +
236G SER 3.3 0.2 - - - -
237G TRP* 1.3 102.8 - - + +
239G LYS* 1.3 56.3 + - - +
241G THR* 3.1 7.8 + - - -
242G MET* 2.9 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G LEU* 5.7 5.6 - - + -
235G THR 3.7 14.2 + - - +
236G SER* 3.8 2.7 + - - +
237G TRP 3.5 0.2 - - - -
238G ILE* 1.3 76.6 - - - +
240G ASP* 1.3 59.9 + - - +
242G MET* 3.7 18.9 - - + +
243G ALA* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G SER 3.1 21.2 + - - +
237G TRP* 3.6 7.6 - - + +
238G ILE 3.2 0.6 - - - -
239G LYS* 1.3 76.6 - - - +
241G THR* 1.3 61.3 + - + +
243G ALA* 3.1 6.2 + - - +
244G LYS* 3.0 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G TRP* 3.8 4.9 - - - -
89G ILE* 4.6 13.0 - - + -
105G LEU* 3.2 19.5 - - - +
237G TRP* 2.8 52.4 + - + +
238G ILE* 3.1 7.1 + - - -
240G ASP* 1.3 78.1 - - + +
242G MET* 1.3 56.4 + - - +
243G ALA 3.4 0.2 - - - -
244G LYS* 3.9 7.2 - - + +
246G PRO* 2.8 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G LEU* 5.0 9.6 - - + -
48G ASP* 4.7 16.4 - - + +
51G TRP* 3.5 48.1 + - + +
105G LEU* 4.5 5.6 - - - -
107G ARG* 5.4 0.2 + - - -
123G LEU* 4.7 11.2 - - + -
238G ILE* 2.9 38.2 + - + +
239G LYS* 3.7 20.6 - - + +
240G ASP 3.1 0.2 - - - -
241G THR* 1.3 77.1 - - - +
243G ALA* 1.3 65.3 + - - +
244G LYS 3.3 0.2 - - - -
245G ASN* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G LYS* 2.9 22.3 + - + +
240G ASP* 3.5 6.1 - - - +
242G MET* 1.3 75.0 - - - +
244G LYS* 1.3 58.5 + - + +
245G ASN* 3.0 13.1 + - - +
----------------------------------------------------------
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