Contacts of the helix formed by residues 198 - 214 (chain A) in PDB entry 3SN5
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 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP* 5.8 7.9 - - + +
193A THR* 5.4 16.2 - - - +
199A LYS* 1.4 66.9 + - - +
200A ALA* 3.3 4.2 - - - +
201A HIS* 3.2 25.8 + - + +
202A ILE* 3.8 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 1.4 74.3 - - - +
200A ALA* 1.3 63.6 + - - +
202A ILE* 3.3 18.1 + - - +
203A LEU* 3.3 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN* 3.3 1.7 - - - +
199A LYS* 1.3 77.4 - - - +
201A HIS* 1.4 51.3 + - - +
203A LEU* 3.3 15.9 + - + +
204A ASN* 2.8 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TYR* 5.1 1.8 - + - -
191A ASP* 5.9 3.1 + - - +
198A GLN* 3.2 17.8 + - + +
200A ALA* 1.4 75.1 - - - +
202A ILE* 1.3 65.8 + - - +
204A ASN* 3.4 12.8 + - + +
205A ASN* 3.1 49.2 + - - +
241A SER* 4.2 19.2 - - - -
250A ARG* 5.0 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 4.7 3.8 - - - -
181A GLU* 4.5 29.6 - - + +
198A GLN 3.8 4.4 + - - +
199A LYS* 3.3 13.2 + - - +
201A HIS* 1.3 78.0 + - - +
203A LEU* 1.4 52.6 + - - +
205A ASN* 3.4 7.6 + - - +
206A LEU* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS 3.3 11.0 + - - +
200A ALA* 3.3 19.0 + - + +
202A ILE* 1.4 78.8 - - - +
204A ASN* 1.4 61.3 + - - +
206A LEU* 3.6 17.1 - - + +
207A ASP* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 2.8 28.5 + - - +
201A HIS* 3.6 15.5 - - + +
202A ILE 3.3 0.2 - - - -
203A LEU* 1.4 81.4 - - - +
205A ASN* 1.3 59.6 + - - +
207A ASP* 3.3 6.2 + - - +
208A ASN* 2.8 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 3.9 15.3 - - + -
184A TYR* 3.0 38.9 + - + -
201A HIS* 3.1 38.6 + - - +
202A ILE* 3.7 6.2 - - - +
204A ASN* 1.3 73.4 - - - +
206A LEU* 1.4 57.2 + - - +
208A ASN* 3.6 1.2 - - - +
209A PHE* 2.9 32.2 + - - +
238A LEU* 3.7 7.6 - - + +
241A SER* 3.5 9.6 + - - -
2205A UNX 1.8 36.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.4 35.7 - - + +
177A ARG* 4.3 24.5 - - + +
180A PHE* 3.7 31.1 - - + -
202A ILE 2.9 17.8 + - - +
203A LEU* 3.6 19.1 - - + +
205A ASN* 1.4 77.0 - - - +
207A ASP* 1.4 62.0 + - - +
209A PHE* 3.4 2.8 + - - +
210A LYS* 3.2 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU 3.1 14.9 + - - +
204A ASN* 3.8 5.6 - - - +
206A LEU* 1.4 76.5 - - - +
208A ASN* 1.4 69.6 + - - +
210A LYS* 3.1 13.2 + - - +
211A GLN* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASN* 2.8 27.1 + - - +
205A ASN 3.6 4.0 - - - +
207A ASP* 1.4 74.2 - - - +
209A PHE* 1.3 58.5 + - - +
211A GLN* 3.2 3.0 + - - +
212A PHE* 3.0 26.5 + - - +
234A ALA* 3.4 22.7 - - - +
237A LYS* 3.5 38.0 + - - +
238A LEU* 3.8 17.3 - - + -
2205A UNX 2.7 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.5 27.1 - + - -
180A PHE* 3.5 26.9 - + + -
205A ASN 2.9 17.0 + - - +
206A LEU 3.6 3.1 - - - +
208A ASN* 1.3 77.2 - - - +
210A LYS* 1.4 53.7 - - - +
212A PHE* 3.3 5.0 + + - +
213A ASP* 2.9 46.6 + - + +
238A LEU* 3.8 16.5 - - + +
280A LEU* 5.1 1.1 - - + -
283A LEU* 4.1 17.0 - - + -
284A TRP* 3.7 48.7 - + + -
287A GLN* 3.8 25.1 - - + -
288A ALA* 4.2 8.3 - - - -
291A ILE* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER* 4.9 13.7 + - - +
176A TYR* 3.5 60.2 - - + +
177A ARG* 6.0 0.6 - - - +
206A LEU* 3.2 32.3 + - + +
207A ASP* 3.1 16.0 + - - +
209A PHE* 1.4 74.1 - - - +
211A GLN* 1.3 65.6 + - - +
213A ASP* 4.0 1.5 - - - +
214A LYS* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 3.0 37.6 + - - +
208A ASN* 3.2 7.6 + - - +
210A LYS* 1.3 80.5 - - - +
212A PHE* 1.3 62.1 + - - +
214A LYS* 3.5 29.6 - - - +
215A VAL* 4.1 2.1 + - - +
230A THR* 3.4 31.6 - - + +
231A ALA* 3.4 17.4 - - - +
234A ALA* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 3.7 6.3 - - - -
109A PHE* 3.6 39.7 - + - -
208A ASN 3.0 16.1 + - - +
209A PHE* 3.9 6.3 - + - +
211A GLN* 1.3 73.9 - - - +
213A ASP* 1.3 66.4 + - - +
214A LYS 3.2 1.0 + - - -
215A VAL* 3.2 18.4 + - - +
216A PHE* 3.5 15.1 + + - -
219A LEU* 3.6 21.3 - - + -
225A ILE* 3.9 9.0 - - + -
231A ALA* 4.3 12.8 - - - +
234A ALA* 4.1 0.4 - - - +
235A ARG* 3.5 37.9 - - + +
238A LEU* 4.1 20.0 - - + -
280A LEU* 4.5 9.9 - - + -
284A TRP* 4.0 17.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.9 12.9 + - - +
209A PHE* 2.9 40.5 + - + +
210A LYS 4.1 2.5 - - - +
212A PHE* 1.3 76.5 - - - +
214A LYS* 1.3 57.4 + - - +
215A VAL 3.3 0.2 - - - -
216A PHE* 3.3 12.7 + - - +
284A TRP* 3.0 19.6 + - + +
288A ALA* 4.4 6.8 - - - +
483A ARG* 2.8 61.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LYS 3.1 18.0 + - - +
211A GLN* 3.5 27.4 - - - +
213A ASP* 1.3 77.4 - - - +
215A VAL* 1.3 63.7 + - + +
216A PHE 3.9 0.2 + - - -
217A PRO* 3.9 8.8 - - - +
483A ARG* 4.8 2.9 + - - +
----------------------------------------------------------
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