Contacts of the helix formed by residues 185 - 198 (chain S) in PDB entry 3TDD
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 ASN 185 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 3.2 32.6 + - - +
44S THR* 4.8 0.2 + - - -
45S HIS* 4.8 2.3 - - - -
183S ASP 3.1 6.2 - - - +
184S GLY* 1.3 81.8 - - - +
186S PRO* 1.3 70.7 - - - +
187S ASP* 3.3 23.4 + - - +
188S GLU* 3.0 29.0 + - + +
189S LEU* 3.4 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S HIS* 4.1 20.4 - - + +
184S GLY 3.9 5.4 - - - +
185S ASN* 1.3 86.9 - - - +
187S ASP* 1.3 79.4 + - - +
189S LEU* 2.9 7.6 + - + +
190S ILE* 2.9 30.1 + - + +
214S ILE* 3.5 29.8 - - + -
219S THR* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185S ASN* 3.3 11.8 + - - +
186S PRO* 1.3 83.4 - - - +
188S GLU* 1.3 60.0 + - - +
190S ILE 4.0 0.2 - - - -
191S LYS* 3.1 47.0 + - - +
231S LYS* 5.6 2.4 - - - +
232S TYR* 2.7 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 3.2 28.5 - - + +
185S ASN* 3.0 27.4 + - + +
186S PRO 3.0 0.8 - - - -
187S ASP* 1.3 78.5 - - + +
189S LEU* 1.3 60.9 + - - +
191S LYS* 3.2 25.9 + - - +
192S ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 3.5 36.2 + - + +
40S LEU* 3.6 33.5 - - + +
41S ARG* 4.3 2.7 - - - -
42S SER* 3.6 29.4 - - - +
45S HIS* 3.6 34.8 - - + +
46S ALA 4.3 0.2 - - - +
47S VAL* 3.9 14.1 - - + -
185S ASN 3.4 7.6 + - - +
186S PRO* 2.9 9.7 + - + +
188S GLU* 1.3 77.1 - - - +
190S ILE* 1.3 58.6 + - - +
192S ALA* 3.4 1.2 + - - +
193S GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S VAL* 4.1 24.9 - - + -
49S VAL* 4.4 0.7 - - + +
186S PRO* 2.9 21.8 + - + +
189S LEU* 1.3 74.5 - - - +
191S LYS* 1.3 59.5 + - - +
193S GLY* 3.1 2.1 + - - -
194S VAL* 2.8 33.9 + - + +
212S ILE* 3.4 43.5 - - + -
214S ILE* 4.3 18.8 - - + -
224S TYR* 5.0 11.2 - - + -
232S TYR* 3.2 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187S ASP* 3.1 34.2 + - - +
188S GLU* 3.2 24.8 + - - +
190S ILE* 1.3 76.2 - - - +
192S ALA* 1.3 62.8 + - - +
194S VAL* 3.1 9.6 + - - +
195S GLU* 2.9 24.2 + - - +
231S LYS* 4.2 18.0 + - - +
232S TYR* 3.9 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 4.1 24.0 - - + +
40S LEU* 4.1 12.6 - - + +
175S TYR* 3.7 17.5 + - + +
179S THR* 5.3 3.4 - - + -
188S GLU 2.9 16.8 + - - +
189S LEU 3.5 5.8 - - - +
191S LYS* 1.3 76.1 - - - +
193S GLY* 1.3 62.2 + - - +
195S GLU* 3.3 7.2 + - - +
196S ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S VAL* 4.5 3.1 - - - +
40S LEU* 3.7 28.7 - - - +
49S VAL* 3.7 15.3 - - - +
189S LEU 2.9 10.7 + - - -
190S ILE 3.1 4.9 + - - -
192S ALA* 1.3 78.4 - - - +
194S VAL* 1.3 55.2 + - - +
196S ALA* 3.2 6.3 + - - +
197S ILE* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S VAL* 4.2 7.0 - - + -
190S ILE* 2.8 23.7 + - + +
191S LYS* 3.1 8.7 + - - +
193S GLY* 1.3 76.0 - - - +
195S GLU* 1.3 56.2 + - - +
197S ILE* 2.9 20.9 - - - +
198S SER* 2.8 15.3 + - - -
207S LEU* 3.2 28.9 - - + -
210S LEU* 4.5 3.1 - - + -
212S ILE* 3.9 26.7 - - + -
232S TYR* 4.0 26.9 - - + +
233S ILE* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175S TYR* 2.6 34.5 + - + +
191S LYS 2.9 12.2 + - - +
192S ALA* 3.5 11.0 - - - +
193S GLY 3.1 0.2 - - - -
194S VAL* 1.3 75.6 - - - +
196S ALA* 1.3 62.6 + - - +
198S SER* 2.9 18.2 + - - +
199S GLN* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S VAL* 4.1 9.2 - - + -
172S ALA* 2.7 26.8 - - + +
175S TYR* 3.2 35.6 - - + -
176S LEU* 3.6 22.4 - - + -
192S ALA 3.1 7.1 + - - +
193S GLY* 3.5 9.0 - - - +
195S GLU* 1.3 78.4 - - - +
197S ILE* 1.3 53.5 + - - +
199S GLN* 3.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S VAL* 4.2 15.7 - - + +
38S VAL* 3.8 19.9 - - + +
49S VAL* 3.7 29.6 - - + +
50S ALA 3.8 1.1 - - - -
51S LEU* 3.6 38.4 - - + +
172S ALA* 4.3 1.1 - - - -
193S GLY 3.0 11.3 + - - +
194S VAL* 2.9 32.5 - - - +
196S ALA* 1.3 73.8 - - - +
198S SER* 1.3 56.0 + - - +
199S GLN 3.0 5.4 - - - -
200S SER* 3.0 23.6 + - - -
201S LEU* 3.7 8.2 + - + +
207S LEU* 3.9 18.2 - - + -
210S LEU* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194S VAL* 2.8 17.2 + - - -
195S GLU* 2.9 19.2 + - - +
197S ILE* 1.3 75.0 - - - +
199S GLN* 1.3 61.4 + - - +
200S SER 3.0 6.4 + - - -
201S LEU* 3.3 41.8 + - - +
207S LEU* 4.1 7.4 - - - -
----------------------------------------------------------
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