Contacts of the helix formed by residues 184 - 198 (chain S) in PDB entry 1I84
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 THR 184 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182S GLY* 3.0 2.8 + - - -
183S LYS* 1.3 73.7 - - - +
185S GLU* 1.3 59.5 + - + +
186S ASN 3.2 1.8 - - - -
187S THR* 2.4 38.9 + - - -
188S LYS* 3.1 29.2 + - + -
228S ASN* 5.0 0.7 - - - +
232S GLU* 4.8 7.2 - - - +
244S ASN* 5.7 4.7 - - - +
246S SER* 2.9 27.5 + - - +
250S LYS* 4.4 16.2 - - - +
465S ASP* 3.9 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182S GLY* 3.6 13.5 + - - +
184S THR* 1.3 79.9 - - - +
186S ASN* 1.3 60.9 + - - +
187S THR 2.7 1.4 + - - -
188S LYS* 2.6 52.1 + - - +
189S LYS* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S TYR* 3.4 34.8 + - - -
123S VAL* 3.7 15.6 - - - +
153S ILE* 3.8 14.6 - - + +
175S CYS* 4.2 13.4 - - - -
182S GLY* 3.2 23.1 + - - +
183S LYS 4.2 4.5 - - - +
184S THR 3.0 0.8 + - - -
185S GLU* 1.3 84.5 - - - +
187S THR* 1.3 58.0 + - - +
189S LYS* 3.9 8.7 - - - -
190S VAL* 2.9 28.2 + - - +
682S VAL* 4.1 5.9 - - + +
684S CYS* 4.6 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175S CYS* 3.9 7.9 - - - -
183S LYS 3.1 15.1 + - - -
184S THR* 2.4 27.0 + - - -
185S GLU 2.7 0.2 + - - -
186S ASN* 1.3 70.9 - - - +
188S LYS* 1.3 64.9 + - + +
189S LYS 3.0 2.6 + - - -
190S VAL* 3.1 8.5 + - - +
191S ILE* 3.1 26.7 + - + +
228S ASN* 5.1 2.2 - - - +
250S LYS* 5.0 4.5 - - - -
252S ILE* 3.6 22.7 - - + -
463S ILE* 3.2 30.6 - - + +
465S ASP* 4.0 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184S THR* 3.9 24.7 - - + +
185S GLU* 2.6 41.5 + - - +
187S THR* 1.3 77.1 - - - +
189S LYS* 1.3 62.1 + - - +
191S ILE* 3.5 7.4 + - - +
192S GLN* 2.9 27.9 + - - +
225S LEU* 5.8 0.3 - - - +
228S ASN* 4.5 24.2 - - + +
229S PRO 6.1 0.2 - - - -
232S GLU* 2.7 34.3 + - - +
244S ASN* 5.6 1.6 - - - +
250S LYS* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S TYR* 4.9 0.9 - - - +
133S TYR* 3.6 45.9 - - + +
153S ILE* 3.8 20.4 - - + -
154S TYR* 4.1 3.3 - - + -
185S GLU* 3.5 30.7 - - + +
186S ASN* 3.9 8.5 - - - +
187S THR 3.0 0.8 - - - -
188S LYS* 1.3 78.7 - - - +
190S VAL* 1.3 55.7 + - - +
191S ILE 3.0 1.6 - - - -
192S GLN* 2.6 56.2 + - - +
193S TYR* 2.7 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S ILE* 4.0 21.1 - - + +
154S TYR* 5.9 0.7 - - - -
157S ALA* 4.0 14.8 - - + +
173S ILE* 3.6 39.7 - - + -
175S CYS* 6.0 0.4 - - - -
186S ASN 2.9 20.4 - - - +
187S THR* 3.1 9.2 + - - +
189S LYS* 1.3 74.9 - - - +
191S ILE* 1.3 61.7 + - - +
193S TYR* 4.0 1.4 - - - +
194S LEU* 3.2 36.8 + - + +
461S LEU* 4.4 0.4 - - + -
463S ILE* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187S THR* 3.1 15.6 + - + +
188S LYS* 3.8 6.1 - - - +
189S LYS 3.0 0.8 - - - -
190S VAL* 1.3 73.8 - - - +
192S GLN* 1.3 58.3 + - - +
194S LEU* 3.3 4.1 + - + -
195S ALA* 2.7 38.0 + - - +
224S LEU* 3.7 46.4 - - + +
225S LEU* 4.5 9.4 - - + -
228S ASN* 4.2 22.2 - - + +
252S ILE* 4.3 27.8 - - + -
254S ILE* 4.4 5.6 - - + -
262S ILE* 6.1 0.2 - - + -
463S ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133S TYR* 4.0 12.7 + - - +
134S SER* 4.6 2.6 - - - +
138S ILE* 4.5 7.3 - - + +
154S TYR* 2.6 28.3 + - + +
188S LYS 2.9 14.2 + - - +
189S LYS* 2.6 55.3 + - - +
191S ILE* 1.3 73.7 - - - +
193S TYR* 1.3 62.4 + - - +
195S ALA* 3.5 10.6 + - - +
196S VAL* 3.8 8.7 + - - +
217S TYR* 4.8 8.7 - - - +
225S LEU* 4.3 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 4.0 26.5 - - + -
141S TYR* 3.8 5.4 + - + -
142S LYS* 3.6 12.2 - - - -
154S TYR* 3.2 52.0 - + + -
157S ALA* 4.1 13.2 - - + -
158S ASP* 2.5 49.3 + - + +
161S TYR* 5.8 1.6 - + - -
189S LYS 2.7 16.5 + - - +
190S VAL 4.0 3.8 - - - +
192S GLN* 1.3 70.0 - - - +
194S LEU* 1.3 66.3 + - + +
195S ALA 2.8 9.9 + - - -
196S VAL* 2.8 16.9 + - - +
197S VAL* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157S ALA* 3.9 23.1 - - + +
161S TYR* 3.8 22.2 - - + -
190S VAL* 3.2 39.4 + - + +
191S ILE* 3.9 4.0 - - - +
193S TYR* 1.3 85.3 - - + +
195S ALA* 1.3 59.9 + - - +
196S VAL 3.1 0.2 - - - -
197S VAL* 4.5 2.5 - - + +
198S ALA* 3.3 26.5 + - + +
199S SER 3.8 2.4 + - - -
254S ILE* 5.0 7.4 - - + -
256S PHE* 3.3 39.3 - - + -
262S ILE* 4.0 12.9 - - + +
461S LEU* 4.0 16.8 - - + -
463S ILE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191S ILE* 2.7 23.9 + - + +
192S GLN 3.5 9.2 - - - +
193S TYR 2.8 0.6 + - - -
194S LEU* 1.3 74.5 - - - +
196S VAL* 1.3 57.9 + - - +
199S SER* 3.1 21.6 + - - -
217S TYR* 3.8 12.7 - - + -
221S GLU* 3.7 24.3 - - + +
224S LEU* 5.3 3.1 - - + -
225S LEU* 3.9 22.4 - - + -
262S ILE* 4.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135S GLU* 3.7 22.7 - - + +
138S ILE* 3.5 31.4 - - + -
139S ASP* 6.4 0.2 - - - -
142S LYS* 5.1 7.4 + - + +
192S GLN 4.3 5.8 - - - +
193S TYR 2.8 9.4 + - - +
195S ALA* 1.3 79.7 - - - +
197S VAL* 1.3 69.5 + - + +
198S ALA 3.2 2.6 + - - -
199S SER* 3.8 14.9 + - - +
215S PHE* 3.9 29.0 - - + -
217S TYR* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 3.4 27.6 - - + -
142S LYS* 4.0 35.1 + - + +
158S ASP* 4.0 7.2 - - - +
161S TYR* 4.8 14.1 + - + -
193S TYR* 2.9 55.9 + - + +
194S LEU* 4.6 1.3 - - + -
196S VAL* 1.3 82.6 - - + +
198S ALA* 1.3 56.8 + - - +
199S SER 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161S TYR* 3.6 39.9 - - + +
194S LEU* 3.3 19.2 + - + +
196S VAL 3.2 0.4 - - - -
197S VAL* 1.3 77.2 - - + +
199S SER* 1.3 69.3 + - - +
256S PHE* 4.4 11.2 - - + -
260S GLY 3.7 3.8 - - - +
261S TYR* 3.4 25.5 - - - -
262S ILE* 3.5 2.8 + - + +
----------------------------------------------------------
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