Contacts of the helix formed by residues 152 - 168 (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 HIS 152 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 3.2 28.3 - - + -
114S TYR* 3.7 13.6 - + - +
116S TYR* 4.1 2.3 + - - -
132S ILE* 2.7 32.3 + - + -
133S TYR* 3.4 9.1 - + - -
141S TYR* 3.3 28.5 - + + +
150S PRO 3.1 1.8 + - - -
151S PRO* 1.3 75.2 - - - +
153S ILE* 1.3 80.3 + - + +
154S TYR* 2.6 62.3 + + - +
155S ALA* 3.0 18.3 + - - +
156S ILE* 3.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S TYR* 3.1 32.1 - - + +
133S TYR* 3.8 7.2 - - + -
152S HIS* 1.3 89.5 + - + +
154S TYR* 1.3 76.5 + - + +
155S ALA 2.6 16.0 + - - -
156S ILE* 2.7 37.1 + - + -
157S ALA* 3.1 8.8 + - - +
175S CYS* 6.1 0.2 - - - -
186S ASN* 3.8 31.6 - - + +
189S LYS* 3.8 9.4 - - + -
190S VAL* 4.0 21.3 - - + +
682S VAL* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132S ILE 3.8 2.0 - - - -
133S TYR* 2.9 39.4 - + - +
134S SER 4.0 2.9 - - - -
137S ILE* 4.2 20.0 - - + -
138S ILE* 3.1 28.2 - - + +
141S TYR* 4.3 10.2 - - + +
152S HIS* 2.6 34.5 + + - +
153S ILE* 1.3 78.0 - - + +
155S ALA* 1.3 54.6 + - - +
157S ALA* 4.0 4.9 - - + -
158S ASP* 3.2 20.1 + - - +
189S LYS* 4.1 9.6 - - + -
192S GLN* 2.6 40.5 + - - -
193S TYR* 3.2 47.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116S TYR* 3.4 21.3 - - - +
141S TYR* 4.2 22.4 - - + -
145S LYS 5.8 3.8 - - - +
146S ARG* 5.9 2.5 - - - +
150S PRO 4.6 0.4 - - - +
152S HIS* 3.0 21.4 + - - +
153S ILE 2.6 4.9 + - - -
154S TYR* 1.3 72.9 - - - +
156S ILE* 1.3 50.2 + - - +
157S ALA 3.2 1.3 - - - -
158S ASP* 3.2 5.9 + - - +
159S THR* 2.7 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114S TYR* 4.9 1.3 - - + -
116S TYR* 4.9 11.2 + - + +
121S CYS* 3.5 33.4 - - + -
152S HIS 4.0 11.2 - - - +
153S ILE* 2.7 33.2 + - + +
155S ALA* 1.3 72.4 - - - +
157S ALA* 1.3 62.8 + - - +
159S THR* 3.3 7.2 + - - -
160S ALA* 3.1 23.4 + - - +
173S ILE* 4.5 9.6 - - + -
680S ASN* 4.4 22.3 - - + +
681S PHE 5.6 1.3 - - - +
682S VAL* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S ILE* 3.1 8.2 + - - +
154S TYR* 3.8 10.8 - - - +
156S ILE* 1.3 82.5 - - - +
158S ASP* 1.3 57.6 + - - +
160S ALA* 3.8 2.1 - - - +
161S TYR* 2.9 30.4 + - - +
173S ILE* 4.4 11.4 - - - -
190S VAL* 4.0 19.5 - - + +
193S TYR* 4.1 12.8 - - + -
194S LEU* 3.9 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S TYR 4.3 6.1 - - - +
143S GLY* 3.3 29.1 + - - +
144S LYS 4.3 8.8 - - - +
146S ARG* 5.2 4.5 + - - -
154S TYR 3.2 8.0 + - - +
155S ALA* 3.2 6.0 + - - +
157S ALA* 1.3 78.3 - - - +
159S THR* 1.3 66.0 + - - +
161S TYR* 3.9 8.5 - - - -
162S ARG* 3.1 36.7 + - - +
193S TYR* 2.5 37.3 + - + +
197S VAL* 4.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116S TYR* 5.5 1.4 + - - -
145S LYS 5.7 0.7 + - - -
146S ARG* 3.2 52.9 + - + +
155S ALA* 2.7 30.9 + - - +
156S ILE* 3.7 8.8 - - - -
157S ALA 3.3 0.2 - - - -
158S ASP* 1.3 73.5 - - - +
160S ALA* 1.3 57.1 + - - +
162S ARG* 4.1 1.7 - - - +
163S SER* 3.2 26.4 + - - -
680S ASN* 5.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156S ILE 3.1 16.1 + - - +
157S ALA 3.8 2.7 - - - +
159S THR* 1.3 74.4 - - - +
161S TYR* 1.3 55.1 + - - +
162S ARG 2.7 16.2 + - - -
163S SER* 2.8 18.2 + - - -
164S MET* 2.8 13.3 + - - +
171S GLN* 4.3 8.3 - - + +
173S ILE* 4.4 10.3 - - + -
461S LEU* 4.4 14.6 - - + -
680S ASN* 3.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157S ALA 2.9 18.6 + - - +
158S ASP* 4.0 16.2 - - - +
160S ALA* 1.3 74.7 - - - +
162S ARG* 1.3 65.4 + - - +
164S MET* 4.0 5.3 - - - +
165S LEU* 2.7 52.4 + - + +
193S TYR* 5.8 0.9 - + + -
194S LEU* 3.8 30.5 - - + -
197S VAL* 4.8 13.9 + - + -
198S ALA* 3.6 26.5 - - + +
256S PHE* 4.0 20.2 - + - -
260S GLY* 2.6 27.3 + - - -
461S LEU* 3.8 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 162 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143S GLY* 4.9 10.9 + - - -
146S ARG* 4.8 15.7 - - - +
158S ASP* 3.1 32.7 + - - +
159S THR 4.1 2.2 - - - +
160S ALA 2.7 4.2 + - - -
161S TYR* 1.3 83.4 + - - +
163S SER* 1.3 59.6 + - - +
164S MET 2.9 1.8 - - - -
165S LEU* 2.6 47.3 + - - +
166S GLN* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146S ARG* 5.9 0.9 + - - -
159S THR* 3.2 20.2 + - - +
160S ALA* 2.8 6.4 + - - -
162S ARG* 1.3 79.4 - - - +
164S MET* 1.3 57.9 + - - +
166S GLN* 3.7 8.3 - - - -
167S ASP* 2.6 46.1 + - - +
171S GLN* 3.7 19.0 + - - -
678S ASN* 5.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160S ALA 2.8 12.0 + - - +
161S TYR* 4.0 11.7 - - - +
162S ARG 2.7 0.8 + - - -
163S SER* 1.3 76.9 - - - +
165S LEU* 1.3 65.7 + - + +
168S ARG* 2.9 34.1 + - - -
169S GLU 4.4 6.7 - - - +
170S ASP* 5.2 4.5 - - - +
171S GLN* 3.8 19.6 - - + +
256S PHE* 3.0 48.7 - - + -
459S SER* 3.8 22.0 - - - +
460S PHE 3.7 20.2 - - - +
461S LEU* 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161S TYR* 2.7 55.9 - - + +
162S ARG* 2.6 26.9 + - - +
164S MET* 1.3 85.5 - - + +
166S GLN* 1.3 63.7 + - - +
168S ARG* 4.3 7.8 - - - +
256S PHE* 5.7 0.7 - - + -
257S ASP 5.1 2.7 - - - +
258S VAL 4.5 7.2 - - - +
259S THR 4.6 1.8 - - - +
260S GLY* 3.2 34.3 - - - +
459S SER* 5.7 1.6 - - - +
400V ARG* 5.8 3.1 + - - -
406V ARG* 5.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162S ARG* 2.8 47.0 + - + +
163S SER* 3.7 7.9 - - - +
164S MET 3.0 0.6 + - - -
165S LEU* 1.3 83.1 + - - +
167S ASP* 1.3 63.8 + - + +
168S ARG* 3.2 11.3 + - - +
733S ARG* 5.2 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163S SER* 2.6 36.1 + - - +
166S GLN* 1.3 75.9 - - + +
168S ARG* 1.3 77.4 + - - +
169S GLU* 3.6 32.8 + - + +
171S GLN* 4.0 0.9 + - - -
415V GLN* 4.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164S MET 2.9 14.9 + - - +
165S LEU* 4.6 6.7 - - - +
166S GLN 3.2 10.5 - - - +
167S ASP* 1.3 80.4 - - - +
169S GLU* 1.3 54.2 + - - +
400V ARG* 2.4 39.8 - - - +
401V SER 4.5 0.2 - - - +
404V THR* 1.8 62.9 + - - -
406V ARG* 2.2 74.1 - - + +
415V GLN* 2.2 77.6 - - + +
608V ASN* 3.2 9.5 - - - +
----------------------------------------------------------
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