Contacts of the helix formed by residues 160 - 178 (chain M) in PDB entry 1J0B
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 SER 160 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61M LEU* 3.9 3.3 - - - +
155M PRO* 3.7 26.9 - - - -
158M GLY 2.4 21.4 + - - -
159M ALA 1.3 70.8 - - - -
161M PRO* 1.3 77.9 - - - +
162M ILE* 3.3 17.2 - - - +
163M GLY 3.2 15.8 + - - -
164M THR* 3.2 19.2 + - - -
230M LEU* 4.1 3.6 - - - -
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Residues in contact with PRO 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M SER* 1.3 88.4 - - - +
162M ILE* 1.3 59.7 + - + +
164M THR* 3.0 27.4 - - - +
165M LEU* 3.5 5.7 + - - +
230M LEU* 4.1 13.9 - - + -
233M GLU* 4.0 28.0 - - + +
234M ALA* 4.1 23.3 - - + +
237M LEU* 4.7 12.6 - - + -
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Residues in contact with ILE 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 5.0 6.3 - - + -
60M TYR* 3.5 14.8 - - + +
61M LEU* 3.2 49.4 - - + +
64M ASP* 3.9 24.0 - - + +
152M TYR* 4.4 2.9 - - - +
160M SER* 3.3 6.7 - - - +
161M PRO* 1.3 72.4 - - + +
163M GLY* 1.3 86.4 + - - +
164M THR 3.0 1.8 - - - -
165M LEU* 3.0 37.9 + - + +
237M LEU* 4.0 24.0 - - + -
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Residues in contact with GLY 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M LYS* 3.4 27.9 - - - +
61M LEU* 3.8 12.8 - - - -
158M GLY 3.6 20.2 - - - -
160M SER* 3.2 4.9 + - - -
162M ILE* 1.3 92.1 - - - +
164M THR* 1.3 62.2 + - - +
166M GLY 3.1 11.3 + - - -
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Residues in contact with THR 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M LYS* 5.4 0.7 - - - -
158M GLY 4.7 0.2 + - - -
160M SER 3.2 11.3 + - - -
161M PRO* 3.0 16.3 + - - +
163M GLY* 1.3 71.7 - - - +
165M LEU* 1.3 66.4 + - - +
166M GLY 2.9 2.5 - - - -
167M TYR* 2.6 20.5 + - - +
168M VAL* 3.4 14.2 + - + -
193M GLY* 3.9 14.3 + - - -
196M ALA* 3.6 23.9 - - + +
197M GLY* 3.2 24.9 - - - +
200M LEU* 5.0 1.3 - - + -
230M LEU* 3.8 8.9 - - + +
231M ILE* 6.2 0.4 - - - -
234M ALA* 4.3 15.0 - - + -
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Residues in contact with LEU 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LEU* 4.3 5.1 - - + +
12M PHE* 3.6 47.8 - - + -
60M TYR* 3.8 22.3 - - + -
161M PRO 4.2 6.1 - - - +
162M ILE* 3.0 31.8 + - + +
164M THR* 1.3 76.1 - - - +
166M GLY* 1.3 54.3 + - - +
168M VAL* 2.7 30.7 + - + +
169M ARG* 3.0 12.0 + - - +
234M ALA* 4.7 9.4 - - + +
237M LEU* 5.4 2.9 - - + -
238M LEU* 3.4 37.0 - - + -
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Residues in contact with GLY 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M ARG* 3.5 40.4 - - - +
57M LYS 4.1 0.4 - - - -
60M TYR* 3.7 13.5 - - - -
163M GLY 3.1 10.6 + - - -
164M THR 2.7 6.9 + - - -
165M LEU* 1.3 74.5 - - - +
167M TYR* 1.3 60.2 + - - -
169M ARG* 3.4 8.0 - - - +
170M ALA 3.3 15.6 + - - -
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Residues in contact with TYR 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M ASP* 2.6 27.3 + - - +
53M ASN* 3.3 44.5 - - + +
56M ARG* 3.3 21.5 + - + -
57M LYS* 3.9 20.9 - - + -
163M GLY 4.4 0.2 + - - -
164M THR 2.6 15.7 + - - +
166M GLY* 1.3 74.4 - - - -
168M VAL* 1.3 62.2 + - - -
169M ARG 3.0 1.3 - - - -
170M ALA* 3.5 15.4 - - + +
171M VAL* 3.3 26.9 + - - +
193M GLY 4.8 0.9 - - - +
194M THR* 4.0 28.5 - - + +
197M GLY* 3.9 5.2 - - - -
198M LEU* 3.5 26.9 + - + +
306M ILE* 4.3 17.2 - - + +
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Residues in contact with VAL 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M ILE* 3.4 14.5 - - + +
9M LEU* 3.6 27.4 - - + -
164M THR* 3.4 16.7 + - + +
165M LEU* 2.7 26.8 + - + +
167M TYR* 1.3 78.4 - - - +
169M ARG* 1.3 56.4 + - - +
171M VAL* 2.9 27.4 - - + +
197M GLY 4.1 7.9 - - - +
200M LEU* 4.0 22.0 - - + -
201M GLY* 4.3 6.3 - - - +
204M ILE* 4.5 10.5 - - + -
238M LEU* 3.9 12.6 - - + -
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Residues in contact with ARG 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 4.4 19.7 - - - +
5M ILE* 4.5 2.5 - - - -
6M PHE* 5.4 11.1 - - - -
9M LEU* 3.6 22.2 + - + +
14M ARG* 3.3 43.2 - - - +
56M ARG* 5.7 6.7 - - - +
59M GLU* 4.0 9.6 - - - -
60M TYR* 2.5 34.2 + - + -
165M LEU 3.0 8.2 + - - +
166M GLY* 3.4 12.3 - - - +
168M VAL* 1.3 75.9 - - - +
170M ALA* 1.3 58.0 + - - +
171M VAL 3.0 1.8 - - - -
172M GLY* 2.6 25.2 + - - +
173M GLU* 3.0 12.0 + - + +
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Residues in contact with ALA 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M LYS* 4.6 2.8 - - - -
43M ASP* 5.0 0.4 - - - +
56M ARG* 3.8 30.9 - - - +
166M GLY 3.3 3.4 + - - -
167M TYR* 3.4 37.4 + - + +
169M ARG* 1.3 79.2 - - - +
171M VAL* 1.3 57.5 + - + +
173M GLU* 3.3 6.5 + - - +
174M ILE* 3.0 39.2 + - + +
198M LEU* 6.1 0.4 - - + -
306M ILE* 5.8 0.7 - - + -
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Residues in contact with VAL 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ILE* 3.3 15.5 - - + -
167M TYR 3.3 12.3 + - - +
168M VAL 2.9 24.0 - - - +
169M ARG 2.9 1.4 + - - -
170M ALA* 1.3 73.5 - - - +
172M GLY* 1.3 65.3 + - - +
173M GLU 3.1 0.7 - - - -
174M ILE* 4.1 7.6 - - + +
175M ALA* 3.1 27.0 + - - +
198M LEU* 3.4 45.1 - - + +
201M GLY* 3.4 21.1 - - - +
202M LEU* 3.9 12.8 - - + +
205M LEU* 3.8 4.6 - - + +
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Residues in contact with GLY 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 3.6 18.1 - - - -
2M HIS* 3.3 11.9 + - - -
5M ILE* 3.5 20.8 - - - +
169M ARG 2.6 15.7 + - - -
171M VAL* 1.3 79.9 - - - +
173M GLU* 1.3 56.4 + - - -
175M ALA* 3.9 2.0 - - - +
176M THR* 3.1 26.3 + - - -
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Residues in contact with GLU 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 4.4 5.8 - - - +
20M TRP 3.9 5.2 - - - +
21M GLU* 3.2 52.4 - - - +
22M THR 3.5 6.6 + - - -
41M LYS* 2.8 28.6 + - - -
56M ARG* 3.6 20.2 + - - -
169M ARG* 3.0 10.6 + - + +
170M ALA* 3.5 9.4 - - - +
171M VAL 3.1 0.2 - - - -
172M GLY* 1.3 75.1 - - - +
174M ILE* 1.3 56.0 - - - +
176M THR* 2.7 8.7 + - - -
177M GLN* 2.6 40.8 + - - +
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Residues in contact with ILE 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ILE* 4.2 7.6 - - + -
41M LYS* 3.5 33.2 - - + -
170M ALA* 3.0 20.8 + - + +
171M VAL* 4.1 8.3 - - - +
173M GLU* 1.3 74.9 - - - +
175M ALA* 1.3 60.5 + - - +
177M GLN* 3.0 9.9 + - - +
178M SER* 2.6 37.7 + - - -
182M PHE* 3.9 29.4 - - + -
185M ILE* 4.0 23.3 - - + -
198M LEU* 4.8 3.6 - - + -
304M LEU* 4.1 6.5 - - + -
306M ILE* 4.2 11.7 - - + -
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Residues in contact with ALA 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M HIS* 5.2 7.4 - - + -
171M VAL 3.1 18.0 + - - +
172M GLY* 3.9 4.9 - - - +
174M ILE* 1.3 81.2 - - - +
176M THR* 1.3 61.3 + - - +
178M SER* 3.8 11.6 - - - +
205M LEU* 3.5 23.1 - - + -
207M GLU* 5.9 2.9 - - - +
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Residues in contact with THR 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 2.7 39.8 + - - +
2M HIS* 3.5 2.8 + - - -
21M GLU* 4.4 12.3 - - - +
172M GLY 3.1 8.7 + - - -
173M GLU* 2.7 15.0 + - - +
175M ALA* 1.3 74.4 - - - +
177M GLN* 1.3 65.7 + - - +
178M SER 4.1 2.6 - - - +
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Residues in contact with GLN 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLU* 3.7 18.5 - - + +
22M THR 2.5 25.4 - - - +
23M PRO* 4.3 1.7 - - - +
24M ILE* 3.4 20.7 + - + +
41M LYS* 2.6 29.2 - - - +
173M GLU* 2.6 22.2 + - - +
174M ILE* 3.2 28.3 - - - +
176M THR* 1.3 75.8 - - - +
178M SER* 1.3 77.7 + - - +
179M GLU* 3.6 6.8 + - - +
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Residues in contact with SER 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M ILE* 4.1 12.3 - - - +
174M ILE* 2.6 22.3 + - - -
175M ALA* 3.8 13.3 - - - +
176M THR 4.1 2.9 - - - +
177M GLN* 1.3 78.3 - - - +
179M GLU* 1.3 64.1 + - - +
180M VAL* 3.1 14.5 + - - +
182M PHE* 2.9 39.8 - - - -
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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) + - + + + + + -
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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