Contacts of the helix formed by residues 144 - 162 (chain M) in PDB entry 1JH0
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 LYS 144 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L GLU* 3.0 34.1 + - - +
134M TYR* 3.7 58.5 + - + +
137M ALA* 4.5 4.3 - - + -
138M GLN* 4.2 15.0 - - - +
142M MET 3.4 17.2 + - - +
143M GLY* 1.3 74.1 - - - +
145M HIS* 1.3 67.3 + - - +
146M THR 3.4 2.2 - - - -
147M ALA* 2.9 18.1 + - + +
148M TRP* 3.0 34.2 + - + +
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Residues in contact with HIS 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L ALA* 3.4 29.2 - - + +
195L LEU* 3.5 33.8 + - + +
196L SER* 3.5 15.1 - - - -
199L ASN* 3.9 29.5 + - + +
143M GLY* 3.3 8.3 - - - -
144M LYS* 1.3 72.8 + - - +
146M THR* 1.3 64.2 + - - +
148M TRP* 3.0 10.8 + - - +
149M ALA* 2.8 24.9 + - - +
267M ARG* 5.4 5.9 + - - -
270M ILE* 5.2 5.8 - - + +
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Residues in contact with THR 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L LEU* 3.8 18.3 + - + +
192L ALA* 3.5 23.8 + - - +
193L LEU* 4.3 4.0 + - - +
196L SER* 4.6 5.9 + - - -
215L PHE* 3.9 36.0 - - + -
216L PHE* 5.4 0.5 - - - -
219L LEU* 5.0 2.7 - - + -
133M THR* 4.6 8.7 - - - -
137M ALA* 6.2 1.3 - - - -
143M GLY 4.9 1.6 + - - -
144M LYS 3.3 0.8 + - - -
145M HIS* 1.3 77.6 - - - +
147M ALA* 1.3 62.3 + - - +
149M ALA* 3.6 2.8 + - - +
150M PHE* 3.2 22.2 + - - +
854M BPH 3.5 21.0 - - - +
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Residues in contact with ALA 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M TRP* 2.7 30.6 + - + +
133M THR* 3.7 29.9 + - - +
134M TYR* 4.0 28.7 - - + -
137M ALA* 6.4 0.2 - - + -
144M LYS* 2.9 13.9 + - + +
146M THR* 1.3 79.2 - - - +
148M TRP* 1.3 65.0 + - + +
150M PHE* 3.3 2.2 + - - +
151M LEU* 3.2 9.2 + - - +
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Residues in contact with TRP 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M TRP* 3.7 32.3 - + - -
134M TYR* 5.1 12.8 - + - -
144M LYS* 3.0 33.2 + - + +
145M HIS* 3.6 9.4 - - - +
147M ALA* 1.3 76.5 - - + +
149M ALA* 1.3 63.4 + - - +
151M LEU* 3.0 40.4 + - + +
152M SER* 3.5 5.0 + - - -
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Residues in contact with ALA 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L ALA* 4.4 4.3 - - + +
192L ALA* 4.6 1.6 - - + -
145M HIS 2.8 19.2 + - - +
146M THR 4.1 1.3 - - - +
148M TRP* 1.3 72.9 - - - +
150M PHE* 1.3 59.6 + - - +
152M SER* 3.3 18.1 - - - -
153M ALA 3.8 2.8 + - - -
270M ILE* 4.1 20.2 - - + -
274M VAL* 3.8 27.9 - - + +
854M BPH 3.6 26.2 - - + +
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Residues in contact with PHE 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M VAL* 4.6 6.3 - - + -
129M TRP* 3.8 10.1 - + - -
130M TRP* 3.3 49.4 - + + -
133M THR* 4.0 7.6 - - + +
146M THR 3.2 18.4 + - - +
147M ALA* 3.5 5.2 - - - +
148M TRP 3.1 0.4 - - - -
149M ALA* 1.3 74.7 - - - +
151M LEU* 1.3 66.9 + - - +
153M ALA* 3.1 4.0 + - + +
154M ILE* 3.0 27.0 + - + +
852M BCL 4.6 14.8 - - + -
854M BPH 3.3 81.0 - + + +
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Residues in contact with LEU 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M TRP* 3.9 32.8 - - + -
130M TRP* 4.1 10.3 - - + +
147M ALA 3.2 10.8 + - - +
148M TRP* 3.0 37.4 + - + +
150M PHE* 1.3 77.6 - - - +
152M SER* 1.3 51.5 + - - +
154M ILE* 2.8 17.0 + - + +
155M TRP* 2.6 36.4 + - + +
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Residues in contact with SER 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M TRP 3.5 4.4 + - - -
149M ALA 3.3 14.6 + - - -
151M LEU* 1.3 78.7 - - - +
153M ALA* 1.3 61.0 + - - +
155M TRP* 3.1 21.8 - - - +
156M LEU 3.6 0.5 + - - -
274M VAL* 2.6 45.9 + - - +
277M THR* 2.8 27.3 + - - +
278M LEU* 3.8 10.5 + - - +
854M BPH 5.1 0.9 - - - -
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Residues in contact with ALA 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M ALA 3.8 1.0 + - - -
150M PHE* 3.1 11.5 + - + +
152M SER* 1.3 75.8 - - - +
154M ILE* 1.3 67.3 + - - +
155M TRP 3.2 0.3 + - - -
156M LEU* 3.4 2.8 + - - +
157M TRP 3.2 16.1 + - - -
277M THR* 3.6 11.4 + - - -
852M BCL 3.5 27.1 - - + +
854M BPH 3.8 44.6 - - + +
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Residues in contact with ILE 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M VAL* 3.7 28.9 - - + -
127M TRP* 3.7 29.8 - - + -
130M TRP* 3.8 41.3 - - + -
150M PHE* 3.0 21.5 + - + +
151M LEU* 2.8 16.2 + - + +
153M ALA* 1.3 75.9 - - - +
155M TRP* 1.3 54.0 + - - +
157M TRP* 3.1 10.2 + - + +
158M MET* 2.6 52.8 + - + +
852M BCL 4.4 2.2 - - + -
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Residues in contact with TRP 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M LEU* 2.6 15.5 + - + +
152M SER* 3.1 13.0 - - - +
154M ILE* 1.3 74.6 - - - +
156M LEU* 1.3 56.5 + - - +
158M MET* 3.2 8.0 + - + +
159M VAL* 2.9 51.2 + - + +
163M ILE* 5.0 11.7 - - + -
277M THR 3.2 24.2 - - - -
278M LEU* 3.2 35.0 + - + +
281M GLY* 3.4 13.4 - - - -
282M ILE* 3.5 31.1 - - + +
285M LEU* 4.2 17.5 - - + -
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Residues in contact with LEU 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152M SER 3.6 1.2 + - - -
153M ALA 3.4 7.6 + - - +
155M TRP* 1.3 75.8 - - - +
157M TRP* 1.3 69.1 + - - +
159M VAL* 3.1 2.3 + - + -
160M LEU* 2.9 43.8 + - + +
277M THR* 4.0 26.2 - - + +
280M GLY 3.9 13.0 - - - +
281M GLY* 3.9 11.0 - - - -
284M ILE* 4.3 5.8 - - + -
850M BCL 4.9 0.7 - - + -
852M BCL 3.3 76.5 - - + +
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Residues in contact with TRP 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M MET* 3.9 20.0 - - + +
123M PHE* 3.9 19.1 - + - -
126M VAL* 3.6 44.4 - - + +
127M TRP* 3.7 17.5 - + - -
153M ALA 3.2 4.0 + - - +
154M ILE* 3.1 15.0 + - + +
156M LEU* 1.3 81.6 - - - +
158M MET* 1.3 93.7 + - + +
160M LEU* 3.5 7.6 + - - +
161M GLY 3.4 16.3 + - - -
850M BCL 3.0 26.3 + - - -
852M BCL 3.5 32.2 - - + +
859M SPO 3.2 51.2 - - + +
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Residues in contact with MET 158 (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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123M PHE* 4.2 15.5 - - + -
127M TRP* 3.9 21.8 - - + +
154M ILE* 2.6 34.7 + - + +
155M TRP* 3.4 11.2 - - + +
157M TRP* 1.3 95.2 - - + +
159M VAL* 1.3 59.2 + - - +
162M PHE* 2.9 42.6 + - + +
163M ILE* 2.8 40.7 + - + -
859M SPO 4.2 3.4 - - - -
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Residues in contact with VAL 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M TRP* 2.9 52.1 + - + +
156M LEU* 3.1 8.2 + - + +
158M MET* 1.3 76.8 - - - +
160M LEU* 1.3 65.3 + - - +
161M GLY 3.2 0.2 + - - -
163M ILE* 3.7 12.1 - - + -
164M ARG* 2.9 30.5 + - + +
165M PRO* 3.5 1.0 - - - +
281M GLY* 3.8 24.2 - - - +
284M ILE* 4.1 13.2 - - + -
285M LEU* 3.8 29.4 - - + +
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Residues in contact with LEU 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 2.9 37.9 + - + +
157M TRP 3.8 3.8 - - - +
159M VAL* 1.3 78.7 - - - +
161M GLY* 1.3 57.9 + - - +
164M ARG* 4.6 4.5 + - - +
165M PRO* 3.6 12.5 - - - +
173M GLU 4.3 3.6 - - - +
174M ALA* 3.9 9.2 - - - -
175M VAL* 4.5 4.7 + - + +
185M TRP* 3.9 22.6 - - + -
284M ILE* 3.6 28.9 - - + -
850M BCL 3.4 41.5 - - + -
852M BCL 3.6 16.4 - - + +
859M SPO 3.9 15.9 - - + -
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Residues in contact with GLY 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M TRP* 4.5 1.2 - - - -
157M TRP 3.4 6.9 + - - -
159M VAL 3.3 0.4 - - - -
160M LEU* 1.3 79.0 - - - +
162M PHE* 1.3 61.1 + - - +
165M PRO* 3.2 19.9 - - - +
171M TRP* 4.1 8.3 - - - -
174M ALA* 3.9 16.4 - - - +
859M SPO 4.0 32.7 - - - +
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Residues in contact with PHE 162 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M PHE* 4.6 10.3 - + - -
158M MET* 2.9 36.8 + - + +
161M GLY* 1.3 77.3 - - - +
163M ILE* 1.3 78.1 + - + +
164M ARG 3.4 0.7 - - - -
165M PRO* 3.1 3.8 - - - +
166M ILE* 3.1 38.8 + - + +
171M TRP* 4.2 15.3 - + - -
859M SPO 3.5 78.2 - - + +
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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