Contacts of the helix formed by residues 147 - 159 (chain M) in PDB entry 2X17
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 147 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1496 GLN* 3.3 18.1 + - - -
144M ALA* 4.0 17.4 - - - +
145M LYS 3.3 5.4 + - - -
146M ASP* 1.3 78.5 - - - +
148M PRO* 1.3 62.7 - - - +
149M GLN* 3.1 17.4 + - - +
150M ILE* 3.4 32.5 + - - +
151M LEU* 3.5 18.7 + - - +
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Residues in contact with PRO 148 (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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1438 PHE* 3.5 45.6 - - + +
1478 SER* 6.3 0.2 - - - -
1508 ILE* 4.0 13.2 - - + +
146M ASP 3.7 7.9 - - - +
147M SER* 1.3 84.5 - - - +
149M GLN* 1.3 77.6 + - - +
151M LEU* 3.9 5.3 - - + +
152M PHE* 3.3 18.9 + - - +
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Residues in contact with GLN 149 (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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1496 GLN* 3.6 25.3 + - + +
1478 SER* 3.3 30.9 + - - +
1498 GLN* 4.1 21.4 + - + +
1508 ILE* 4.0 15.1 - - + +
1538 MET* 4.1 8.4 - - + +
146M ASP 5.2 0.2 - - - +
147M SER* 3.1 18.6 + - - +
148M PRO* 1.3 98.4 - - - +
150M ILE* 1.3 61.5 + - - +
152M PHE* 3.4 6.2 + - - +
153M MET* 3.3 28.7 + - + +
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Residues in contact with ILE 150 (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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1486 PRO* 4.1 15.9 - - + +
1496 GLN* 3.8 38.1 - - + +
1526 PHE* 4.1 31.6 - - + -
140M LYS 4.9 2.2 - - - +
143M PHE* 4.7 7.6 - - + +
144M ALA* 3.6 29.8 - - + -
147M SER* 3.4 20.9 + - - +
149M GLN* 1.3 74.1 - - - +
151M LEU* 1.3 59.8 + - - +
152M PHE 3.2 0.4 - - - -
153M MET* 3.2 10.9 + - + -
154M LEU* 2.8 36.4 + - + +
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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
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1438 PHE* 3.8 26.7 - - + -
36M LEU* 4.3 22.2 - - + -
39M PHE* 4.0 14.5 - - + -
83M PRO* 4.4 18.6 - - + -
141M LEU* 3.8 28.0 - - + -
144M ALA* 4.7 7.2 - - + +
147M SER 3.5 14.7 + - - +
148M PRO* 3.9 7.2 - - + +
149M GLN 3.4 0.4 - - - -
150M ILE* 1.3 77.6 - - - +
152M PHE* 1.3 57.4 + - - +
154M LEU* 3.5 7.4 + - - +
155M ASP* 3.1 27.0 + - - +
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Residues in contact with PHE 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1408 LYS* 4.7 23.3 - - + -
1438 PHE* 4.9 11.4 - + + -
1508 ILE* 4.3 21.8 - - + -
1538 MET* 3.8 43.5 - - + -
1548 LEU* 4.7 11.0 - - + -
1578 GLU* 3.3 40.8 - - + -
36M LEU* 5.7 2.0 - - - -
148M PRO 3.3 11.8 + - - +
149M GLN* 3.4 10.8 - - - +
150M ILE 3.2 0.6 - - - -
151M LEU* 1.3 78.8 - - - +
153M MET* 1.3 62.9 + - + +
155M ASP* 3.2 18.7 + - + +
156M LYS* 3.3 14.7 + - + +
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Residues in contact with MET 153 (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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1496 GLN* 4.1 13.5 - - + +
1526 PHE* 3.7 32.3 - - + -
1536 MET* 3.7 22.9 - - + +
11736 AG 2.6 30.5 - - - -
1538 MET* 3.8 14.4 - - + -
149M GLN* 3.3 18.8 + - + +
150M ILE* 3.2 19.1 + - + +
152M PHE* 1.3 75.8 - - + +
154M LEU* 1.3 63.4 + - - +
156M LYS* 3.6 7.7 + - - +
157M GLU* 3.3 26.9 + - - +
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Residues in contact with LEU 154 (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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1526 PHE* 4.4 10.3 - - + -
39M PHE* 4.1 9.6 - - + -
137M ILE* 4.5 15.3 - - + -
140M LYS* 3.7 57.2 - - + +
141M LEU* 4.1 18.6 - - + -
144M ALA* 5.5 1.6 - - + -
150M ILE* 2.8 26.0 + - + +
151M LEU* 3.7 7.6 - - - +
153M MET* 1.3 74.5 - - - +
155M ASP* 1.3 64.8 + - - +
157M GLU* 3.3 12.9 + - + +
158M LEU* 3.1 37.9 + - + +
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Residues in contact with ASP 155 (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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1408 LYS* 5.7 4.3 + - - -
35M GLY 4.7 1.9 - - - +
36M LEU* 3.4 21.8 - - + +
37M GLU* 3.8 6.8 + - - +
38M GLY* 3.0 36.4 + - - -
39M PHE* 3.1 26.8 + - + +
151M LEU 3.1 13.3 + - - +
152M PHE* 3.2 15.8 + - + +
154M LEU* 1.3 77.9 - - - +
156M LYS* 1.3 59.4 + - - +
158M LEU* 3.7 0.4 + - - -
159M SER* 3.3 18.0 + - - -
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Residues in contact with LYS 156 (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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1566 LYS* 5.1 13.9 - - - +
1568 LYS* 4.8 17.0 - - - +
1578 GLU* 4.6 22.6 - - + +
152M PHE* 3.3 11.5 + - + +
153M MET* 3.9 10.3 - - - +
154M LEU 3.3 0.4 - - - -
155M ASP* 1.3 78.9 - - - +
157M GLU* 1.3 63.5 + - + +
159M SER* 2.6 25.4 + - - +
160M ALA* 4.1 2.8 + - - +
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Residues in contact with GLU 157 (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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1526 PHE* 3.6 26.0 - - - -
1566 LYS* 3.8 38.2 - - - +
140M LYS* 3.6 23.3 + - - -
153M MET 3.3 12.1 + - - +
154M LEU* 3.3 14.0 + - + +
156M LYS* 1.3 79.7 - - + +
158M LEU* 1.3 63.8 + - + +
160M ALA* 3.7 17.9 - - - +
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Residues in contact with LEU 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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38M GLY 3.8 17.5 - - - +
39M PHE* 3.6 43.3 - - + +
42M TRP* 3.6 30.7 - - + +
87M PHE* 4.9 1.6 - - + -
137M ILE* 3.8 33.0 - - + -
154M LEU* 3.1 25.6 + - + +
155M ASP 4.3 0.2 - - - +
156M LYS 3.3 0.2 - - - -
157M GLU* 1.3 76.0 - - + +
159M SER* 1.3 60.1 + - - +
160M ALA 3.0 6.6 + - - -
161M ARG* 3.2 23.4 + - - +
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Residues in contact with SER 159 (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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37M GLU 5.4 0.4 - - - -
38M GLY* 3.9 14.8 - - - -
41M ASN* 5.3 7.8 + - - -
155M ASP* 3.3 14.8 + - - -
156M LYS* 2.6 30.0 + - - +
158M LEU* 1.3 74.3 - - - +
160M ALA* 1.3 63.1 + - - +
161M ARG 3.2 8.4 - - - +
162M ALA* 4.8 5.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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