Contacts of the helix formed by residues 147 - 159 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1493 GLN* 3.5 12.4 + - - -
144Q ALA* 3.8 16.4 + - - +
145Q LYS 3.5 4.2 + - - -
146Q ASP* 1.3 78.7 - - - +
148Q PRO* 1.3 61.9 - - - +
149Q GLN* 3.1 16.9 + - - +
150Q ILE* 3.4 36.9 + - - +
151Q LEU* 3.4 19.1 + - - +
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Residues in contact with PRO 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439 PHE* 3.9 33.5 - - + +
1509 ILE* 4.2 11.7 - - + +
146Q ASP 3.6 7.6 - - - +
147Q SER* 1.3 85.3 - - - +
149Q GLN* 1.3 74.7 + - - +
150Q ILE 3.3 0.2 - - - -
151Q LEU* 3.8 10.7 - - + +
152Q PHE* 3.0 30.1 + - - +
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Residues in contact with GLN 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493 GLN* 4.3 21.4 + - + +
1479 SER* 3.5 29.8 + - - +
1499 GLN* 4.3 19.3 + - + +
1509 ILE* 3.9 19.5 - - + +
1539 MET* 4.1 7.7 - - + +
146Q ASP 5.0 0.5 - - - +
147Q SER* 3.1 18.8 + - - +
148Q PRO* 1.3 95.9 - - - +
150Q ILE* 1.3 61.4 + - - +
152Q PHE* 3.7 4.0 - - - +
153Q MET* 3.5 29.4 + - + +
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Residues in contact with ILE 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483 PRO* 4.2 22.0 - - + +
1493 GLN* 4.0 31.6 - - + +
1523 PHE* 4.4 29.8 - - + -
140Q LYS 5.0 0.9 - - - +
143Q PHE* 4.5 10.3 - - + +
144Q ALA* 3.7 28.0 - - + -
147Q SER* 3.4 25.2 + - - +
148Q PRO 3.3 0.2 - - - -
149Q GLN* 1.3 73.0 - - - +
151Q LEU* 1.3 61.1 + - - +
152Q PHE 3.2 1.8 - - - -
153Q MET* 3.0 12.5 + - + +
154Q LEU* 2.8 34.8 + - + +
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Residues in contact with LEU 151 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439 PHE* 4.0 23.6 - - + -
36Q LEU* 4.5 15.2 - - + +
39Q PHE* 3.9 16.6 - - + -
83Q PRO* 4.4 23.3 - - + -
141Q LEU* 3.8 29.2 - - + -
144Q ALA* 4.6 5.3 - - + +
147Q SER 3.4 15.0 + - - +
148Q PRO* 3.8 7.9 - - + +
149Q GLN 3.5 0.2 - - - -
150Q ILE* 1.3 78.2 - - - +
152Q PHE* 1.3 60.2 + - - +
154Q LEU* 3.5 8.5 + - - +
155Q ASP* 3.2 21.5 + - - +
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Residues in contact with PHE 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409 LYS* 4.5 27.1 - - + -
1439 PHE* 4.7 16.5 - + + -
1509 ILE* 4.2 20.6 - - + -
1539 MET* 3.9 41.3 - - + -
1549 LEU* 4.6 13.2 - - + -
1579 GLU* 3.3 34.1 - - - -
36Q LEU* 5.6 2.2 - - - -
148Q PRO 3.0 18.4 + - - +
149Q GLN* 3.7 7.0 - - - +
151Q LEU* 1.3 78.6 - - - +
153Q MET* 1.3 64.7 + - + +
155Q ASP* 3.4 20.9 + - + +
156Q LYS* 3.5 10.3 + - + +
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Residues in contact with MET 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493 GLN* 4.5 11.9 - - + +
1523 PHE* 3.9 31.9 - - + -
1533 MET* 4.0 18.2 - - + +
11723 AG 2.8 28.7 - - - -
1539 MET* 3.9 18.4 - - + +
149Q GLN* 3.5 21.7 + - + +
150Q ILE* 3.0 19.1 + - + +
152Q PHE* 1.3 76.5 - - + +
154Q LEU* 1.3 64.4 + - - +
156Q LYS* 3.4 8.9 + - - +
157Q GLU* 3.3 25.7 + - - +
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Residues in contact with LEU 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523 PHE* 4.7 9.6 - - + -
39Q PHE* 3.9 11.0 - - + -
137Q ILE* 4.7 13.5 - - + -
140Q LYS* 3.8 54.1 - - + +
141Q LEU* 4.1 22.7 - - + +
144Q ALA* 5.3 1.6 - - + -
150Q ILE* 2.8 23.0 + - + +
151Q LEU* 3.7 10.5 - - - +
152Q PHE 3.3 0.2 - - - -
153Q MET* 1.3 73.8 - - - +
155Q ASP* 1.3 63.0 + - - +
157Q GLU* 3.3 15.4 + - - +
158Q LEU* 3.1 36.2 + - + +
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Residues in contact with ASP 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409 LYS* 5.8 3.5 + - - -
35Q GLY 4.8 2.1 - - - +
36Q LEU* 3.3 22.8 - - + -
37Q GLU* 3.8 8.5 + - - +
38Q GLY* 2.9 39.2 + - - -
39Q PHE* 3.2 25.7 + - + +
151Q LEU 3.2 13.2 + - - +
152Q PHE* 3.4 13.6 - - + +
153Q MET 3.3 0.2 - - - -
154Q LEU* 1.3 76.8 - - - +
156Q LYS* 1.3 56.6 + - - +
159Q SER* 3.1 24.9 + - - -
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Residues in contact with LYS 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563 LYS* 5.4 10.6 - - - +
1569 LYS* 5.3 10.3 - - - +
1579 GLU* 4.5 25.1 - - + +
152Q PHE* 3.5 10.1 + - + +
153Q MET* 3.4 12.7 + - - +
154Q LEU 3.3 0.6 - - - -
155Q ASP* 1.3 77.8 + - - +
157Q GLU* 1.3 60.7 + - + +
159Q SER* 2.6 23.8 + - - +
160Q ALA* 4.1 3.3 + - - +
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Residues in contact with GLU 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523 PHE* 3.3 31.5 - - - -
1563 LYS* 4.8 20.9 - - - +
140Q LYS* 3.7 22.1 + - - -
153Q MET 3.3 10.3 + - - +
154Q LEU* 3.6 15.0 - - + +
155Q ASP 3.3 0.2 - - - -
156Q LYS* 1.3 80.0 - - + +
158Q LEU* 1.3 66.8 + - + +
160Q ALA* 3.5 19.8 - - - +
161Q ARG 4.8 0.2 + - - -
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Residues in contact with LEU 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q GLY 3.2 22.9 - - - +
39Q PHE* 3.7 43.7 - - + -
42Q TRP* 3.6 31.8 - - + +
87Q PHE* 4.7 2.2 - - + -
137Q ILE* 3.8 35.7 - - + -
154Q LEU* 3.1 22.0 + - + +
157Q GLU* 1.3 78.9 - - + +
159Q SER* 1.3 59.4 + - - +
160Q ALA 3.1 5.6 - - - -
161Q ARG* 3.3 19.0 + - - +
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Residues in contact with SER 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q GLU* 5.3 0.7 - - - -
38Q GLY* 3.7 15.9 - - - -
41Q ASN* 5.0 9.9 + - - +
155Q ASP* 3.1 15.6 + - - -
156Q LYS* 2.6 30.5 + - - +
158Q LEU* 1.3 75.4 - - - +
160Q ALA* 1.3 62.8 + - - +
161Q ARG 3.2 8.9 + - - +
162Q ALA* 4.5 6.4 + - - +
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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