Contacts of the helix formed by residues 147 - 159 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144J ALA* 4.2 15.0 - - - +
145J LYS 3.5 4.2 + - - -
146J ASP* 1.3 78.9 - - - +
148J PRO* 1.3 62.0 - - - +
149J GLN* 3.1 18.1 + - - -
150J ILE* 3.4 31.2 + - - +
151J LEU* 3.3 20.0 + - - +
149Y GLN* 3.4 18.6 + - - +
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Residues in contact with PRO 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435 PHE* 4.0 25.5 - - + +
1475 SER* 6.4 0.4 - - - -
1505 ILE* 3.7 20.2 - - + +
146J ASP 3.6 8.7 - - - +
147J SER* 1.3 84.0 - - - +
149J GLN* 1.3 72.3 + - - +
150J ILE 3.4 0.2 - - - -
151J LEU* 3.9 11.9 - - + +
152J PHE* 3.2 26.5 + - - +
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Residues in contact with GLN 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465 ASP 5.7 0.2 + - - -
1475 SER* 3.4 23.4 + - - +
1495 GLN* 3.6 35.7 + - + +
1505 ILE* 4.2 12.4 - - + +
1535 MET* 4.1 7.7 - - + +
146J ASP 5.2 0.2 - - - +
147J SER* 3.1 19.4 + - - +
148J PRO* 1.3 94.1 - - - +
150J ILE* 1.3 61.1 + - - +
152J PHE* 3.5 5.4 + - - +
153J MET* 3.3 31.1 + - + +
149L GLN* 6.3 0.9 - - + -
149Y GLN* 4.2 22.0 + - + +
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Residues in contact with ILE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LYS* 5.0 1.3 - - + +
143J PHE* 4.3 17.5 - - + +
144J ALA* 3.6 24.2 - - + -
147J SER* 3.4 25.4 + - - +
148J PRO 3.4 0.2 - - - -
149J GLN* 1.3 74.4 - - - +
151J LEU* 1.3 60.2 + - - +
152J PHE 3.2 0.4 - - - -
153J MET* 3.3 9.9 + - + -
154J LEU* 2.9 38.2 + - + +
148Y PRO* 4.0 23.8 - - + +
149Y GLN* 4.0 26.0 - - + +
152Y PHE* 4.3 26.9 - - + -
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435 PHE* 3.7 26.5 - - + -
36J LEU* 4.5 14.9 - - + +
39J PHE* 4.2 14.5 - - + -
83J PRO* 4.3 23.6 - - + -
141J LEU* 3.9 28.3 - - + -
144J ALA* 4.7 7.0 - - + +
147J SER 3.3 16.4 + - - +
148J PRO* 3.9 7.9 - - + +
149J GLN 3.4 0.2 - - - -
150J ILE* 1.3 75.8 - - - +
152J PHE* 1.3 61.7 + - - +
154J LEU* 3.6 6.4 + - - +
155J ASP* 3.2 22.5 + - - +
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Residues in contact with PHE 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405 LYS* 4.8 16.8 - - + -
1435 PHE* 5.0 13.9 - + + -
1505 ILE* 3.9 24.9 - - + -
1535 MET* 3.6 50.5 - - + -
1545 LEU* 4.5 12.3 - - + -
1575 GLU* 3.4 36.1 - - - -
36J LEU* 5.8 1.1 - - - -
148J PRO 3.2 18.6 + - - +
149J GLN* 3.5 7.6 - - - +
150J ILE 3.2 0.2 - - - -
151J LEU* 1.3 78.0 - - - +
153J MET* 1.3 61.6 + - + +
155J ASP* 3.4 17.0 + - + +
156J LYS* 3.4 14.3 + - + +
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Residues in contact with MET 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535 MET* 3.7 19.5 - - + +
11745 AG 2.9 26.0 - - - -
149J GLN* 3.3 26.2 + - + +
150J ILE* 3.3 10.2 + - + +
152J PHE* 1.3 75.8 - - + +
154J LEU* 1.3 63.0 + - - +
155J ASP 3.4 0.2 - - - -
156J LYS* 3.7 8.5 + - + +
157J GLU* 3.5 26.2 + - - +
149Y GLN* 4.3 10.1 - - + +
152Y PHE* 3.7 34.1 - - + -
153Y MET* 3.7 26.0 - - + +
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Residues in contact with LEU 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J PHE* 4.1 10.1 - - + -
137J ILE* 4.7 13.7 - - + -
140J LYS* 3.8 55.2 - - + +
141J LEU* 4.2 21.8 - - + -
144J ALA* 5.1 2.0 - - + -
150J ILE* 2.9 30.0 + - + +
151J LEU* 3.8 7.4 - - - +
153J MET* 1.3 76.5 - - - +
155J ASP* 1.3 63.6 + - - +
157J GLU* 3.2 14.7 + - - +
158J LEU* 3.1 36.3 + - + +
152Y PHE* 4.9 6.9 - - + -
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Residues in contact with ASP 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405 LYS* 5.5 5.9 + - - -
35J GLY 4.6 2.1 - - - +
36J LEU* 3.2 24.0 - - + +
37J GLU* 3.7 6.8 + - - +
38J GLY* 2.9 51.4 + - - -
39J PHE* 3.1 26.4 + - + +
151J LEU 3.2 12.4 + - - +
152J PHE* 3.4 13.2 + - + +
154J LEU* 1.3 78.5 - - - +
156J LYS* 1.3 60.7 + - - +
158J LEU 3.6 0.2 + - - -
159J SER* 3.3 7.8 + - - -
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Residues in contact with LYS 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565 LYS* 4.9 15.6 - - - +
1575 GLU* 4.4 25.1 - - + +
152J PHE* 3.4 12.6 + - + +
153J MET* 3.9 11.7 - - + +
154J LEU 3.2 1.0 - - - -
155J ASP* 1.3 78.3 + - - +
157J GLU* 1.3 62.7 + - + +
159J SER* 2.6 25.5 + - - +
160J ALA* 4.1 2.4 + - - +
156Y LYS* 5.6 8.2 - - - +
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Residues in contact with GLU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LYS* 4.0 17.3 + - - -
153J MET 3.5 10.0 + - - +
154J LEU* 3.2 15.9 + - + +
156J LYS* 1.3 79.0 - - + +
158J LEU* 1.3 67.0 + - + +
159J SER 3.4 0.3 + - - -
160J ALA* 3.4 21.1 - - - +
152Y PHE* 3.4 30.7 - - + -
156Y LYS* 4.0 31.9 - - - +
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Residues in contact with LEU 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J GLY 3.4 19.5 - - - +
39J PHE* 3.6 44.0 - - + -
42J TRP* 3.6 38.9 - - + +
87J PHE* 4.8 1.6 - - + -
137J ILE* 3.8 32.1 - - + -
154J LEU* 3.1 20.1 + - + +
156J LYS 3.4 0.2 - - - -
157J GLU* 1.3 76.8 - - + +
159J SER* 1.3 56.2 + - - +
160J ALA 3.1 5.6 - - - -
161J ARG 3.2 22.0 + - - +
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Residues in contact with SER 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J GLU 5.3 0.7 - - - -
38J GLY* 3.8 15.3 - - - -
41J ASN* 5.2 8.5 + - - -
155J ASP 3.3 15.4 + - - -
156J LYS* 2.6 27.2 + - - +
158J LEU* 1.3 75.2 - - - +
160J ALA* 1.3 63.2 + - - +
161J ARG 3.2 9.3 + - - +
162J ALA* 4.5 7.3 - - - +
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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