Contacts of the helix formed by residues 144 - 156 (chain B) in PDB entry 2PA2
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 ASN 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B SER 4.6 1.7 - - - +
80B CYS* 3.5 38.3 + - - +
84B GLY* 4.2 3.0 + - - -
140B THR* 3.1 30.9 + - + -
141B LYS* 3.0 15.3 + - - +
143B GLN* 1.3 79.1 - - - +
145B LYS* 1.3 64.4 + - - +
146B GLU 3.1 3.4 - - - -
147B HIS* 2.8 32.2 + - + +
148B VAL* 3.1 12.7 + - - +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.2 36.6 - - + +
142B LEU 3.4 16.6 + - - +
143B GLN 3.2 4.1 - - - +
144B ASN* 1.3 75.4 - - - +
146B GLU* 1.3 76.2 + - + +
148B VAL* 3.3 4.3 + - - +
149B ILE* 3.3 40.3 + - + +
167B ILE* 4.3 13.2 - - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLN 4.2 12.3 - - - +
144B ASN 3.1 1.0 - - - -
145B LYS* 1.3 96.5 + - + +
147B HIS* 1.3 65.0 + - + +
149B ILE* 3.4 9.9 + - + +
150B GLU* 3.1 26.9 + - - +
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Residues in contact with HIS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 3.4 23.3 + - - -
76B MET* 3.8 2.0 - - - +
79B SER* 3.4 51.3 + - - +
80B CYS* 3.7 9.9 - - - -
143B GLN 5.2 1.8 - - - -
144B ASN* 2.8 31.4 + - - +
146B GLU* 1.3 80.5 - - + +
148B VAL* 1.3 60.7 - - - +
150B GLU* 4.5 0.2 - - - -
151B ALA* 2.8 30.1 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 11.0 - - + -
50B GLY* 3.7 32.5 - - - +
76B MET* 4.2 15.7 - - + -
138B ILE* 4.0 20.4 - - + +
140B THR* 3.4 28.3 - - + -
144B ASN 3.1 13.9 + - - +
145B LYS 3.5 6.7 - - - +
146B GLU 3.3 0.2 - - - -
147B HIS* 1.3 75.5 - - - +
149B ILE* 1.3 63.7 + - - +
151B ALA* 3.3 1.2 + - - +
152B LEU* 3.0 30.5 + - + +
167B ILE* 4.1 5.4 - - + -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS* 3.3 34.0 + - + +
146B GLU* 3.6 10.5 - - + +
147B HIS 3.3 0.2 - - - -
148B VAL* 1.3 77.9 - - - +
150B GLU* 1.3 57.3 + - - +
152B LEU 3.4 0.5 + - - -
153B ARG* 2.8 62.2 + - - +
165B ILE* 3.8 21.4 - - + +
167B ILE* 3.9 24.7 - - + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 3.5 34.5 - - + +
146B GLU 3.1 17.2 + - - +
148B VAL 3.3 0.2 - - - -
149B ILE* 1.3 78.7 - - - +
151B ALA* 1.3 62.0 - - - +
153B ARG* 3.1 29.7 + - - +
154B ARG* 2.8 59.6 + - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.1 13.9 - - + +
75B TYR* 3.9 17.0 - - + -
76B MET* 3.8 24.7 - - + -
138B ILE* 3.9 11.2 - - + -
147B HIS 2.8 19.3 + - - +
148B VAL 3.5 5.4 - - - +
149B ILE 3.2 0.2 - - - -
150B GLU* 1.3 77.4 - - - +
152B LEU* 1.3 59.8 + - - +
154B ARG* 3.3 3.0 + - - +
155B ALA* 3.1 28.2 + - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY* 3.5 37.7 - - - +
51B HIS 3.7 13.2 - - - +
52B MET* 3.5 17.3 - - + +
72B ALA* 4.9 2.2 - - + -
136B MET* 4.2 30.3 - - + +
138B ILE* 3.7 24.5 - - + -
148B VAL* 3.0 20.9 + - + +
149B ILE 4.0 2.7 - - - +
151B ALA* 1.3 73.5 - - - +
153B ARG* 1.3 64.1 + - - +
155B ALA* 4.2 2.2 - - - -
156B LYS* 3.1 23.6 + - - +
165B ILE* 4.0 20.6 - - + -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE* 2.8 43.8 + - - +
150B GLU* 3.1 34.2 + - - +
151B ALA 3.3 0.2 - - - -
152B LEU* 1.3 76.8 - - - +
154B ARG* 1.3 57.4 + - + +
156B LYS* 3.1 29.5 - - + +
157B PHE* 3.4 14.2 - - + -
165B ILE* 3.5 16.9 - - + +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B CYS* 3.9 19.5 - - - -
75B TYR* 3.6 39.1 + - + +
78B LYS* 4.6 11.5 - - - +
150B GLU* 2.8 46.5 + - - +
151B ALA 3.9 2.9 - - - +
153B ARG* 1.3 77.0 - - + +
155B ALA* 1.3 66.1 + - - +
157B PHE* 3.1 27.6 + - - +
158B LYS* 4.4 2.3 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 3.5 18.8 - - + -
68B ALA* 3.5 27.9 - - - +
71B CYS* 3.9 10.7 - - - -
72B ALA* 3.9 10.3 - - + +
136B MET* 3.9 4.5 - - + -
151B ALA 3.1 17.7 + - - +
152B LEU* 3.4 2.0 + - - +
154B ARG* 1.3 73.1 - - - +
156B LYS* 1.3 52.9 + - - +
157B PHE 2.7 16.7 + - - -
158B LYS* 2.9 22.8 + - - +
159B PHE* 4.3 0.9 + - - -
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B K 2.8 25.3 - - - -
52B MET* 3.2 17.4 - - + +
152B LEU 3.1 9.9 + - - +
153B ARG* 3.1 27.6 - - + +
155B ALA* 1.3 75.1 - - - +
157B PHE* 1.3 66.0 + - + +
158B LYS 3.2 0.4 - - - -
159B PHE* 3.2 9.7 - - - +
162B ARG* 4.5 5.1 - - - +
163B GLN* 2.7 48.7 + - + +
164B LYS* 4.1 1.8 - - - +
165B ILE* 3.5 39.1 - - - +
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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