Contacts of the helix formed by residues 139 - 147 (chain A) in PDB entry 3PII
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 3.9 3.1 - - - +
138A LEU* 1.3 77.8 - - - +
140A PHE* 1.3 67.7 + - - +
141A GLU* 3.7 21.3 + - - +
142A GLU* 3.1 37.5 + - - +
143A ALA* 3.0 23.3 + - - +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 4.0 30.1 - - + -
34A ALA* 4.4 5.6 - - + +
64A VAL* 3.6 32.3 - - + +
65A GLY* 3.2 30.5 - - - -
66A ILE* 3.6 17.7 - - + -
82A ARG* 3.3 49.8 - - + +
134A ILE* 4.0 10.3 - - + -
139A SER* 1.3 72.0 - - - +
141A GLU* 1.3 67.4 + - + +
143A ALA* 4.6 2.7 - - - -
144A ALA* 3.2 20.4 + - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 4.8 3.0 - - - +
139A SER* 3.2 17.4 + - - +
140A PHE* 1.3 80.2 - - + +
142A GLU* 1.3 62.7 + - + +
144A ALA* 3.8 0.7 + - - +
145A PRO* 3.4 14.2 - - - +
308A ILE* 3.6 28.0 - - + +
310A VAL* 4.1 16.7 - - + +
333A VAL* 3.8 22.4 - - - +
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN 5.2 1.4 - - - +
138A LEU* 3.7 24.7 - - + +
139A SER* 3.1 28.7 + - - +
141A GLU* 1.3 78.6 - - + +
143A ALA* 1.3 60.3 + - - +
145A PRO* 2.9 17.2 - - - +
146A ILE* 3.8 6.4 - - - +
299A ALA* 5.6 1.3 - - + +
304A VAL 5.1 1.4 - - - +
305A LYS* 3.8 37.7 + - - +
306A THR* 3.7 24.7 + - - +
308A ILE* 4.9 9.9 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE* 4.0 31.6 - - + -
138A LEU* 3.4 24.5 - - + -
139A SER 3.0 16.9 + - - +
140A PHE 4.0 2.0 - - - +
142A GLU* 1.3 76.3 - - - +
144A ALA* 1.3 57.7 + - - +
146A ILE* 2.6 34.5 + - - +
147A PHE* 3.3 11.5 - - + -
296A LEU* 4.6 0.4 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A CYS* 4.5 1.3 - - - -
36A GLY* 3.8 14.8 - - - +
62A GLU* 3.1 34.2 - - - +
64A VAL* 3.9 16.3 - - + +
140A PHE 3.2 13.8 + - - +
141A GLU 4.1 2.9 - - - +
143A ALA* 1.3 77.2 - - - +
145A PRO* 1.3 68.6 - - + +
147A PHE* 3.3 16.6 + - - +
333A VAL* 4.2 11.9 - - + -
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Residues in contact with PRO 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY* 5.9 0.2 - - - -
62A GLU* 3.2 11.4 - - - +
141A GLU 3.4 9.2 - - - +
142A GLU 2.9 26.7 - - - +
144A ALA* 1.3 83.3 - - + +
146A ILE* 1.3 63.6 + - - +
148A CYS* 3.1 1.7 + - - -
149A ALA* 2.9 26.9 + - + +
150A GLY 3.2 4.1 + - - -
306A THR* 3.6 32.5 - - + -
308A ILE* 4.1 5.8 - - + -
331A ARG* 4.2 19.5 - - + +
333A VAL* 4.0 17.7 - - + -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU 3.8 14.4 - - - +
143A ALA* 2.6 18.7 + - - +
145A PRO* 1.3 71.4 - - - +
147A PHE* 1.3 55.0 + - - -
148A CYS 3.2 0.2 + - - -
150A GLY* 3.8 15.5 - - - +
151A VAL 3.0 28.1 + - - -
179A VAL* 5.5 2.9 - - + -
183A TYR* 3.9 3.8 - - + +
292A LEU* 3.6 4.2 - - + +
295A ALA* 3.8 25.8 - - + +
296A LEU* 3.1 29.6 - - + +
299A ALA* 4.1 15.0 - - + -
304A VAL* 4.0 24.9 - - + +
306A THR* 3.9 18.4 - - + +
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS 4.5 4.4 - - - +
62A GLU* 4.3 13.0 - - - -
63A GLY 5.2 0.4 - - - -
64A VAL* 3.8 20.4 - - + -
84A GLY* 3.3 43.5 - - - -
85A ILE 4.3 1.6 - - - -
86A PRO* 3.9 26.9 - - + +
87A TRP 4.9 1.9 + - - -
132A VAL* 4.1 8.7 - - + -
134A ILE* 3.8 17.3 - - + -
143A ALA* 3.3 14.6 - - + -
144A ALA 3.3 10.5 - - - +
145A PRO 3.1 0.4 - - - -
146A ILE* 1.3 76.2 - - - +
148A CYS* 1.3 58.2 + - - +
151A VAL* 3.5 12.0 - - - +
286A VAL* 5.2 3.1 - - - +
292A LEU* 3.6 28.9 - - + +
296A LEU* 3.8 28.7 - - + -
600A BMD 5.5 0.2 + - - -
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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
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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