Contacts of the helix formed by residues 139 - 147 (chain B) in PDB entry 3P9K
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 TYR 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B GLU* 3.4 29.9 + - - -
136B SER 2.9 9.2 + - - +
138B TYR* 1.3 89.6 - - + +
140B LEU* 1.3 62.0 + - - +
141B LYS 3.3 2.9 - - - -
142B ASP* 3.2 28.0 + - - +
143B ALA* 3.1 20.4 + - - +
150B PRO* 3.6 20.4 - - + +
153B LYS* 4.1 22.4 - - + +
154B ALA* 3.3 35.8 + - + -
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Residues in contact with LEU 140 (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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32A THR* 4.7 4.9 - - - -
35A ASN* 3.6 33.7 - - + +
73A MET* 5.8 0.7 - - - -
77A ILE* 4.1 18.4 - - + -
136B SER 3.4 4.5 + - - +
137B TRP* 3.5 20.2 + - + +
139B TYR* 1.3 76.9 - - - +
141B LYS* 1.3 65.1 + - - +
143B ALA* 3.1 6.0 + - + +
144B VAL* 3.0 23.0 + - + +
150B PRO* 3.8 19.7 - - + -
315B MET* 4.0 21.5 - - + -
318B LEU* 3.9 32.1 - - + -
319B ALA* 5.3 3.6 - - + -
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Residues in contact with LYS 141 (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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35A ASN* 3.0 17.9 + - - +
38A GLU* 3.4 41.7 - - + +
39A LEU* 3.8 31.3 - - + +
138B TYR* 3.8 20.9 + - - +
140B LEU* 1.3 74.5 - - - +
142B ASP* 1.3 91.8 + - - +
144B VAL* 3.1 4.3 + - - +
145B LEU* 3.1 29.6 + - + +
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Residues in contact with ASP 142 (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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139B TYR* 3.2 34.8 + - - +
141B LYS* 1.3 103.3 + - - +
143B ALA* 1.3 52.3 + - - +
145B LEU* 3.1 8.0 + - - +
146B ASP* 2.6 48.2 + - - +
153B LYS* 3.9 17.0 - - + +
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Residues in contact with ALA 143 (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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67A ASN* 3.3 2.9 + - - -
73A MET* 3.5 8.7 - - - +
139B TYR 3.1 2.9 + - - +
140B LEU* 3.1 10.6 + - + +
142B ASP* 1.3 79.9 - - - +
144B VAL* 1.3 59.4 + - - +
147B GLY* 2.6 31.9 + - - -
148B GLY 3.7 17.5 - - - +
150B PRO* 3.5 29.4 - - + -
153B LYS* 3.6 15.2 - - - +
318B LEU* 6.2 0.4 - - + -
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Residues in contact with VAL 144 (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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39A LEU* 3.9 24.7 - - + -
62A LEU* 4.0 26.9 - - + -
64A SER* 3.9 1.2 - - - -
67A ASN* 2.8 24.3 + - - +
70A ALA* 3.8 13.2 - - + +
73A MET* 3.7 21.5 - - + -
74A VAL* 4.3 12.3 - - + -
77A ILE* 4.0 20.4 - - + -
140B LEU* 3.0 21.3 + - + +
141B LYS 3.1 7.4 + - - +
143B ALA* 1.3 75.5 - - - +
145B LEU* 1.3 60.9 + - + +
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Residues in contact with LEU 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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39A LEU* 3.7 23.6 - - + -
62A LEU* 4.3 6.5 - - + -
63A PRO* 4.0 43.1 - - + +
64A SER* 3.8 29.1 - - - -
66A ALA* 4.4 8.8 - - - +
67A ASN* 4.0 4.6 - - - +
141B LYS* 3.1 15.9 + - + +
142B ASP* 3.7 9.2 - - - +
144B VAL* 1.3 79.1 - - + +
146B ASP* 1.3 68.1 + - - +
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Residues in contact with ASP 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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66A ALA* 4.0 19.2 - - - +
67A ASN* 4.0 4.5 - - - -
142B ASP* 2.6 27.9 + - - +
145B LEU* 1.3 84.7 - - - +
147B GLY* 1.3 64.8 + - - +
153B LYS* 3.4 20.8 + - - +
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Residues in contact with GLY 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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67A ASN* 3.4 25.1 - - - -
69A GLU* 5.8 0.7 - - - -
73A MET* 4.2 2.2 - - - -
143B ALA* 2.6 24.8 + - - -
146B ASP* 1.3 79.3 - - - +
148B GLY* 1.3 60.3 + - - -
153B LYS* 3.3 20.8 + - - -
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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