Contacts of the helix formed by residues 130 - 135 (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 ASP 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LYS* 4.1 8.9 + - - +
126B LEU 3.4 14.2 + - - +
127B MET* 3.1 18.9 + - - +
128B ASN 3.2 0.2 - - - -
129B GLN* 1.3 81.3 - - - +
131B LYS* 1.3 66.1 + - - +
132B VAL* 3.1 22.8 + - - +
133B LEU* 3.2 3.1 + - - +
134B MET* 3.1 18.8 + - - +
168B ARG* 2.8 46.5 + - - -
169B PHE* 3.5 17.3 - - + -
172B VAL* 4.4 5.6 - - - +
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Residues in contact with LYS 131 (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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131A LYS* 5.1 9.3 - - - +
135A GLU* 2.8 36.3 + - - +
138A TYR* 3.6 46.1 - - + +
129B GLN 3.7 1.6 + - - -
130B ASP* 1.3 77.0 + - - +
132B VAL* 1.3 66.2 + - + +
134B MET* 3.1 11.5 + - + +
135B GLU* 3.3 25.0 + - - +
168B ARG* 5.4 2.7 - - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.1 16.2 + - - +
131B LYS* 1.3 79.7 - - + +
133B LEU* 1.3 60.3 + - - +
135B GLU* 3.6 2.9 - - - +
136B SER 4.5 0.9 + - - -
151B PHE* 4.2 10.0 - - + -
155B TYR* 2.6 37.0 + - + +
162B TYR* 3.6 31.6 - - + +
166B ASP* 3.9 16.8 - - - +
168B ARG* 3.5 15.9 - - - +
169B PHE* 3.9 24.5 - - + -
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Residues in contact with LEU 133 (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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127B MET* 3.6 31.6 - - + +
128B ASN* 4.0 23.8 - - - +
130B ASP* 3.2 4.6 + - - +
131B LYS 3.2 0.4 - - - -
132B VAL* 1.3 74.1 - - - +
134B MET* 1.3 66.2 + - - +
135B GLU 3.1 2.8 + - - -
136B SER* 3.5 5.9 + - - -
137B TRP* 3.5 7.1 + - - +
151B PHE* 4.2 18.4 - - + -
159B ALA* 6.0 2.0 - - + -
163B HIS* 5.9 0.7 - - - +
169B PHE* 3.4 31.2 - - + -
173B PHE* 5.6 2.5 - - + -
316B ILE* 5.9 0.2 - - + -
320B HIS* 3.2 59.0 - - + +
602B CIY 5.8 3.1 - - + -
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Residues in contact with MET 134 (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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27A SER* 3.9 22.7 - - - -
31A MET* 3.9 30.5 - - + -
134A MET* 3.5 29.2 - - + -
138A TYR* 3.2 25.1 - - + +
31B MET* 4.7 3.4 - - - +
128B ASN 3.8 16.8 - - - +
129B GLN* 4.0 13.2 - - - +
130B ASP 3.1 17.1 + - - +
131B LYS* 3.1 2.9 + - + +
133B LEU* 1.3 78.1 - - - +
135B GLU* 1.3 64.3 + - - +
137B TRP* 3.1 27.1 + - - +
138B TYR* 3.6 17.6 - - + +
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Residues in contact with GLU 135 (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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131A LYS* 2.6 43.2 + - - +
131B LYS* 3.3 17.5 + - - +
132B VAL 3.6 2.2 - - - +
133B LEU 3.1 0.2 - - - -
134B MET* 1.3 79.7 - - - +
136B SER* 1.3 62.8 + - - +
138B TYR* 3.0 30.2 + - - +
139B TYR* 3.4 25.8 + - + -
154B ALA* 4.0 18.2 - - + +
155B TYR* 3.3 31.1 + - + +
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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