Contacts of the helix formed by residues 2124 - 2135 (chain A) in PDB entry 5NP1
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 TYR2124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2123A SER* 1.3 78.4 - - - +
2125A HIS* 1.3 50.1 + - - +
2127A SER* 3.1 9.3 - - - -
2128A LEU* 2.1 43.1 + - - +
2150A ALA* 5.6 0.2 - - - +
2153A LYS* 5.6 5.2 - - + -
2154A GLU* 5.8 7.0 - - - +
2157A GLU* 5.6 9.9 - - + -
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Residues in contact with HIS2125 (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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2097A GLU* 3.4 28.4 - - + +
2100A TYR* 3.3 5.9 - - - +
2101A GLN* 3.5 24.7 - - + +
2104A TRP* 5.3 4.0 - - + +
2123A SER* 4.2 0.6 - - - -
2124A TYR* 1.3 76.4 - - - +
2126A GLU* 1.3 50.8 + - - +
2128A LEU* 2.9 8.1 + - - +
2129A TYR* 2.1 40.7 + - - +
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Residues in contact with GLU2126 (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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2096A GLU* 3.7 20.2 - - + -
2100A TYR* 3.1 13.4 - - + +
2123A SER* 2.7 31.6 + - - +
2125A HIS* 1.3 69.9 - - - +
2127A SER* 1.3 53.5 + - - +
2129A TYR* 2.7 2.4 + - - -
2130A ASN* 2.2 41.7 + - - +
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Residues in contact with SER2127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123A SER 2.2 29.4 + - - -
2124A TYR* 3.3 10.1 - - - -
2126A GLU* 1.3 65.0 - - - +
2128A LEU* 1.3 52.8 + - - +
2130A ASN* 3.2 7.3 - - - +
2131A ALA* 2.3 41.4 + - - +
2150A ALA* 4.3 23.2 - - - +
2153A LYS* 4.6 9.6 - - - -
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Residues in contact with LEU2128 (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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2104A TRP* 5.9 5.2 - - + -
2124A TYR 2.1 33.3 + - - +
2125A HIS* 3.1 9.6 - - - +
2127A SER* 1.3 66.2 - - - +
2129A TYR* 1.3 49.9 + - - +
2131A ALA* 2.6 11.1 + - - +
2132A LEU* 2.1 41.9 + - + -
2150A ALA* 4.9 4.1 - - - +
2179A ILE* 6.5 1.1 - - + -
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Residues in contact with TYR2129 (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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2100A TYR* 3.3 24.4 + - + +
2103A ALA* 3.8 19.3 - - + -
2104A TRP* 5.0 2.4 - - - +
2108A GLN* 4.1 4.4 - - + +
2112A CYS* 5.8 2.6 - - + +
2125A HIS 2.1 30.4 + - - +
2126A GLU* 2.7 4.6 + - - +
2128A LEU* 1.3 66.0 - - - +
2130A ASN* 1.3 50.7 - - - +
2132A LEU* 3.1 9.7 - - - +
2133A GLN* 2.2 40.6 + - - +
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Residues in contact with ASN2130 (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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2126A GLU 2.2 31.6 + - - +
2127A SER* 3.2 9.4 - - - +
2129A TYR* 1.3 66.3 - - - +
2131A ALA* 1.3 50.4 - - - +
2133A GLN* 2.9 9.4 + - - +
2134A SER* 2.1 41.3 + - - -
2146A SER* 5.8 0.7 - - - -
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Residues in contact with ALA2131 (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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2127A SER 2.3 32.8 + - - +
2128A LEU* 2.6 8.4 + - - +
2130A ASN* 1.3 68.1 - - - +
2132A LEU* 1.3 50.2 + - - +
2134A SER* 3.0 14.1 - - - -
2135A LEU* 2.5 34.0 + - - +
2143A PHE* 3.8 6.3 - - + +
2146A SER* 4.7 4.2 - - - -
2147A LEU* 4.5 21.1 - - + +
2150A ALA* 4.6 9.6 - - + -
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Residues in contact with LEU2132 (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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2104A TRP* 6.4 1.6 - - - -
2108A GLN* 3.4 23.9 - - + +
2109A TRP* 4.8 3.1 + - - +
2128A LEU* 2.1 32.8 + - + +
2129A TYR* 3.1 10.1 - - - +
2131A ALA* 1.3 63.5 - - - +
2133A GLN* 1.3 61.2 + - - +
2135A LEU* 2.7 29.5 + - - +
2136A ARG* 3.3 2.6 + - - -
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Residues in contact with GLN2133 (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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2108A GLN* 4.1 1.6 - - - +
2109A TRP* 4.3 13.9 - - - +
2112A CYS* 4.5 21.3 - - + -
2129A TYR 2.2 29.0 + - - +
2130A ASN* 3.1 14.8 - - - +
2132A LEU* 1.3 66.2 - - - +
2134A SER* 1.3 51.3 + - - +
2136A ARG* 2.3 40.0 + - + +
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Residues in contact with SER2134 (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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2130A ASN 2.1 30.4 + - - -
2131A ALA* 3.0 16.2 - - - -
2133A GLN* 1.3 66.8 - - - +
2135A LEU* 1.3 57.6 + - - +
2136A ARG 3.2 1.5 + - - -
2137A ASP* 4.1 3.5 + - - +
2141A SER 3.8 10.4 + - - -
2142A THR* 4.7 3.9 + - - -
2143A PHE* 3.0 36.7 + - - +
2146A SER* 3.8 10.1 - - - -
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Residues in contact with LEU2135 (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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2131A ALA 2.5 13.4 + - - +
2132A LEU* 2.7 17.9 + - - +
2134A SER* 1.3 72.6 - - - +
2136A ARG* 1.3 59.9 + - - +
2137A ASP 2.7 20.4 - - - +
2141A SER 5.4 1.1 - - - +
2143A PHE* 4.3 5.6 - - + -
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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