Contacts of the helix formed by residues 2117 - 2130 (chain A) in PDB entry 5DZZ
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 ASP2117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2085A GLN* 4.7 4.0 + - - +
2111A ILE* 4.6 0.2 - - - +
2116A ILE* 1.3 89.9 - - - +
2118A ARG* 1.3 64.3 + - - +
2119A GLU* 3.4 11.3 + - + +
2120A THR* 2.7 43.5 + - - -
2121A GLY* 3.2 18.0 + - - -
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Residues in contact with ARG2118 (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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2111A ILE* 4.1 21.3 - - + +
2116A ILE 3.7 0.8 + - - -
2117A ASP* 1.3 73.2 - - - +
2119A GLU* 1.3 64.3 + - + +
2121A GLY* 3.3 1.3 + - - +
2122A MET* 3.0 59.6 + - + +
2157A ASP 5.0 1.2 + - - -
2158A LEU* 3.7 16.6 - - - +
2161A SER* 3.5 21.8 + - - -
2167A ASP* 4.6 6.7 + - - -
2168A SER* 4.2 15.6 + - - -
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Residues in contact with GLU2119 (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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2117A ASP* 3.3 9.3 - - + +
2118A ARG* 1.3 81.0 - - + +
2120A THR* 1.3 64.5 + - - +
2122A MET* 3.2 12.8 + - - +
2123A ARG* 3.3 35.1 + - - +
2171A ASN* 4.7 2.8 - - - +
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Residues in contact with THR2120 (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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2050A GLU* 3.7 16.2 - - + +
2085A GLN* 3.3 29.4 + - - +
2088A ALA* 5.9 0.4 - - + -
2089A ALA* 5.2 4.5 - - + +
2116A ILE* 4.3 9.9 - - + -
2117A ASP* 2.7 33.7 + - - -
2119A GLU* 1.3 73.3 - - - +
2121A GLY* 1.3 62.3 + - - +
2123A ARG* 3.1 29.9 + - - +
2124A LEU* 3.1 34.4 + - + +
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Residues in contact with GLY2121 (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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2107A VAL* 3.9 14.8 - - - +
2111A ILE* 3.7 22.0 - - - -
2116A ILE* 4.4 4.0 - - - +
2117A ASP 3.2 11.5 + - - -
2118A ARG 3.7 4.0 - - - -
2119A GLU 3.2 0.2 - - - -
2120A THR* 1.3 79.3 - - - +
2122A MET* 1.3 56.4 + - - +
2124A LEU* 3.5 5.1 + - - +
2125A LEU* 3.1 32.6 + - - +
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Residues in contact with MET2122 (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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2111A ILE* 4.2 7.9 - - + -
2118A ARG* 3.0 63.7 + - + +
2119A GLU* 3.6 4.9 - - - +
2121A GLY* 1.3 75.2 - - - +
2123A ARG* 1.3 61.1 + - - +
2125A LEU* 3.5 12.2 + - - +
2126A GLU* 3.0 30.3 + - - +
2158A LEU* 3.6 30.3 - - + +
2161A SER* 4.3 2.2 - - - +
2162A LEU* 3.6 22.9 - - + +
2168A SER* 4.2 12.3 - - - +
2171A ASN* 3.5 25.1 + - - +
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Residues in contact with ARG2123 (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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2047A MET* 3.4 41.1 - - - +
2050A GLU* 3.1 34.5 + - + +
2085A GLN* 5.7 0.4 - - - -
2119A GLU* 3.5 27.7 + - - +
2120A THR* 3.1 30.5 + - - +
2122A MET* 1.3 79.2 - - - +
2124A LEU* 1.3 59.0 + - + +
2126A GLU* 3.2 3.5 + - - +
2127A ALA* 2.9 30.7 + - - +
2171A ASN* 3.1 39.6 + - + +
2172A PHE* 3.7 18.1 - - + -
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Residues in contact with LEU2124 (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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2050A GLU* 3.7 24.5 - - + +
2051A ALA 4.9 0.4 - - - +
2054A ALA* 3.7 25.5 - - + +
2088A ALA 4.6 4.0 - - - +
2089A ALA* 3.8 29.6 - - + -
2092A ALA* 3.9 17.7 - - + -
2096A PHE* 5.0 3.8 - - + -
2107A VAL* 4.1 20.0 - - + -
2116A ILE* 5.4 3.1 - - + -
2120A THR* 3.1 26.6 + - + +
2121A GLY* 3.8 6.3 - - - +
2123A ARG* 1.3 77.9 - - + +
2125A LEU* 1.3 56.9 + - - +
2127A ALA* 3.3 4.3 + - - +
2128A GLN* 3.0 36.3 + - - +
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Residues in contact with LEU2125 (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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2107A VAL* 4.4 16.4 - - + -
2108A SER* 3.6 26.0 - - - +
2111A ILE* 4.3 15.3 - - + -
2121A GLY 3.1 17.7 + - - +
2122A MET* 3.9 13.7 - - - +
2124A LEU* 1.3 77.2 - - - +
2126A GLU* 1.3 61.7 + - - +
2128A GLN* 3.4 16.3 + - - +
2129A ILE* 3.0 31.2 + - + +
2134A VAL* 4.6 13.0 - - + -
2154A ILE* 4.3 22.2 - - + -
2158A LEU* 4.6 7.9 - - + -
2162A LEU* 3.9 15.5 - - + -
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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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2122A MET 3.0 16.1 + - - +
2123A ARG 3.5 4.0 - - - +
2125A LEU* 1.3 77.4 - - - +
2127A ALA* 1.3 60.4 + - - +
2129A ILE* 3.5 4.8 + - - +
2130A ALA* 3.2 23.9 + - + +
2162A LEU* 4.3 12.3 - - + +
2169A GLN 3.2 21.0 - - - +
2171A ASN* 2.6 41.2 + - - +
2172A PHE* 3.7 12.1 - - - -
2182A SER* 3.2 11.3 - - - -
2183A TYR* 2.9 30.3 + - + -
2184A VAL* 5.8 2.2 - - + +
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Residues in contact with ALA2127 (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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2051A ALA* 3.7 35.9 - - + -
2054A ALA* 5.3 0.4 - - + -
2055A THR* 3.7 8.1 - - + -
2123A ARG 2.9 16.2 + - - +
2124A LEU* 3.7 5.4 - - - +
2125A LEU 3.3 0.2 - - - -
2126A GLU* 1.3 77.5 - - - +
2128A GLN* 1.3 56.3 + - - +
2130A ALA* 3.6 3.3 + - - +
2131A SER* 2.7 32.2 + - - -
2172A PHE* 4.2 4.9 - - + -
2183A TYR* 4.2 16.5 - - + -
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Residues in contact with GLN2128 (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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2054A ALA 3.0 29.4 + - - +
2055A THR* 3.9 8.1 - - + -
2092A ALA* 3.4 36.0 + - - +
2107A VAL* 4.2 7.1 - - - +
2124A LEU 3.0 22.2 + - - +
2125A LEU* 3.8 12.2 - - + +
2127A ALA* 1.3 75.4 - - - +
2129A ILE* 1.3 61.2 + - - +
2131A SER* 2.8 18.9 + - - -
2132A GLY 3.1 8.5 + - - -
2133A GLY 2.9 18.0 + - - +
2134A VAL* 4.0 7.7 - - - +
2135A VAL* 3.1 31.9 + - + +
2142A PHE* 3.5 5.6 - - + -
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Residues in contact with ILE2129 (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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2125A LEU* 3.0 18.3 + - + +
2126A GLU* 3.9 5.6 - - - +
2128A GLN* 1.3 75.4 - - - +
2130A ALA* 1.3 62.8 + - - +
2131A SER 3.2 0.9 + - - -
2132A GLY 3.2 14.7 + - - -
2133A GLY 3.5 17.7 - - - +
2134A VAL* 4.6 6.1 - - + -
2145A LYS* 3.7 39.7 - - + +
2154A ILE* 4.6 8.3 - - + -
2159A TYR* 4.5 13.7 - - + -
2162A LEU* 3.7 30.3 - - + -
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Residues in contact with ALA2130 (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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2015A ALA* 4.8 1.7 - - - +
2126A GLU* 3.2 17.7 + - + +
2127A ALA 3.9 0.9 - - - +
2128A GLN 3.2 0.2 - - - -
2129A ILE* 1.3 76.7 - - - +
2131A SER* 1.3 56.2 + - - +
2132A GLY 3.4 0.4 - - - -
2183A TYR* 3.9 25.1 - - + -
2184A VAL* 4.0 25.8 - - + -
2187A LYS* 2.7 32.7 + - + +
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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