Contacts of the helix formed by residues 2142 - 2154 (chain A) in PDB entry 4D0O
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 GLY2142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2024A TYR* 4.0 0.2 - - - -
2115A PHE* 6.0 0.7 - - - -
2133A MET* 3.4 22.6 - - - +
2140A ARG 2.9 8.7 + - - -
2141A LEU* 1.3 76.2 - - - +
2143A ILE* 1.3 66.2 + - - -
2144A PRO* 3.3 8.5 - - - -
2145A GLU* 3.2 12.4 + - - +
2146A CYS* 3.0 22.7 + - - -
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Residues in contact with ILE2143 (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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2024A TYR* 3.9 34.6 + - + -
2028A MET* 3.6 32.3 - - + -
2042A LEU* 4.4 6.5 - - + -
2043A PHE* 4.0 17.7 - - + -
2115A PHE* 3.6 38.3 - - + -
2125A PHE* 4.4 3.1 - - + -
2129A VAL* 4.8 3.4 - - + -
2141A LEU 4.1 0.2 + - - -
2142A GLY* 1.3 71.2 - - - -
2144A PRO* 1.3 72.0 - - + +
2146A CYS* 3.3 7.8 + - - +
2147A ILE* 3.0 41.6 + - + +
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Residues in contact with PRO2144 (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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2112A VAL* 4.2 27.7 - - + +
2115A PHE* 3.5 35.4 - - + -
2116A LYS* 4.8 1.3 - - - -
2142A GLY* 3.3 7.6 - - - -
2143A ILE* 1.3 94.6 - - + +
2145A GLU* 1.3 60.9 + - - +
2147A ILE* 3.4 2.8 + - - +
2148A LEU* 3.0 27.6 + - + +
2145B GLU* 3.2 37.9 - - + +
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Residues in contact with GLU2145 (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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2140A ARG 3.8 0.9 - - - +
2141A LEU* 3.5 17.8 - - + +
2142A GLY* 3.2 22.2 + - - +
2144A PRO* 1.3 75.8 - - - +
2146A CYS* 1.3 66.2 + - - +
2148A LEU* 3.2 4.5 + - - +
2149A LEU* 2.8 37.1 + - + +
2112B VAL* 3.9 8.8 - - - +
2116B LYS* 2.7 40.0 + - - -
2144B PRO* 4.0 21.5 - - + +
2145B GLU* 4.7 6.3 - - + +
2148B LEU* 4.1 20.1 - - + +
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Residues in contact with CYS2146 (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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2016A THR* 4.3 9.6 - - + -
2019A ILE* 5.2 1.8 - - - -
2020A MET* 3.6 35.2 - - + -
2024A TYR* 4.4 11.7 - - - -
2043A PHE* 5.7 0.2 - - + -
2141A LEU* 3.9 31.4 - - - -
2142A GLY 3.0 21.0 + - - -
2143A ILE* 3.3 10.5 + - + +
2145A GLU* 1.3 75.8 - - - +
2147A ILE* 1.3 64.0 + - + +
2149A LEU* 3.1 6.2 + - - +
2150A VAL* 3.0 26.5 + - - +
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Residues in contact with ILE2147 (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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2020A MET* 5.0 0.9 - - + -
2042A LEU* 4.4 6.3 - - + +
2043A PHE* 4.3 13.9 - - + -
2104A PHE* 3.6 29.4 - - + -
2108A HIS* 3.7 29.6 - - - +
2111A SER* 4.1 21.8 - - - -
2112A VAL* 3.8 27.8 - - + +
2143A ILE* 3.0 34.2 + - + +
2144A PRO* 3.7 3.4 - - + +
2146A CYS* 1.3 78.1 - - + +
2148A LEU* 1.3 59.1 + - - +
2150A VAL 3.3 0.3 + - - -
2151A THR* 2.9 32.4 + - - -
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Residues in contact with LEU2148 (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 HIS* 3.4 29.2 - - + -
2112A VAL* 5.6 3.1 - - + -
2144A PRO* 3.0 19.0 + - + +
2145A GLU 3.5 4.9 - - - +
2147A ILE* 1.3 78.2 - - + +
2149A LEU* 1.3 61.3 + - - +
2151A THR* 3.3 4.4 + - - -
2152A GLN* 3.0 29.6 + - - +
2145B GLU* 4.1 22.0 - - + +
2148B LEU* 3.7 32.1 - - + -
2149B LEU* 4.3 18.8 - - + +
2152B GLN* 3.6 25.4 + - - +
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Residues in contact with LEU2149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2013A HIS* 4.7 3.0 + - - +
2016A THR* 4.4 21.8 - - + +
2141A LEU* 3.8 26.9 - - + -
2145A GLU* 2.8 30.9 + - + +
2146A CYS* 3.1 6.0 + - - +
2148A LEU* 1.3 72.5 - - - +
2150A VAL* 1.3 63.0 + - - +
2152A GLN* 3.3 15.4 + - - +
2153A ARG* 3.2 21.5 + - - +
2156A LYS* 5.8 0.2 - - - -
2108B HIS* 5.9 2.2 - - - +
2109B ASN* 6.1 0.9 - - - +
2148B LEU* 4.2 24.5 - - + -
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Residues in contact with VAL2150 (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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2013A HIS* 4.0 13.0 - - + +
2016A THR* 4.4 8.7 - - + -
2017A LEU* 3.5 34.3 - - + -
2020A MET* 3.7 16.8 - - - -
2049A LEU* 4.3 4.9 - - + -
2101A TYR* 3.4 25.8 - - + -
2104A PHE* 3.4 36.1 - - + -
2146A CYS 3.0 17.3 + - - +
2149A LEU* 1.3 76.0 - - - +
2151A THR* 1.3 62.8 + - - +
2153A ARG* 3.3 10.9 + - - +
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Residues in contact with THR2151 (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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2101A TYR* 4.9 0.3 - - - -
2104A PHE* 3.7 12.9 - - - -
2105A CYS* 4.0 31.6 - - + -
2108A HIS* 3.4 37.8 + - + +
2147A ILE 2.9 19.5 + - - -
2148A LEU* 3.6 6.5 - - - -
2149A LEU 3.3 0.2 - - - -
2150A VAL* 1.3 77.9 - - - +
2152A GLN* 1.3 62.6 + - - +
2153A ARG 3.4 0.7 + - - -
2154A ILE* 4.3 10.6 - - - +
2155A THR* 5.0 2.4 - - - +
2152B GLN* 5.2 5.8 - - - +
2156B LYS* 5.7 6.3 - - - +
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Residues in contact with GLN2152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2148A LEU 3.0 12.7 + - - +
2149A LEU* 3.6 20.4 - - - +
2150A VAL 3.3 0.2 - - - -
2151A THR* 1.3 75.9 - - - +
2153A ARG* 1.3 65.4 + - - +
2155A THR* 2.5 33.8 + - - +
2156A LYS* 3.3 33.6 + - - +
2108B HIS* 5.5 1.7 + - - -
2148B LEU* 3.6 30.1 + - - +
2151B THR* 5.1 4.5 - - - +
2152B GLN* 2.9 53.6 - - + +
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Residues in contact with ARG2153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2006A LEU 3.8 3.4 + - - -
2009A THR* 3.0 42.8 + - - -
2010A GLU* 2.9 32.9 + - - +
2013A HIS* 3.3 49.5 - - + +
2101A TYR* 4.3 3.6 - - - +
2149A LEU 3.2 6.6 + - - +
2150A VAL 3.6 5.6 - - - +
2151A THR 3.3 2.0 - - - -
2152A GLN* 1.3 77.7 - - - +
2154A ILE* 1.3 59.3 + - - +
2156A LYS* 2.9 53.5 + - - +
2157A TYR* 3.3 38.1 + - + +
2160A LEU* 4.2 7.0 - - - +
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Residues in contact with ILE2154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2089A PHE* 5.2 2.9 - - + -
2097A LEU* 5.0 5.8 - - + +
2101A TYR* 4.1 40.8 - - + -
2105A CYS* 5.3 1.8 - - - -
2150A VAL 4.6 1.2 + - - -
2151A THR 4.3 9.8 + - - +
2152A GLN 3.1 0.4 + - - -
2153A ARG* 1.3 79.0 - - - +
2155A THR* 1.3 73.4 + - + +
2156A LYS 3.3 0.9 + - - -
2157A TYR* 3.5 28.0 - - + +
2158A PRO* 3.7 3.8 - - - +
2185A VAL* 4.3 5.0 - - + +
2188A VAL* 3.5 32.8 - - + -
2189A ILE* 3.6 25.4 - - + +
2192A VAL* 4.2 16.8 - - + -
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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