Contacts of the helix formed by residues 2142 - 2154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2115B PHE* 6.0 0.7 - - - -
2133B MET* 3.4 22.4 - - - -
2140B ARG 2.9 8.9 + - - -
2141B LEU* 1.3 76.8 - - - +
2143B ILE* 1.3 66.6 + - - -
2144B PRO* 3.3 8.5 - - - -
2145B GLU* 3.2 15.8 + - - +
2146B CYS* 3.0 22.3 + - - -
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Residues in contact with ILE2143 (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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2024B TYR* 3.9 34.9 + - + -
2028B MET* 3.5 30.7 - - + -
2042B LEU* 4.4 3.6 - - + -
2043B PHE* 4.0 17.7 - - + -
2115B PHE* 3.6 40.2 - - + -
2125B PHE* 4.4 3.6 - - + -
2129B VAL* 4.8 3.8 - - + +
2142B GLY* 1.3 71.6 - - - -
2144B PRO* 1.3 71.6 - - + +
2146B CYS* 3.3 8.8 + - - +
2147B ILE* 3.0 41.4 + - + +
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Residues in contact with PRO2144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2140A ARG 5.9 0.7 - - - +
2145A GLU* 4.0 30.5 - - + +
2112B VAL* 4.2 23.0 - - + +
2115B PHE* 3.5 35.2 - - + -
2116B LYS* 4.8 2.9 - - - -
2142B GLY* 3.3 7.2 - - - -
2143B ILE* 1.3 95.8 - - + +
2145B GLU* 1.3 62.6 + - + +
2147B ILE* 3.4 2.6 + - + +
2148B LEU* 3.0 28.3 + - - +
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Residues in contact with GLU2145 (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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2112A VAL* 5.3 0.3 - - - +
2116A LYS* 3.3 25.0 + - - -
2144A PRO* 3.2 41.1 - - + +
2145A GLU* 4.7 7.0 - - + +
2148A LEU* 4.1 10.9 - - + +
2133B MET* 5.0 3.3 - - - +
2140B ARG 3.6 10.2 - - - +
2141B LEU* 3.7 13.1 - - + +
2142B GLY* 3.2 25.7 + - - +
2144B PRO* 1.3 76.1 - - + +
2146B CYS* 1.3 61.1 + - - +
2148B LEU* 3.2 8.5 + - - +
2149B LEU* 2.8 38.1 + - + +
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Residues in contact with CYS2146 (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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2016B THR* 4.3 10.3 - - + +
2019B ILE* 5.2 1.3 - - - -
2020B MET* 3.6 35.7 - - + -
2024B TYR* 4.4 13.0 - - - -
2043B PHE* 5.7 0.2 - - + -
2141B LEU* 3.9 31.4 - - - -
2142B GLY 3.0 20.3 + - - -
2143B ILE* 3.3 10.7 + - + +
2145B GLU* 1.3 74.5 - - - +
2147B ILE* 1.3 63.0 + - + +
2149B LEU* 3.1 6.3 + - - +
2150B VAL* 3.0 26.9 + - - +
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Residues in contact with ILE2147 (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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2020B MET* 5.0 0.4 - - + -
2042B LEU* 4.4 6.1 - - + +
2043B PHE* 4.3 15.7 - - + -
2104B PHE* 3.6 28.4 - - + -
2108B HIS* 3.7 30.3 - - - +
2111B SER* 4.1 20.6 - - - +
2112B VAL* 3.8 28.7 - - + +
2143B ILE* 3.0 34.4 + - + +
2144B PRO* 3.7 3.8 - - + +
2146B CYS* 1.3 78.4 - - - +
2148B LEU* 1.3 57.9 + - - +
2150B VAL* 3.3 0.6 + - - -
2151B THR* 2.9 32.6 + - - -
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Residues in contact with LEU2148 (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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2145A GLU* 3.9 29.8 - - + +
2148A LEU* 3.7 33.0 - - + -
2149A LEU* 4.2 20.0 - - + +
2152A GLN* 3.6 22.9 + - - +
2108B HIS* 3.4 28.9 - - + +
2112B VAL* 5.5 3.8 - - + -
2144B PRO 3.0 17.8 + - - +
2145B GLU 3.5 4.7 - - - +
2146B CYS 3.2 0.2 - - - -
2147B ILE* 1.3 78.8 - - + +
2149B LEU* 1.3 61.0 + - - +
2151B THR* 3.3 4.3 + - - -
2152B GLN* 3.0 30.5 + - - +
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Residues in contact with LEU2149 (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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2108A HIS* 6.3 0.4 - - - +
2148A LEU* 4.3 20.0 - - + -
2013B HIS* 4.8 2.5 + - - +
2016B THR* 4.4 22.2 - - + +
2141B LEU* 3.8 27.6 - - + -
2145B GLU* 2.8 25.7 + - + +
2146B CYS* 3.5 4.3 - - - +
2148B LEU* 1.3 73.0 - - - +
2150B VAL* 1.3 62.7 + - - +
2152B GLN* 3.4 20.6 + - - +
2153B ARG* 3.2 21.5 + - - +
2156B LYS* 5.8 0.6 - - - -
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Residues in contact with VAL2150 (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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2013B HIS* 4.0 14.1 - - + -
2016B THR* 4.4 9.0 - - + -
2017B LEU* 3.5 32.8 - - + -
2020B MET* 3.7 16.6 - - - -
2049B LEU* 4.3 5.2 - - + -
2101B TYR* 3.4 25.8 - - + -
2104B PHE* 3.4 36.3 - - + -
2146B CYS 3.0 17.7 + - - +
2149B LEU* 1.3 74.3 - - - +
2151B THR* 1.3 62.9 + - - +
2153B ARG* 3.3 10.4 + - - +
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Residues in contact with THR2151 (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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2152A GLN* 5.1 6.3 - - - +
2156A LYS* 5.4 8.3 - - - +
2101B TYR* 4.9 0.2 - - - -
2104B PHE* 3.7 12.9 - - - -
2105B CYS* 4.0 33.9 - - + -
2108B HIS* 3.4 36.3 + - + +
2147B ILE 2.9 19.6 + - - -
2148B LEU* 3.6 7.0 - - - -
2150B VAL* 1.3 78.2 - - - +
2152B GLN* 1.3 61.4 + - - +
2153B ARG 3.4 0.7 + - - -
2154B ILE* 4.2 10.4 - - - +
2155B THR* 5.0 2.6 - - - +
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Residues in contact with GLN2152 (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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2108A HIS* 5.7 1.2 + - - -
2148A LEU* 3.6 29.7 + - - +
2151A THR* 5.2 5.2 - - - +
2152A GLN* 2.9 53.5 - - + +
2148B LEU 3.0 12.7 + - - +
2149B LEU* 3.6 20.3 - - - +
2151B THR* 1.3 76.2 - - - +
2153B ARG* 1.3 66.5 + - - +
2155B THR* 2.5 32.7 + - - +
2156B LYS* 3.2 32.5 + - - +
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Residues in contact with ARG2153 (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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2006B LEU 3.8 3.6 + - - -
2009B THR* 3.0 43.5 + - - -
2010B GLU* 2.9 32.5 + - - +
2013B HIS* 3.3 48.3 - - + +
2101B TYR* 4.3 3.8 - - - +
2149B LEU 3.2 7.3 + - - +
2150B VAL 3.6 6.1 - - - +
2151B THR 3.3 2.2 - - - -
2152B GLN* 1.3 77.9 - - - +
2154B ILE* 1.3 58.8 + - - +
2156B LYS* 2.9 52.7 + - - +
2157B TYR* 3.3 37.9 + - + +
2160B LEU* 4.2 7.0 - - - +
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Residues in contact with ILE2154 (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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2089B PHE* 5.2 2.9 - - + -
2097B LEU* 5.0 5.6 - - + +
2101B TYR* 4.1 40.5 - - + -
2105B CYS* 5.3 1.6 - - - -
2150B VAL 4.6 1.0 + - - -
2151B THR 4.2 10.9 + - - +
2152B GLN 3.1 0.4 + - - -
2153B ARG* 1.3 78.6 - - - +
2155B THR* 1.3 73.4 + - + +
2156B LYS 3.5 0.5 + - - -
2157B TYR* 3.6 27.7 - - + +
2158B PRO* 3.6 4.0 - - - +
2185B VAL* 4.3 5.0 - - + +
2188B VAL* 3.5 32.5 - - + -
2189B ILE* 3.6 25.5 - - + +
2192B VAL* 4.2 17.5 - - + -
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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