Contacts of the helix formed by residues 2160 - 2172 (chain D) in PDB entry 2C5L
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 THR2160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2158D VAL 3.6 2.5 + - - -
2159D SER* 1.3 76.1 - - - +
2161D ALA* 1.3 60.8 + - - +
2162D GLN* 3.4 15.7 - - + +
2163D ASP* 3.0 55.1 + - - +
2164D VAL* 3.0 15.4 + - - +
2215D GLN* 2.9 51.6 + - - +
2216D GLU 3.5 5.6 - - - -
2217D CYS* 4.8 0.4 - - - +
2218D VAL* 4.3 1.6 - - - -
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Residues in contact with ALA2161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2160D THR* 1.3 74.6 + - - +
2162D GLN* 1.3 58.4 + - - +
2164D VAL* 3.4 2.9 + - - +
2165D ILE* 2.9 39.4 + - + +
2189D LEU* 4.1 12.4 - - + +
2212D LEU* 4.5 13.0 - - + -
2213D LEU 3.6 24.2 - - - +
2214D ASP* 3.7 3.6 - - - +
2216D GLU 3.0 11.6 + - - +
2218D VAL* 3.8 17.3 - - + -
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Residues in contact with GLN2162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2160D THR* 3.3 10.5 - - + -
2161D ALA* 1.3 77.7 - - - +
2163D ASP* 1.3 58.4 + - - +
2165D ILE* 3.8 9.3 - - - +
2166D GLN* 2.9 28.8 + - - +
2184D PRO* 2.7 50.5 + - - +
2185D SER* 3.3 15.2 + - - +
2187D TYR 3.4 16.0 + - - -
2214D ASP* 3.2 36.0 + - + +
2215D GLN* 4.7 6.7 - - - +
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Residues in contact with ASP2163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2158D VAL 5.0 0.5 - - - +
2159D SER* 3.9 15.9 + - - +
2160D THR* 3.0 45.7 + - - +
2162D GLN* 1.3 76.3 - - - +
2164D VAL* 1.3 58.7 + - - +
2166D GLN* 3.4 8.1 + - - +
2167D GLN* 3.0 33.7 + - - +
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Residues in contact with VAL2164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137D PHE* 5.3 0.4 - - + -
2139D VAL* 4.4 17.0 - - + -
2141D VAL* 4.1 22.4 - - + -
2153D ILE* 4.6 5.3 - - + +
2155D ALA* 4.6 12.6 - - + -
2159D SER* 4.3 13.5 - - - -
2160D THR 3.0 13.4 + - - +
2161D ALA 3.8 6.1 - - - +
2163D ASP* 1.3 72.0 - - - +
2165D ILE* 1.3 59.7 + - - +
2167D GLN* 3.1 10.3 + - - +
2168D THR* 2.8 31.3 + - - +
2189D LEU* 3.9 19.5 - - + -
2218D VAL* 3.7 22.0 - - + -
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Residues in contact with ILE2165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2161D ALA* 2.9 27.8 + - + +
2162D GLN* 3.8 14.1 - - - +
2164D VAL* 1.3 75.2 - - - +
2166D GLN* 1.3 56.9 + - - +
2168D THR* 3.3 7.8 + - - -
2169D LEU* 2.8 42.4 + - + +
2184D PRO* 3.8 12.3 - - + +
2187D TYR* 3.6 43.1 - - + +
2188D VAL* 3.8 17.7 - - - -
2189D LEU* 3.8 18.4 - - + +
2214D ASP* 6.5 0.2 - - - -
2233D LEU* 3.9 14.6 - - + -
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Residues in contact with GLN2166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2162D GLN 2.9 19.9 + - - +
2163D ASP* 3.5 9.6 - - - +
2164D VAL 3.2 0.4 - - - -
2165D ILE* 1.3 78.0 - - - +
2167D GLN* 1.3 62.4 + - + +
2169D LEU* 3.4 5.5 + - - +
2170D CYS* 3.2 46.1 + - - -
2182D PRO 5.4 0.2 - - - +
2184D PRO* 3.4 31.1 - - + +
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Residues in contact with GLN2167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2153D ILE* 3.5 23.5 - - + +
2154D LYS 3.0 20.5 + - - +
2155D ALA* 3.4 30.3 - - - +
2156D PRO* 4.7 4.0 - - - +
2159D SER* 4.6 5.1 + - - -
2163D ASP* 3.0 21.1 + - - +
2164D VAL* 3.1 11.6 + - - +
2166D GLN* 1.3 78.8 - - + +
2168D THR* 1.3 61.1 + - - +
2170D CYS* 3.2 10.4 + - - +
2171D LYS* 3.2 26.4 + - - +
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Residues in contact with THR2168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2141D VAL* 3.5 23.8 - - + +
2144D VAL* 3.7 35.4 - - + +
2151D THR* 4.1 5.8 - - + -
2153D ILE* 3.3 19.7 - - - +
2164D VAL* 2.8 18.1 + - - +
2165D ILE* 3.5 11.8 - - - -
2167D GLN* 1.3 73.1 - - - +
2169D LEU* 1.3 62.4 + - - +
2171D LYS* 3.2 6.6 + - - +
2172D ALA* 3.1 21.5 + - - +
2189D LEU* 5.4 0.2 - - - +
2233D LEU* 4.2 13.2 - - + -
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Residues in contact with LEU2169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2165D ILE* 2.8 27.5 + - + +
2166D GLN* 4.0 6.3 - - - +
2167D GLN 3.4 0.2 - - - -
2168D THR* 1.3 73.4 - - - +
2170D CYS* 1.3 62.6 + - - +
2172D ALA 3.7 1.2 - - - -
2173D LYS* 3.3 21.1 + - - +
2178D ILE* 3.7 40.3 - - + +
2181D ASN 4.4 1.8 - - - +
2182D PRO* 4.0 13.0 - - + +
2183D ASN 4.0 5.4 - - - -
2184D PRO* 3.5 41.5 - - + -
2187D TYR* 3.8 29.4 - - + +
2233D LEU* 4.6 3.8 - - + -
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Residues in contact with CYS2170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP* 5.4 2.6 - - - +
2166D GLN* 3.2 38.5 + - - +
2167D GLN* 3.4 12.6 - - - +
2168D THR 3.2 0.2 - - - -
2169D LEU* 1.3 75.4 - - - +
2171D LYS* 1.3 64.4 + - + +
2173D LYS* 3.2 41.6 + - - +
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Residues in contact with LYS2171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP* 4.5 20.1 + - - +
34B PRO 5.3 6.3 + - - -
35B THR* 6.4 0.2 - - - +
36B ILE* 5.2 10.1 - - - +
38B ASP* 4.6 9.0 - - - +
40B TYR* 5.6 1.4 + - - -
2148D GLN* 4.4 9.7 - - - +
2151D THR* 3.6 31.2 - - + +
2152D VAL 3.7 18.3 + - - -
2153D ILE* 3.7 18.2 - - + +
2154D LYS 5.3 0.8 - - - +
2167D GLN* 3.2 16.4 + - - +
2168D THR* 3.2 11.4 + - - +
2170D CYS* 1.3 79.7 - - + +
2172D ALA* 1.3 58.4 + - + +
2173D LYS* 3.2 11.2 + - - +
2174D TYR* 4.7 4.3 + - - +
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Residues in contact with ALA2172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2144D VAL* 3.4 33.2 - - + -
2148D GLN* 4.0 13.5 - - - +
2168D THR 3.1 7.0 + - - +
2169D LEU 3.7 3.6 - - - -
2170D CYS 3.4 0.2 - - - -
2171D LYS* 1.3 76.7 - - + +
2173D LYS* 1.3 63.5 + - - +
2174D TYR 2.9 5.0 + - - +
2175D SER* 3.0 24.6 + - - +
2178D ILE* 3.5 24.6 - - + +
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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