Contacts of the helix formed by residues 2139 - 2156 (chain A) in PDB entry 4UXL
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 THR2139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2076A ILE* 3.1 16.7 - - - +
2109A ILE* 6.4 1.6 - - - -
2131A GLU* 4.8 3.6 + - - -
2137A ILE* 4.1 16.6 - - + -
2138A PHE* 1.3 79.8 - - - +
2140A THR* 1.3 64.4 + - - +
2141A GLN* 3.1 36.5 + - - +
2142A SER* 2.7 27.5 + - - -
2143A ASP 3.1 5.5 + - - -
2202A PRO* 5.4 0.3 - - - +
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Residues in contact with THR2140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2071A GLU* 3.9 24.8 + - - +
2075A PHE 5.9 3.1 - - - -
2076A ILE* 4.3 4.9 - - - +
2109A ILE* 6.1 7.1 - - - +
2139A THR* 1.3 73.8 - - - +
2141A GLN* 1.3 85.1 + - + +
2143A ASP* 3.1 13.5 - - - +
2144A VAL* 3.0 28.9 + - - +
2208A PHE* 3.7 21.3 - - - -
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Residues in contact with GLN2141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2139A THR* 3.0 21.4 + - - +
2140A THR* 1.3 101.8 - - + +
2142A SER* 1.3 57.7 + - - +
2144A VAL* 3.6 10.4 + - + +
2145A TRP 3.3 9.2 + - - -
2202A PRO* 3.5 40.4 + - + +
2203A ASP* 5.1 3.6 - - - +
2205A ARG* 2.6 36.6 + - + +
2206A PRO 6.0 1.1 - - - +
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Residues in contact with SER2142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2076A ILE* 4.2 1.6 - - - +
2129A ALA* 3.8 12.8 + - - +
2131A GLU* 3.9 7.2 - - - -
2132A SER* 3.6 21.9 + - - -
2137A ILE 4.6 0.4 - - - -
2138A PHE* 3.5 12.9 - - - +
2139A THR* 2.7 37.9 + - - -
2141A GLN* 1.3 75.3 - - - +
2143A ASP* 1.3 65.5 + - - +
2144A VAL 3.2 0.2 - - - -
2145A TRP* 3.2 4.2 + - - +
2146A SER* 3.1 24.6 + - - -
2205A ARG* 3.5 7.8 - - - +
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Residues in contact with ASP2143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2070A LEU* 5.4 1.9 - - - +
2075A PHE 4.6 1.7 - - - +
2076A ILE* 3.5 16.9 - - - +
2077A HIS* 2.9 27.0 + - - +
2078A ARG* 3.0 28.5 + - - -
2080A LEU* 3.5 22.8 + - + +
2139A THR 3.1 5.3 + - - -
2140A THR* 3.1 18.7 - - - +
2142A SER* 1.3 79.3 + - - +
2144A VAL* 1.3 54.2 + - - +
2146A SER* 3.3 4.4 + - - -
2147A PHE* 2.9 24.8 + - - +
2208A PHE* 4.0 16.6 - - + -
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Residues in contact with VAL2144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2140A THR* 3.0 19.7 + - - +
2141A GLN* 3.6 15.0 - - + +
2143A ASP* 1.3 74.5 - - - +
2145A TRP* 1.3 65.8 + - - +
2147A PHE* 3.8 3.2 - - - +
2148A GLY 3.1 16.6 + - - -
2197A CYS* 3.4 28.1 - - - +
2205A ARG* 3.9 16.8 - - + -
2206A PRO* 3.6 26.7 - - + +
2207A THR* 5.0 0.7 - - - -
2208A PHE* 3.9 29.4 - - + +
2211A ILE* 3.9 7.0 - - + -
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Residues in contact with TRP2145 (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 ARG 4.9 0.8 + - - -
2127A TRP 3.4 21.7 + - - -
2128A MET 3.3 14.8 + - - -
2129A ALA* 3.5 21.1 - - + -
2130A PRO* 3.6 27.8 - - + -
2141A GLN 3.3 3.4 + - - -
2142A SER 3.2 9.5 + - - +
2144A VAL* 1.3 78.2 - - - +
2146A SER* 1.3 61.4 + - - +
2148A GLY 3.2 3.8 + - - -
2149A ILE* 3.2 14.5 + - + +
2162A TYR* 4.3 14.2 + - - -
2174A VAL* 3.9 15.3 - - + -
2179A ARG* 3.6 31.6 - - - -
2197A CYS 3.4 12.8 - - - +
2198A TRP* 3.1 70.9 + + + -
2199A ALA 4.0 4.5 - - - -
2205A ARG* 3.8 17.5 - - - +
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Residues in contact with SER2146 (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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2078A ARG 5.6 3.8 + - - -
2079A ASP* 5.8 0.5 - - - -
2080A LEU* 3.8 32.9 + - - +
2127A TRP* 2.4 30.3 + - - +
2128A MET* 4.5 1.9 - - - -
2142A SER 3.1 11.1 + - - -
2143A ASP* 3.3 10.4 + - - -
2145A TRP* 1.3 76.5 - - - +
2147A PHE* 1.3 59.4 + - - +
2149A ILE* 3.1 8.8 + - - +
2150A LEU* 2.8 25.5 + - - +
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Residues in contact with PHE2147 (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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2060A CYS 3.7 7.2 - - - -
2063A ILE* 3.4 36.6 - - + -
2064A SER* 3.4 28.3 - - - -
2067A CYS* 4.1 9.9 - - - -
2080A LEU* 4.4 6.4 - - + +
2143A ASP 2.9 14.8 + - - +
2144A VAL 3.8 4.9 - - - +
2146A SER* 1.3 72.7 - - - +
2148A GLY* 1.3 62.4 + - - +
2150A LEU* 3.0 11.3 + - + +
2151A ILE* 2.8 62.2 + - + +
2197A CYS* 4.9 0.9 - - - -
2208A PHE* 4.1 13.5 - + + -
2211A ILE* 3.4 38.4 - - + -
2215A LEU* 4.3 2.9 - - + -
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Residues in contact with GLY2148 (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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2144A VAL 3.1 11.1 + - - -
2145A TRP 3.2 1.1 + - - -
2147A PHE* 1.3 78.0 - - - +
2149A ILE* 1.3 60.9 + - - +
2151A ILE* 3.1 16.4 - - - +
2152A TRP 3.1 16.8 + - - -
2194A MET* 3.8 1.7 - - - +
2197A CYS* 3.8 14.8 - - - -
2198A TRP* 3.3 31.5 - - - -
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Residues in contact with ILE2149 (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 ARG 3.8 18.4 - - - +
2127A TRP* 3.4 28.7 - - + +
2145A TRP* 3.4 25.4 - - + +
2146A SER* 3.1 13.1 + - - +
2148A GLY* 1.3 72.2 - - - +
2150A LEU* 1.3 60.8 + - - +
2152A TRP* 3.2 5.0 + - - +
2153A GLU* 2.9 26.5 + - - +
2161A PRO* 3.8 24.0 - - + -
2162A TYR* 3.9 11.9 - - - +
2180A LEU* 3.8 20.0 - - + -
2198A TRP* 3.6 20.0 - - + +
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Residues in contact with LEU2150 (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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2034A LEU* 4.1 11.7 - - + -
2063A ILE* 3.6 33.4 - - + -
2080A LEU* 4.9 7.2 - - + +
2081A ALA* 4.6 13.0 - - - +
2082A ALA* 3.5 38.6 - - + +
2085A CYS* 4.1 13.9 - - - -
2127A TRP* 4.8 0.8 - - - +
2146A SER 2.8 12.9 + - - +
2147A PHE* 3.0 18.4 + - + +
2149A ILE* 1.3 76.9 - - - +
2151A ILE* 1.3 58.7 + - + +
2153A GLU* 2.8 26.7 + - - +
2154A ILE* 2.9 20.1 + - + +
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Residues in contact with ILE2151 (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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2060A CYS* 3.9 24.0 - - + -
2147A PHE* 2.8 60.2 + - + +
2148A GLY* 3.1 20.6 - - - +
2150A LEU* 1.3 73.0 - - - +
2152A TRP* 1.3 56.7 + - - +
2154A ILE* 3.3 10.5 + - + -
2155A LEU* 2.9 38.1 + - + +
2190A LEU 5.4 0.4 - - - +
2193A LEU* 4.3 23.3 - - + -
2194A MET* 3.4 25.6 - - + -
2197A CYS* 5.0 1.6 - - - -
2215A LEU* 5.4 1.8 - - + -
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Residues in contact with TRP2152 (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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2148A GLY 3.1 14.3 + - - +
2149A ILE 3.3 11.2 - - - +
2151A ILE* 1.3 78.4 - - - +
2153A GLU* 1.3 61.9 + - - +
2155A LEU* 3.3 2.4 + - - +
2156A THR* 3.0 49.1 + - + +
2159A HIS* 3.3 36.8 - - + -
2160A GLN 3.5 14.8 - - - -
2161A PRO* 3.5 24.5 - - + -
2162A TYR 4.9 0.7 - - - -
2163A PRO* 5.1 6.5 - - + -
2180A LEU* 3.6 37.5 - - + +
2181A GLU* 2.8 30.5 + - + -
2183A PRO* 3.9 21.9 - - + +
2191A TRP* 4.6 0.9 - + - -
2194A MET* 3.8 16.6 - - - -
2198A TRP* 4.2 3.6 - + + -
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Residues in contact with GLU2153 (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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2035A LEU* 3.5 25.6 - - - +
2038A LEU* 3.5 3.3 - - + +
2081A ALA* 3.7 1.6 - - - -
2082A ALA* 2.9 38.0 + - + +
2083A ARG 4.9 0.5 + - - -
2127A TRP* 3.0 38.1 + - - +
2149A ILE 2.9 12.2 + - - +
2150A LEU* 2.8 16.0 + - - +
2152A TRP* 1.3 83.7 - - + +
2154A ILE* 1.3 57.7 + - - +
2156A THR* 3.4 6.0 + - - -
2157A LEU 3.2 2.4 + - - -
2158A GLY* 2.7 32.1 + - - +
2159A HIS 4.2 14.8 - - - +
2161A PRO* 4.6 4.9 - - + +
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Residues in contact with ILE2154 (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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2034A LEU* 3.8 31.0 - - + -
2038A LEU* 3.7 10.3 - - + -
2056A LEU* 3.6 51.9 - - + +
2059A LEU* 4.1 18.8 - - + +
2060A CYS* 3.8 26.9 - - - +
2063A ILE* 5.1 3.4 - - + -
2150A LEU* 2.9 26.0 + - + +
2151A ILE* 3.5 11.9 - - + +
2153A GLU* 1.3 76.9 - - - +
2155A LEU* 1.3 58.4 + - + +
2157A LEU* 3.0 20.4 + - - +
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Residues in contact with LEU2155 (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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2053A LEU* 4.0 26.9 - - + -
2056A LEU* 4.4 18.3 - - + +
2057A VAL 5.6 0.2 - - - +
2060A CYS* 3.9 23.8 - - - -
2151A ILE* 2.9 33.1 + - + +
2152A TRP* 3.3 1.5 + - - +
2154A ILE* 1.3 78.4 - - + +
2156A THR* 1.3 59.0 + - - +
2157A LEU* 3.3 9.0 + - - +
2183A PRO* 3.9 26.2 - - + +
2184A ARG 5.5 1.0 - - - +
2186A CYS* 4.7 4.9 - - + -
2187A PRO* 4.9 4.7 - - + -
2190A LEU* 4.2 20.6 - - + -
2194A MET* 4.6 12.8 - - + -
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Residues in contact with THR2156 (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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2042A ARG* 3.6 2.4 + - - -
2152A TRP* 3.0 52.1 + - + +
2153A GLU* 3.4 3.5 + - - -
2154A ILE 3.2 0.2 - - - -
2155A LEU* 1.3 75.3 - - - +
2157A LEU* 1.3 65.9 + - - +
2159A HIS* 2.8 63.6 + - + +
2183A PRO* 3.8 23.1 - - + -
2184A ARG* 6.3 1.1 - - - +
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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
------------------------------------------------------------
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