Contacts of the helix formed by residues 2121 - 2136 (chain D) in PDB entry 3CMT
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 THR2121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2119D PRO* 3.8 4.4 - - - +
2120D ASP* 1.3 85.6 - - + +
2122D GLY* 1.3 63.0 + - - +
2123D GLU* 3.7 15.8 + - - +
2124D GLN* 3.1 28.1 + - - +
2125D ALA* 3.1 21.1 + - - +
2150D THR 3.5 7.6 - - - -
2152D LYS* 3.9 36.3 - - + +
2155D ILE* 3.8 15.0 - - + -
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Residues in contact with GLY2122 (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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2121D THR* 1.3 69.4 - - - +
2123D GLU* 1.3 64.1 + - - +
2125D ALA* 3.2 6.5 + - - +
2126D LEU* 3.0 27.2 + - - +
2149D LEU* 3.9 30.7 - - - +
2150D THR 2.7 22.3 + - - +
2170D MET* 4.1 9.0 - - - -
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Residues in contact with GLU2123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159D ILE* 3.6 32.4 - - + +
1160D GLY* 4.0 14.6 - - - -
2121D THR* 3.3 5.5 - - - +
2122D GLY* 1.3 76.5 - - - +
2124D GLN* 1.3 52.1 + - - +
2126D LEU* 3.3 1.9 + - - +
2127D GLU* 2.8 39.3 + - - +
2151D PRO* 3.5 7.8 - - - +
2152D LYS* 2.6 46.4 + - + +
2153D ALA 5.3 0.2 + - - -
2166D LEU* 4.6 6.2 - - - +
2170D MET* 3.7 25.8 - - + +
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Residues in contact with GLN2124 (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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2118D GLN 4.9 0.3 - - - +
2119D PRO* 3.4 9.5 - - + +
2120D ASP* 3.4 48.1 + - - +
2121D THR* 3.1 20.1 + - - +
2123D GLU* 1.3 78.6 - - - +
2125D ALA* 1.3 63.8 + - - +
2127D GLU* 3.2 1.9 + - - +
2128D ILE* 2.9 34.7 + - + +
3021D PHE* 3.3 59.1 + - + +
3025D SER* 4.2 11.3 - - - +
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Residues in contact with ALA2125 (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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2093D ILE* 4.0 12.5 - - + +
2119D PRO* 3.6 29.5 - - + +
2121D THR 3.1 7.0 + - - +
2122D GLY 3.2 9.6 + - - +
2124D GLN* 1.3 79.2 - - - +
2126D LEU* 1.3 58.0 + - + +
2128D ILE* 3.5 7.3 + - - +
2129D CYS* 3.2 29.4 + - - -
2143D VAL* 5.5 2.0 - - + -
2149D LEU* 3.8 23.3 - - + -
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Residues in contact with LEU2126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159D ILE* 3.7 24.1 - - + +
2122D GLY 3.0 20.4 + - - +
2123D GLU 3.9 2.2 - - - +
2125D ALA* 1.3 74.4 - - + +
2127D GLU* 1.3 60.4 + - - +
2128D ILE 3.2 0.4 - - - -
2129D CYS* 3.3 10.0 + - - +
2130D ASP* 3.0 28.1 + - - +
2143D VAL* 5.5 1.6 - - + -
2149D LEU* 4.1 11.7 - - + -
2170D MET* 3.9 22.7 - - + -
2171D MET* 3.5 35.4 - - + -
2174D ALA* 3.8 21.1 - - + -
2178D LEU* 4.5 6.1 - - + +
2191D PHE* 4.1 19.3 - - + -
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Residues in contact with GLU2127 (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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1158D GLU* 3.3 30.2 - - - +
1159D ILE* 3.1 41.2 + - + +
2123D GLU* 2.8 18.8 + - + +
2124D GLN 3.7 0.4 - - - +
2126D LEU* 1.3 76.9 - - - +
2128D ILE* 1.3 57.1 + - - +
2130D ASP* 3.4 7.5 + - - +
2131D ALA* 3.0 27.9 + - - +
2134D ARG* 5.1 8.8 + - - -
2177D LYS* 3.5 16.3 + - - -
3020D GLN* 4.4 5.2 - - - +
3021D PHE* 3.7 25.2 - - + -
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Residues in contact with ILE2128 (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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2093D ILE* 3.9 22.0 - - + -
2117D SER* 3.5 22.9 - - - +
2119D PRO* 4.7 1.6 - - + -
2124D GLN* 2.9 40.3 + - + +
2125D ALA* 3.6 9.0 - - - +
2127D GLU* 1.3 74.6 - - - +
2129D CYS* 1.3 65.8 + - - +
2131D ALA* 3.2 7.2 + - - +
2132D LEU* 3.0 35.6 + - + +
3017D ILE* 3.8 33.9 - - + -
3021D PHE* 4.2 9.0 - - + -
3025D SER* 4.5 3.8 - - - +
3026D ILE* 4.4 7.9 - - + -
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Residues in contact with CYS2129 (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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2093D ILE* 4.1 5.4 - - - -
2125D ALA 3.2 16.5 + - - -
2126D LEU* 3.4 15.9 - - - +
2128D ILE* 1.3 78.9 - - - +
2130D ASP* 1.3 51.9 + - - +
2132D LEU* 3.3 3.4 + - - +
2133D ALA* 2.8 36.4 + - - +
2141D ILE* 3.9 27.7 - - + +
2143D VAL* 3.7 29.8 - - - -
2178D LEU* 4.1 16.8 - - + -
2189D LEU* 4.8 9.9 - - + -
2191D PHE* 5.7 0.2 - - - -
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Residues in contact with ASP2130 (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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1155D ILE 5.3 0.2 - - - +
1159D ILE* 4.6 2.2 - - + -
2126D LEU 3.0 16.3 + - - +
2127D GLU* 3.7 13.2 - - - +
2128D ILE 3.2 0.2 - - - -
2129D CYS* 1.3 76.2 - - - +
2131D ALA* 1.3 58.0 + - - +
2133D ALA* 3.4 2.1 + - - +
2134D ARG* 2.5 60.5 + - - +
2177D LYS* 3.4 36.8 + - - +
2178D LEU* 3.6 20.7 - - + +
2181D ASN* 2.8 23.8 - - - +
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Residues in contact with ALA2131 (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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2127D GLU* 3.0 17.3 + - - +
2128D ILE 3.2 5.4 + - - +
2130D ASP* 1.3 77.4 - - - +
2132D LEU* 1.3 56.4 + - - +
2134D ARG* 3.4 22.1 + - - +
2135D SER* 3.0 28.6 + - - -
3013D ALA* 4.4 7.5 - - + +
3016D GLN* 5.2 10.5 - - + +
3017D ILE* 4.0 24.0 - - + -
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Residues in contact with LEU2132 (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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2091D ALA* 3.7 29.6 - - + -
2093D ILE* 4.7 4.9 - - + -
2115D LEU* 4.7 2.0 - - + -
2128D ILE* 3.0 34.7 + - + +
2129D CYS 3.7 2.7 - - - +
2131D ALA* 1.3 71.4 - - - +
2133D ALA* 1.3 66.5 + - - +
2135D SER* 2.7 23.9 + - - +
2136D GLY* 3.6 2.4 + - - -
2138D VAL* 3.8 30.3 + - + +
2141D ILE* 3.8 16.4 - - + -
3010D LEU* 5.4 0.9 - - + -
3013D ALA* 4.9 5.8 - - + -
3014D LEU* 4.6 14.8 - - + -
3017D ILE* 4.0 19.1 - - + -
3026D ILE* 4.3 12.3 - - + -
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Residues in contact with ALA2133 (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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2129D CYS 2.8 21.4 + - - +
2130D ASP* 3.5 7.4 - - - +
2132D LEU* 1.3 75.3 - - - +
2134D ARG* 1.3 58.9 + - - +
2136D GLY 3.2 2.4 + - - -
2141D ILE* 4.2 4.6 - - + +
2178D LEU* 4.8 1.8 - - + -
2181D ASN* 4.0 20.6 - - + -
2182D LEU* 4.0 26.9 - - + -
2185D SER* 2.5 31.9 + - - -
2187D THR* 4.1 9.4 + - - -
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Residues in contact with ARG2134 (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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1155D ILE 5.8 1.2 + - - -
2127D GLU* 5.1 8.5 + - - -
2130D ASP* 2.5 54.0 + - - +
2131D ALA* 3.6 24.1 - - - +
2133D ALA* 1.3 72.5 - - - +
2135D SER* 1.3 62.9 + - - +
2136D GLY* 3.2 1.9 + - - -
2177D LYS* 5.0 1.4 - - - +
2181D ASN* 3.2 33.6 + - - +
2185D SER* 4.3 4.9 + - - -
3016D GLN* 5.2 9.5 - - - +
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Residues in contact with SER2135 (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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2131D ALA 3.0 16.0 + - - -
2132D LEU* 2.7 23.1 + - - +
2134D ARG* 1.3 75.8 - - - +
2136D GLY* 1.3 59.7 + - - +
2137D ALA* 3.1 19.1 + - - +
2138D VAL* 4.1 3.3 + - - +
3009D ALA* 3.8 29.2 - - - +
3010D LEU* 5.1 0.6 - - - +
3013D ALA* 3.9 22.6 - - - +
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Residues in contact with GLY2136 (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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2132D LEU 3.6 0.6 + - - -
2133D ALA 3.2 11.6 + - - -
2134D ARG 3.2 4.9 - - - -
2135D SER* 1.3 77.6 + - - +
2137D ALA* 1.3 59.0 + - - +
2138D VAL 3.6 5.5 - - - +
2139D ASP* 5.7 0.3 - - - +
2185D SER* 4.0 23.1 - - - +
3006D LYS* 4.0 15.3 - - - +
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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