Contacts of the helix formed by residues 1002 - 1022 (chain A) 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 ILE1002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A ALA* 1.3 86.7 - - + +
1003A ASP* 1.3 61.7 - - + +
1004A GLU 3.4 0.6 + - - -
1005A ASN* 3.9 13.2 + - - +
1006A LYS* 3.9 14.0 - - + +
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Residues in contact with ASP1003 (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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1001A ALA 4.2 3.5 + - - -
1002A ILE* 1.3 74.4 + - + +
1004A GLU* 1.3 90.0 + - - +
1005A ASN 3.3 0.9 - - - -
1006A LYS* 3.4 20.1 + - + +
1007A GLN* 3.4 26.7 + - - +
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Residues in contact with GLU1004 (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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1001A ALA* 3.2 35.7 + - - +
1002A ILE 3.4 0.4 - - - -
1003A ASP* 1.3 90.4 + - - +
1005A ASN* 1.3 62.3 + - - +
1006A LYS 3.2 0.2 - - - -
1007A GLN* 3.6 13.8 + - - +
1008A LYS* 3.3 21.0 + - - +
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Residues in contact with ASN1005 (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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1001A ALA 3.3 19.6 + - - -
1002A ILE* 3.9 9.9 + - - +
1003A ASP 3.3 0.2 - - - -
1004A GLU* 1.3 78.8 - - - +
1006A LYS* 1.3 62.1 + - + +
1008A LYS* 3.4 24.4 - - - +
1009A ALA* 3.2 21.7 + - - +
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Residues in contact with LYS1006 (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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87A GLY 5.0 6.3 + - - -
89A THR* 4.7 4.8 + - - -
136A GLY 4.2 15.5 - - - +
137A ALA* 3.5 28.3 + - - +
139A ASP* 3.1 34.8 + - - -
1002A ILE* 3.9 12.8 - - + +
1003A ASP* 3.4 23.7 + - + +
1004A GLU 3.2 0.6 - - - -
1005A ASN* 1.3 78.6 - - + +
1007A GLN* 1.3 51.5 + - + +
1009A ALA* 3.2 5.2 + - - -
1010A LEU* 2.8 35.1 + - - +
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Residues in contact with GLN1007 (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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1003A ASP* 3.4 13.6 + - - +
1004A GLU* 4.0 14.6 - - - +
1005A ASN 3.4 0.4 - - - -
1006A LYS* 1.3 74.2 - - + +
1008A LYS* 1.3 66.0 + - - +
1010A LEU* 3.5 19.6 - - + +
1011A ALA* 3.0 28.4 + - - +
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Residues in contact with LYS1008 (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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1004A GLU 3.3 11.5 + - - +
1005A ASN* 3.4 26.9 - - - +
1007A GLN* 1.3 80.6 - - - +
1009A ALA* 1.3 59.7 - - - +
1011A ALA* 4.4 2.6 - - - +
1012A ALA* 3.4 20.3 + - - +
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Residues in contact with ALA1009 (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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135A SER* 3.7 25.3 - - - +
136A GLY 5.7 0.2 - - - -
137A ALA* 4.2 3.1 - - + -
1005A ASN 3.2 8.7 + - - +
1006A LYS* 3.2 9.9 + - - +
1008A LYS* 1.3 78.9 - - + +
1010A LEU* 1.3 64.2 + - - +
1012A ALA* 3.5 7.8 - - - +
1013A ALA* 3.1 22.3 + - - +
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Residues in contact with LEU1010 (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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89A THR* 4.2 19.7 - - + +
115A LEU* 3.8 18.8 - - + -
132A LEU* 5.7 0.2 - - + -
135A SER* 5.7 0.2 - - - +
137A ALA* 3.5 22.0 - - + +
138A VAL* 4.2 7.4 - - + -
1006A LYS 2.8 20.8 + - - +
1007A GLN* 3.2 21.1 + - + +
1009A ALA* 1.3 70.7 - - - +
1011A ALA* 1.3 64.4 + - + +
1013A ALA* 2.9 7.4 + - + +
1014A LEU* 2.9 56.2 + - + +
1028A ARG* 6.3 1.1 - - - +
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Residues in contact with ALA1011 (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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1007A GLN 3.0 15.7 + - - +
1008A LYS* 4.4 3.4 - - - +
1010A LEU* 1.3 79.4 - - + +
1012A ALA* 1.3 56.5 + - - +
1014A LEU* 3.9 8.6 - - - +
1015A GLY* 2.9 28.6 + - - -
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Residues in contact with ALA1012 (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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1008A LYS 3.4 18.0 + - - +
1009A ALA* 3.5 10.1 - - - +
1010A LEU 3.1 0.4 - - - -
1011A ALA* 1.3 78.6 - - - +
1013A ALA* 1.3 57.4 + - - +
1015A GLY* 3.7 1.0 + - - -
1016A GLN* 3.1 26.9 + - - +
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Residues in contact with ALA1013 (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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131A ALA* 4.5 8.5 - - + +
132A LEU* 4.9 6.3 - - + -
135A SER* 3.5 32.5 - - - +
1009A ALA 3.1 5.1 + - - +
1010A LEU* 2.9 9.7 + - + +
1012A ALA* 1.3 74.7 - - - +
1014A LEU* 1.3 55.1 + - - +
1016A GLN* 3.2 9.1 + - - +
1017A ILE* 2.8 48.4 + - + +
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Residues in contact with LEU1014 (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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115A LEU* 3.6 35.2 - - + -
132A LEU* 4.6 11.0 - - + -
1010A LEU* 2.9 53.2 + - + +
1011A ALA* 3.9 8.5 - - - +
1013A ALA* 1.3 77.1 - - - +
1015A GLY* 1.3 57.4 + - - +
1017A ILE* 3.4 7.7 + - - +
1018A GLU* 3.0 37.5 + - + +
1026A ILE* 4.4 16.2 - - + +
1027A MET* 5.9 1.3 - - - -
1028A ARG* 5.4 9.0 - - - +
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Residues in contact with GLY1015 (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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1011A ALA 2.9 17.2 + - - -
1012A ALA 4.0 1.3 - - - -
1014A LEU* 1.3 76.7 - - - +
1016A GLN* 1.3 55.4 + - - +
1018A GLU* 3.4 4.9 + - - +
1019A LYS* 3.0 32.6 + - - +
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Residues in contact with GLN1016 (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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131A ALA* 5.2 8.3 - - + +
134A ARG* 5.1 10.1 - - - +
1012A ALA 3.1 19.7 + - - +
1013A ALA* 3.4 10.1 - - - +
1015A GLY* 1.3 75.4 - - - +
1017A ILE* 1.3 67.3 + - + +
1019A LYS* 3.5 11.9 + - - +
1020A GLN* 3.1 50.4 + - - +
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Residues in contact with ILE1017 (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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128A ILE* 4.1 31.6 - - + -
131A ALA* 4.0 23.6 - - + -
132A LEU* 3.7 34.3 - - + -
1013A ALA* 2.8 26.2 + - + +
1014A LEU* 3.7 8.1 - - - +
1015A GLY 3.3 0.2 - - - -
1016A GLN* 1.3 73.7 - - + +
1018A GLU* 1.3 54.5 + - - +
1020A GLN* 3.1 6.4 + - - +
1021A PHE* 2.7 42.0 + - + +
1025A SER* 4.0 7.9 - - - +
1026A ILE* 3.7 24.7 - - + -
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Residues in contact with GLU1018 (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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1014A LEU* 3.0 23.1 + - + +
1015A GLY* 4.0 4.8 - - - +
1017A ILE* 1.3 75.7 - - - +
1019A LYS* 1.3 58.2 + - - +
1022A GLY* 2.9 38.8 + - - +
1023A LYS 2.9 22.9 - - - +
1024A GLY* 3.6 7.8 - - - -
1025A SER* 3.7 4.1 + - - +
1026A ILE* 2.9 35.5 - - + +
1027A MET* 5.1 0.9 - - - +
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Residues in contact with LYS1019 (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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1015A GLY 3.0 18.4 + - - +
1016A GLN* 3.8 11.9 - - - +
1017A ILE 3.3 0.2 - - - -
1018A GLU* 1.3 77.3 - - - +
1020A GLN* 1.3 63.7 + - - +
1022A GLY 4.6 0.7 + - - -
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Residues in contact with GLN1020 (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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127A GLU* 4.7 8.4 + - - +
1016A GLN* 3.1 44.4 + - - +
1017A ILE* 3.1 4.7 + - - +
1019A LYS* 1.3 82.8 - - + +
1021A PHE* 1.3 93.5 + - + +
1022A GLY 3.6 1.1 - - - -
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Residues in contact with PHE1021 (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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120A ASP* 5.5 2.1 - - - +
124A GLN* 3.7 40.2 + - + +
127A GLU* 3.8 30.5 - - + -
128A ILE* 4.2 18.8 - - + -
131A ALA* 6.3 1.1 - - + -
1017A ILE* 2.7 36.2 + - + +
1020A GLN* 1.3 106.7 - - + +
1022A GLY* 1.3 60.1 + - - +
1025A SER* 3.3 25.2 - - - +
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Residues in contact with GLY1022 (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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1018A GLU* 2.9 21.5 + - - +
1019A LYS 4.6 1.4 + - - -
1020A GLN 3.6 2.0 + - - -
1021A PHE* 1.3 78.9 - - - +
1023A LYS* 1.3 70.5 + - - +
1024A GLY 3.7 0.9 - - - -
1025A SER* 3.1 13.7 + - - -
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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