Contacts of the helix formed by residues 1001 - 1012 (chain A) in PDB entry 5CQR
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 MET1001 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995A HIS* 6.1 0.7 - - - -
996A LEU* 3.1 45.0 + - + +
999A GLU* 3.7 23.1 - - + +
1000A HIS* 1.3 75.2 - - - +
1002A TYR* 1.3 62.8 + - - +
1003A GLU 3.4 2.9 + - - -
1004A PRO* 3.9 26.6 - - + +
1005A ALA 3.7 13.3 + - - -
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Residues in contact with TYR1002 (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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996A LEU 4.8 0.4 - - - -
997A MET* 3.8 39.7 + - + -
1000A HIS* 3.2 53.3 + - + -
1001A MET* 1.3 73.5 - - - +
1003A GLU* 1.3 60.8 + - - +
1005A ALA* 3.6 6.1 + - - +
1006A GLY* 3.1 20.4 + - - -
1021A ALA* 3.7 21.7 - - - +
1024A THR* 3.3 40.3 - - + +
1025A CYS* 4.4 11.9 - - + -
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Residues in contact with GLU1003 (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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1002A TYR* 1.3 75.7 - - - +
1004A PRO* 1.3 77.0 - - + +
1006A GLY* 3.0 11.5 + - - +
1007A LEU* 3.0 27.2 + - + +
1022A PHE* 4.1 9.1 - - + -
1025A CYS* 3.7 25.1 - - + +
1027A ASN* 3.5 27.5 + - - +
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Residues in contact with PRO1004 (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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996A LEU* 3.7 22.3 - - + +
1001A MET* 3.9 29.6 - - + +
1003A GLU* 1.3 96.2 - - + +
1005A ALA* 1.3 61.5 + - - +
1007A LEU* 3.1 13.8 + - + +
1008A MET* 3.0 23.0 + - - +
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Residues in contact with ALA1005 (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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993A GLY* 3.6 13.0 - - - +
996A LEU* 3.4 30.7 - - + +
997A MET* 3.9 20.4 - - - -
1001A MET 3.7 6.0 + - - +
1002A TYR 3.6 9.3 + - - +
1003A GLU 3.2 0.4 - - - -
1004A PRO* 1.3 78.2 - - - +
1006A GLY* 1.3 57.4 + - - +
1008A MET* 4.0 4.1 - - - +
1009A PHE* 2.8 38.7 + - + -
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Residues in contact with GLY1006 (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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1002A TYR 3.1 8.3 + - - -
1003A GLU 3.0 8.8 + - - -
1005A ALA* 1.3 77.2 - - - +
1007A LEU* 1.3 57.1 + - - +
1010A ALA* 3.1 28.4 + - - +
1018A ALA* 3.3 10.6 - - - +
1021A ALA* 3.5 21.7 - - - +
1022A PHE* 3.3 18.1 - - - -
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Residues in contact with LEU1007 (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 GLU* 3.0 27.1 + - - +
1004A PRO* 3.1 13.6 + - + +
1006A GLY* 1.3 75.7 - - - +
1008A MET* 1.3 59.2 + - - +
1010A ALA* 3.4 4.5 + - + +
1011A ARG* 3.0 29.1 + - - +
1022A PHE* 4.0 13.0 - - + -
1030A GLN* 3.5 29.2 - - - +
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Residues in contact with MET1008 (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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975A LEU* 4.4 11.4 - - + -
985A TYR* 5.0 4.0 - - - +
989A SER* 3.0 47.1 - - - +
992A TYR* 3.8 26.9 - - + -
993A GLY* 4.4 8.5 - - - +
996A LEU* 5.1 5.4 - - + -
1004A PRO 3.0 15.4 + - - +
1005A ALA* 4.0 6.5 - - - +
1006A GLY 3.4 0.2 - - - -
1007A LEU* 1.3 72.3 - - - +
1009A PHE* 1.3 66.6 + - - +
1010A ALA 3.0 2.0 + - - -
1011A ARG* 3.1 38.7 + - + +
1012A CYS* 3.1 15.4 + - + -
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Residues in contact with PHE1009 (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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989A SER 5.3 0.2 - - - -
990A ILE* 3.9 20.2 - - + -
993A GLY* 3.3 39.5 - - - -
994A GLU* 3.5 12.1 - - - -
997A MET* 4.3 14.8 - - + -
1005A ALA* 2.8 35.3 + - + +
1008A MET* 1.3 77.6 - - - +
1010A ALA* 1.3 60.0 + - - +
1012A CYS* 3.7 3.4 + - - -
1013A GLY 3.4 2.9 + - - -
1014A ALA* 2.8 43.0 + - + +
1017A LYS* 3.5 50.0 - - + -
1018A ALA* 3.6 20.9 - - + +
1021A ALA* 4.4 1.6 - - + -
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Residues in contact with ALA1010 (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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1006A GLY 3.1 20.8 + - - +
1007A LEU* 3.8 7.9 - - + +
1008A MET 3.0 1.2 - - - -
1009A PHE* 1.3 75.3 - - - +
1011A ARG* 1.3 63.7 + - - +
1013A GLY* 3.9 6.5 + - - +
1014A ALA 5.0 0.7 - - - +
1015A HIS* 4.7 6.6 - - - -
1018A ALA* 3.7 13.7 - - + -
1022A PHE* 4.2 11.2 - - + -
1030A GLN* 6.1 0.2 - - - +
1034A VAL* 4.3 10.5 - - + -
1037A GLN* 4.7 12.9 + - - +
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Residues in contact with ARG1011 (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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985A TYR* 3.7 22.7 + - - +
1007A LEU 3.0 16.7 + - - +
1008A MET* 3.7 19.9 - - + +
1010A ALA* 1.3 76.6 - - - +
1012A CYS* 1.3 57.5 + - - +
1013A GLY* 3.0 10.3 + - - -
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Residues in contact with CYS1012 (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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985A TYR* 5.3 5.8 - - + -
986A GLN* 3.0 31.7 + - - +
989A SER* 3.7 29.2 - - - +
990A ILE* 3.2 34.1 - - - -
1008A MET* 3.1 16.8 + - + +
1009A PHE* 3.9 9.9 - - - -
1011A ARG* 1.3 75.8 - - - +
1013A GLY* 1.3 57.8 + - - +
1014A ALA* 4.1 5.6 - - - -
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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