Contacts of the helix formed by residues 1008 - 1018 (chain A) in PDB entry 3SQD
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 SER1008 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006A GLN 3.7 2.8 + - - -
1007A PRO* 1.3 77.0 - - - +
1009A PHE* 1.3 64.8 + - - +
1010A ARG* 3.5 9.3 + - - +
1011A LYS* 3.0 24.5 + - - +
1012A LEU* 3.1 21.9 + - - +
1039A TYR* 4.2 3.1 - - - -
1034B HIS* 4.8 5.5 - - - -
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Residues in contact with PHE1009 (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 PRO 4.0 0.2 + - - -
1008A SER* 1.3 73.1 - - - +
1010A ARG* 1.3 62.4 + - - +
1012A LEU* 3.3 9.6 + - + +
1013A MET* 3.0 24.4 + - - +
1038A GLU* 3.7 42.0 - - + -
1039A TYR* 3.5 44.1 + + - -
1042A ARG* 3.2 56.5 - - + +
1044A ILE* 4.9 3.6 - - + -
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Residues in contact with ARG1010 (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 SER* 3.1 9.1 + - - +
1009A PHE* 1.3 79.8 - - - +
1011A LYS* 1.3 64.0 + - - +
1013A MET* 3.2 6.4 + - - +
1014A GLU* 2.9 46.3 + - - +
1034B HIS* 5.1 7.1 + - + +
1035B LEU* 6.1 3.4 - - - +
1037B ARG* 3.4 26.3 - - - +
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Residues in contact with LYS1011 (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 LEU* 4.1 13.5 - - - -
1005A LYS 6.0 0.4 - - - -
1007A PRO* 3.8 19.1 - - + -
1008A SER* 3.0 24.5 + - - +
1010A ARG* 1.3 75.1 - - - +
1012A LEU* 1.3 63.7 + - - +
1014A GLU* 3.3 1.0 + - - -
1015A HIS* 3.0 60.8 + - + -
1024A ILE* 4.0 14.6 - - + -
1030B GLU 3.0 23.6 + - - -
1031B ASN* 3.1 14.3 + - - +
1034B HIS* 3.0 48.1 + - + +
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Residues in contact with LEU1012 (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 PRO* 3.8 17.0 - - + +
1008A SER 3.1 16.8 + - - +
1009A PHE* 3.6 10.1 - - - +
1011A LYS* 1.3 77.0 - - - +
1013A MET* 1.3 63.6 + - - +
1015A HIS* 3.4 2.9 + - - +
1016A LYS* 3.2 36.6 + - - +
1024A ILE* 3.7 37.0 - - + +
1026A LEU* 4.4 8.5 - - + -
1039A TYR* 3.6 37.0 - - + -
1044A ILE* 4.1 24.7 - - + -
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Residues in contact with MET1013 (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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1009A PHE 3.0 16.9 + - - +
1010A ARG* 3.2 5.6 + - - +
1012A LEU* 1.3 77.2 - - - +
1014A GLU* 1.3 57.5 + - + +
1016A LYS* 3.0 26.9 + - - +
1017A GLN* 2.9 63.6 + - - +
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Residues in contact with GLU1014 (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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1010A ARG* 2.9 48.1 + - + +
1011A LYS 3.9 2.9 - - - +
1012A LEU 3.3 0.2 - - - -
1013A MET* 1.3 78.9 - - + +
1015A HIS* 1.3 64.3 + - - +
1017A GLN* 4.3 10.5 - - - +
1018A ASN* 3.0 31.7 + - - +
1021A LEU* 3.7 4.2 - - + +
1034B HIS* 3.4 38.6 + - + +
1035B LEU* 5.9 0.3 - - - +
1037B ARG* 3.1 43.3 + - - +
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Residues in contact with HIS1015 (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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977A TYR* 3.9 30.7 - + - -
1011A LYS* 3.0 56.9 + - + +
1012A LEU 3.9 4.5 - - - +
1014A GLU* 1.3 75.2 - - - +
1016A LYS* 1.3 63.4 + - + +
1018A ASN 3.3 20.3 - - - +
1021A LEU* 3.8 35.2 - - + +
1022A SER 2.7 27.8 + - - +
1023A GLU* 5.3 1.9 - - - -
1024A ILE* 3.6 24.7 - - + +
1033B LEU* 4.7 2.5 - - + -
1034B HIS* 4.1 9.6 + - + -
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Residues in contact with LYS1016 (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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1012A LEU* 3.2 21.1 + - - +
1013A MET* 3.0 34.7 + - - +
1015A HIS* 1.3 77.8 - - + +
1017A GLN* 1.3 59.8 + - + +
1018A ASN 3.4 1.8 + - - -
1024A ILE 6.4 0.2 - - - +
1043A GLY 5.9 0.2 + - - -
1044A ILE* 3.8 27.1 - - - +
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Residues in contact with GLN1017 (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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1013A MET* 2.9 49.0 + - - +
1014A GLU* 3.3 10.0 + - + +
1015A HIS 3.2 0.8 - - - -
1016A LYS* 1.3 77.8 - - - +
1018A ASN* 1.3 72.5 + - - +
1019A SER 4.2 1.0 + - - -
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Residues in contact with ASN1018 (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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1014A GLU 3.0 23.0 + - - +
1015A HIS 3.3 11.5 - - - +
1016A LYS 3.4 2.8 - - - -
1017A GLN* 1.3 90.2 + - - +
1019A SER* 1.3 64.4 + - - +
1020A SER* 3.0 14.2 + - - +
1021A LEU* 2.9 25.9 + - + +
1037B ARG* 3.8 43.8 + - + +
1041B ALA* 4.1 15.0 - - - +
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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