Contacts of the helix formed by residues 1008 - 1018 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006B GLN 3.8 1.4 + - - -
1007B PRO* 1.3 77.9 - - - +
1009B PHE* 1.3 65.8 + - - +
1010B ARG* 3.4 10.7 + - - +
1011B LYS* 3.1 24.7 + - - +
1012B LEU* 3.2 19.3 + - - +
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Residues in contact with PHE1009 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B PRO 3.9 0.2 + - - -
1008B SER* 1.3 72.4 - - - +
1010B ARG* 1.3 63.2 + - - +
1012B LEU* 3.0 17.6 + - + +
1013B MET* 3.2 18.6 + - + +
1038B GLU* 3.4 38.6 - - + -
1039B TYR* 3.7 15.5 - + - -
1042B ARG* 3.7 53.4 - - + +
1044B ILE* 3.4 34.1 - - + -
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Residues in contact with ARG1010 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008B SER* 3.3 9.7 + - - +
1009B PHE* 1.3 78.9 - - - +
1011B LYS* 1.3 63.7 + - - +
1013B MET* 3.1 17.6 + - - +
1014B GLU* 3.5 13.4 + - - +
1017B GLN* 5.0 1.2 - - - +
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Residues in contact with LYS1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977B TYR* 4.6 16.1 - - - -
1003B LEU* 3.2 37.3 - - - +
1005B LYS 5.7 0.4 + - - -
1007B PRO* 4.0 13.6 - - + +
1008B SER* 3.1 20.6 + - - +
1010B ARG* 1.3 78.8 - - - +
1012B LEU* 1.3 61.8 + - - +
1014B GLU* 3.2 36.8 + - - +
1015B HIS 4.7 0.9 + - - -
1022B SER 5.1 1.6 - - - +
1024B ILE* 3.5 27.9 - - + +
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Residues in contact with LEU1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B PRO* 4.2 8.1 - - + -
1008B SER 3.2 14.5 + - - +
1009B PHE* 3.0 14.4 + - + +
1011B LYS* 1.3 77.8 - - - +
1013B MET* 1.3 64.4 + - + +
1014B GLU 3.5 0.2 + - - -
1015B HIS* 4.3 7.4 + - - +
1016B LYS* 5.0 6.9 + - - +
1024B ILE* 3.7 42.7 + - + +
1026B LEU* 4.6 7.0 - - + -
1039B TYR* 3.4 28.7 - - + -
1044B ILE* 3.3 41.5 - - + -
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Residues in contact with MET1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B PHE* 3.2 12.9 + - + +
1010B ARG* 3.1 12.1 + - - +
1012B LEU* 1.3 78.5 - - + +
1014B GLU* 1.3 64.9 + - - +
1015B HIS 3.3 1.3 - - - -
1016B LYS* 3.1 53.2 + - + +
1017B GLN* 3.0 43.6 + - + +
1042B ARG* 6.0 3.6 - - - +
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Residues in contact with GLU1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977B TYR* 6.1 1.2 - - - -
1010B ARG 3.5 9.8 + - - +
1011B LYS* 3.2 32.3 + - - +
1012B LEU 3.3 0.2 - - - -
1013B MET* 1.3 76.2 - - - +
1015B HIS* 1.3 64.6 + - - +
1017B GLN* 3.0 15.3 + - - +
1018B ASN* 2.9 25.9 + - - +
1021B LEU* 3.8 34.7 - - + +
1022B SER 5.1 5.8 + - - +
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Residues in contact with HIS1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B LYS 4.7 0.2 + - - -
1012B LEU 4.3 6.7 + - - +
1013B MET 3.3 0.6 - - - -
1014B GLU* 1.3 79.2 - - - +
1016B LYS* 1.3 66.6 + - + +
1018B ASN 3.1 21.7 - - - +
1019B SER* 3.2 36.3 + - - -
1021B LEU* 2.8 23.5 + - - +
1022B SER 3.9 2.6 + - - +
1023B GLU* 3.7 57.9 + - + +
1024B ILE 5.2 0.4 - - - +
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Residues in contact with LYS1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012B LEU 5.0 5.6 + - - +
1013B MET* 3.1 45.3 + - + +
1015B HIS* 1.3 83.6 - - + +
1017B GLN* 1.3 62.2 + - - +
1018B ASN* 3.3 0.7 + - - -
1019B SER 5.0 0.3 + - - -
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Residues in contact with GLN1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B ARG 5.0 1.2 - - - +
1013B MET* 3.0 37.6 + - + +
1014B GLU* 3.0 17.7 + - - +
1016B LYS* 1.3 76.3 - - - +
1018B ASN* 1.3 63.6 + - + +
1021B LEU* 6.1 0.4 - - + -
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Residues in contact with ASN1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014B GLU 2.9 13.4 + - - +
1015B HIS* 3.1 8.9 - - - +
1016B LYS 3.2 1.8 - - - -
1017B GLN* 1.3 83.4 - - + +
1019B SER* 1.3 58.8 + - - +
1020B SER* 2.9 29.3 + - - -
1021B LEU* 2.9 41.2 + - + +
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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