Contacts of the helix formed by residues 1006 - 1020 (chain B) in PDB entry 1XTB
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 ASN1006 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002B ALA 3.1 9.6 + - - +
1003B LEU 3.0 15.1 + - - +
1005B ARG* 1.3 78.6 - - - +
1007B PRO* 1.3 72.5 - - - +
1008B GLN* 2.8 41.6 + - - +
1009B PHE* 2.9 16.3 - - + +
1010B GLN* 3.2 22.7 + - - +
1070B LEU* 3.3 8.9 - - - +
1073B SER* 3.2 27.0 + - - +
1074B ARG* 3.9 16.8 + - - -
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Residues in contact with PRO1007 (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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1005B ARG 3.4 6.5 - - - +
1006B ASN* 1.3 88.2 - - - +
1008B GLN* 1.3 93.0 + - - +
1010B GLN* 3.5 7.6 + - + +
1011B LYS* 3.1 24.3 + - - +
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Residues in contact with GLN1008 (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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1006B ASN* 2.8 17.7 + - - +
1007B PRO* 1.3 99.1 - - - +
1009B PHE* 1.3 56.3 + - - +
1011B LYS* 3.6 12.2 + - + +
1012B LEU* 3.1 27.4 + - - +
1066B MET* 4.9 4.4 - - - +
1069B ASP* 3.8 24.0 - - + +
1070B LEU* 3.8 16.6 - - + +
1073B SER* 3.1 31.0 + - - +
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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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1003B LEU* 3.4 57.9 - - + +
1004B THR* 3.9 22.0 - - + -
1006B ASN* 2.9 9.6 - - + +
1007B PRO 3.2 0.2 - - - -
1008B GLN* 1.3 74.9 - - - +
1010B GLN* 1.3 69.1 + - - +
1012B LEU* 3.2 15.9 + - + +
1013B GLN* 2.8 54.8 + - + +
1070B LEU* 3.9 19.0 - - + +
1324B ILE* 5.2 2.5 - - + -
1328B ASN* 3.9 34.8 - - + -
1329B CYS* 5.1 3.6 - - - -
1372B HIS* 5.3 5.4 - - + -
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Residues in contact with GLN1010 (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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1004B THR* 2.7 32.3 + - - +
1005B ARG 5.2 1.8 - - - +
1006B ASN 3.2 15.5 + - - +
1007B PRO* 3.9 7.6 - - + +
1008B GLN 3.4 0.2 - - - -
1009B PHE* 1.3 88.2 - - - +
1011B LYS* 1.3 57.1 + - - +
1013B GLN* 3.3 27.7 + - - +
1014B GLN* 2.8 32.0 + - - +
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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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1007B PRO 3.1 17.7 + - - +
1008B GLN* 3.7 12.1 - - + +
1010B GLN* 1.3 75.3 - - - +
1012B LEU* 1.3 63.7 + - - +
1014B GLN* 3.3 6.8 + - - +
1015B TRP* 3.0 24.1 + - + +
1065B HIS* 5.3 5.5 + - - -
1066B MET* 4.1 30.8 - - + +
1069B ASP* 4.7 10.5 + - - -
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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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1008B GLN 3.1 14.5 + - - +
1009B PHE* 3.3 14.4 - - + +
1011B LYS* 1.3 76.7 - - - +
1013B GLN* 1.3 62.2 + - - +
1015B TRP* 3.3 4.3 + - - +
1016B HIS* 3.0 22.3 + - - +
1063B VAL* 4.5 2.2 - - + +
1066B MET* 3.7 37.9 - - + +
1067B LEU* 3.7 31.0 - - + +
1070B LEU* 4.0 20.6 - - + -
1324B ILE* 5.2 5.4 - - + -
1325B TRP* 3.6 28.1 - - + -
1329B CYS* 4.0 16.8 - - - -
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Residues in contact with GLN1013 (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* 2.8 44.9 + - + +
1010B GLN* 3.4 28.5 + - - +
1012B LEU* 1.3 77.1 - - - +
1014B GLN* 1.3 61.5 + - - +
1016B HIS* 3.3 3.5 + - - +
1017B ARG* 2.5 71.7 + - + +
1328B ASN 5.2 4.2 - - - +
1329B CYS* 4.3 15.2 - - - -
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Residues in contact with GLN1014 (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 GLN 2.8 20.7 + - - +
1011B LYS* 3.7 7.2 - - - +
1013B GLN* 1.3 70.3 - - - +
1015B TRP* 1.3 65.8 + - - +
1017B ARG* 3.4 27.1 + - - +
1018B GLU* 3.2 48.0 + - - +
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Residues in contact with TRP1015 (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* 3.0 13.4 + - + +
1012B LEU 3.5 8.1 - - - +
1014B GLN* 1.3 76.9 - - - +
1016B HIS* 1.3 59.4 + - - +
1018B GLU* 3.1 10.2 + - - +
1019B HIS* 2.8 72.3 + + + +
1020B GLY 4.2 4.9 - - - -
1023B LEU* 4.1 26.9 - - + -
1060B THR* 4.5 6.3 - - + -
1062B GLU* 3.1 33.5 + - - -
1063B VAL* 3.6 26.5 - - + -
1066B MET* 3.3 30.3 - - + -
1325B TRP* 3.9 16.8 - + - -
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Residues in contact with HIS1016 (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 3.0 12.8 + - - +
1013B GLN* 3.5 10.3 - - - +
1014B GLN 3.3 0.2 - - - -
1015B TRP* 1.3 86.5 - - - +
1017B ARG* 1.3 66.5 + - + +
1020B GLY* 2.7 38.8 + - - +
1021B SER 4.4 1.1 + - - -
1325B TRP* 3.7 24.3 - - + -
1329B CYS* 2.9 35.0 + - + +
1330B PHE* 3.4 47.9 - + - -
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Residues in contact with ARG1017 (chain B).
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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1013B GLN* 2.5 61.6 + - + +
1014B GLN* 3.7 29.5 - - - +
1015B TRP 3.3 0.2 - - - -
1016B HIS* 1.3 83.9 - - + +
1018B GLU* 1.3 62.1 + - + +
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Residues in contact with GLU1018 (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 GLN* 3.2 42.2 + - - +
1015B TRP* 3.1 7.6 + - - +
1017B ARG* 1.3 82.9 - - + +
1019B HIS* 1.3 86.2 + - + +
1020B GLY 3.9 0.2 - - - -
1021B SER* 6.1 0.2 - - - -
1022B GLU* 3.9 9.4 - - - +
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Residues in contact with HIS1019 (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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1015B TRP* 2.8 64.7 + + + +
1018B GLU* 1.3 107.9 + - + +
1020B GLY* 1.3 68.5 + - - +
1021B SER* 3.4 2.7 - - - -
1022B GLU* 2.9 44.2 + - - +
1023B LEU* 3.7 6.2 + - - +
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Residues in contact with GLY1020 (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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1015B TRP* 3.8 7.9 + - - -
1016B HIS* 2.7 47.5 + - - +
1019B HIS* 1.3 71.3 - - - +
1021B SER* 1.3 56.9 + - - +
1022B GLU 3.1 5.2 + - - -
1023B LEU* 3.3 23.4 + - - +
1058B LEU* 5.8 0.2 - - - +
1330B PHE* 4.1 13.0 - - - -
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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