Contacts of the helix formed by residues 1060 - 1074 (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 THR1060 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015B TRP* 4.5 6.5 - - + -
1023B LEU* 3.6 25.1 - - + -
1028B LEU* 4.4 13.7 - - + -
1035B ARG* 5.0 1.8 - - - +
1039B PHE* 3.9 9.9 - - - -
1059B VAL* 1.3 80.3 - - - +
1061B GLU* 1.3 64.4 + - - +
1062B GLU* 3.5 11.0 + - - +
1063B VAL* 2.9 33.2 + - + +
1064B MET* 2.9 14.4 + - - +
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Residues in contact with GLU1061 (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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1038B HIS* 3.4 39.1 + - + +
1039B PHE* 3.7 24.6 - - + -
1060B THR* 1.3 73.6 - - - +
1062B GLU* 1.3 58.2 + - - +
1064B MET* 3.3 5.8 + - - +
1065B HIS* 2.9 29.2 + - - +
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Residues in contact with GLU1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015B TRP* 3.1 37.4 + - + +
1060B THR* 3.5 7.6 + - - +
1061B GLU* 1.3 80.4 - - - +
1063B VAL* 1.3 61.7 + - - +
1065B HIS* 3.3 8.1 + - + +
1066B MET* 3.1 37.6 + - + +
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Residues in contact with VAL1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU* 4.8 1.3 - - + -
1015B TRP* 3.6 37.7 - - + -
1023B LEU* 4.8 0.9 - - + -
1059B VAL* 3.9 16.6 - - + -
1060B THR* 2.9 30.6 + - + +
1062B GLU* 1.3 76.9 - - - +
1064B MET* 1.3 58.2 + - - +
1066B MET* 3.2 10.0 + - + +
1067B LEU* 2.9 38.1 + - + +
1325B TRP* 3.8 35.0 - - + -
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Residues in contact with MET1064 (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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1039B PHE* 3.6 23.3 - - + -
1054B TYR* 3.8 22.9 - - + +
1059B VAL* 3.7 25.6 - - + -
1060B THR 2.9 15.9 + - - +
1061B GLU* 3.7 10.1 - - - +
1063B VAL* 1.3 76.4 - - - +
1065B HIS* 1.3 56.8 + - - +
1067B LEU* 3.6 12.9 - - + +
1068B LEU* 2.9 43.3 + - + +
1318B LEU* 3.8 24.9 - - + +
1321B MET* 5.9 2.0 - - + -
1322B LEU* 4.0 22.2 - - + -
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Residues in contact with HIS1065 (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* 5.3 7.6 - - - -
1061B GLU 2.9 16.8 + - - +
1062B GLU* 3.5 9.0 - - + +
1063B VAL 3.1 0.2 - - - -
1064B MET* 1.3 74.9 - - - +
1066B MET* 1.3 61.5 + - + +
1068B LEU* 3.3 9.2 + - - +
1069B ASP* 2.9 64.9 + - - -
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Residues in contact with MET1066 (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* 4.9 5.7 - - - +
1011B LYS* 4.1 35.0 - - + +
1012B LEU* 3.7 31.5 - - + +
1015B TRP* 3.3 58.3 - - + +
1062B GLU* 3.1 26.6 + - + +
1063B VAL* 3.2 13.4 + - + +
1065B HIS* 1.3 78.1 - - + +
1067B LEU* 1.3 62.0 + - - +
1069B ASP* 3.3 10.0 + - - +
1070B LEU* 3.0 23.4 + - - +
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Residues in contact with LEU1067 (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* 3.7 29.4 - - + -
1059B VAL* 4.7 0.2 - - + -
1063B VAL* 2.9 34.8 + - + +
1064B MET* 3.6 26.2 - - + +
1066B MET* 1.3 77.6 - - - +
1068B LEU* 1.3 61.8 + - + +
1070B LEU* 3.2 8.3 + - - +
1071B ALA* 3.1 18.0 + - - +
1321B MET* 3.5 57.2 - - + +
1322B LEU* 4.6 4.5 - - + -
1324B ILE* 5.2 0.9 - - + -
1325B TRP* 4.1 19.7 - - + +
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Residues in contact with LEU1068 (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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1064B MET* 2.9 29.7 + - + +
1065B HIS* 3.8 8.3 - - - +
1067B LEU* 1.3 73.9 - - + +
1069B ASP* 1.3 66.7 + - - +
1071B ALA* 3.2 5.5 + - + +
1072B LYS* 3.0 23.4 + - - +
1311B LEU* 3.8 40.5 - - + +
1312B GLU* 3.5 30.7 - - + +
1317B VAL* 4.5 10.3 - - + -
1318B LEU* 4.3 16.2 - - + -
1321B MET* 5.3 4.5 - - + -
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Residues in contact with ASP1069 (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* 3.8 17.2 - - + +
1011B LYS* 4.7 7.8 + - - -
1065B HIS* 2.9 57.5 + - - +
1066B MET* 3.6 9.1 - - - +
1068B LEU* 1.3 77.8 - - - +
1070B LEU* 1.3 56.7 + - - +
1072B LYS* 3.3 11.3 + - - +
1073B SER* 2.8 30.1 + - - -
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Residues in contact with LEU1070 (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* 4.1 7.0 - - + -
1006B ASN* 3.3 28.7 - - - +
1008B GLN* 3.8 8.0 - - + +
1009B PHE* 3.9 27.4 - - + +
1012B LEU* 4.0 24.5 - - + -
1066B MET 3.0 12.6 + - - +
1067B LEU* 3.4 8.7 - - + +
1068B LEU 3.1 0.2 - - - -
1069B ASP* 1.3 75.4 - - - +
1071B ALA* 1.3 66.3 + - - +
1073B SER* 3.0 5.7 + - - -
1074B ARG* 2.9 45.5 + - + +
1321B MET* 4.0 19.5 - - + -
1324B ILE* 4.6 4.3 - - + -
1503B VAL* 4.5 5.2 - - + -
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Residues in contact with ALA1071 (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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1067B LEU 3.1 9.1 + - - +
1068B LEU* 3.2 10.5 + - - +
1070B LEU* 1.3 78.2 - - - +
1072B LYS* 1.3 62.6 + - - +
1074B ARG* 3.4 4.9 + - - -
1076B VAL* 3.2 43.3 + - + +
1311B LEU* 4.3 11.7 - - + -
1317B VAL* 4.4 9.0 - - + -
1321B MET* 3.9 30.5 - - + +
1503B VAL* 4.7 0.9 - - - -
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Residues in contact with LYS1072 (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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1068B LEU 3.0 12.6 + - - +
1069B ASP* 3.5 14.4 - - - +
1071B ALA* 1.3 77.9 - - - +
1073B SER* 1.3 57.6 + - - +
1075B GLY* 2.9 22.2 + - - -
1076B VAL 5.1 0.7 - - - +
1077B GLU* 3.7 24.2 + - - +
1311B LEU* 4.1 12.7 - - + +
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Residues in contact with SER1073 (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* 3.2 30.2 + - - +
1008B GLN* 3.1 24.4 + - - -
1069B ASP 2.8 18.5 + - - -
1070B LEU* 3.0 14.0 + - - -
1072B LYS* 1.3 72.6 - - - +
1074B ARG* 1.3 62.1 + - - +
1075B GLY 3.2 1.2 + - - -
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Residues in contact with ARG1074 (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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1002B ALA* 4.0 18.4 + - - +
1003B LEU* 4.3 10.6 - - - +
1006B ASN* 3.9 21.6 + - - +
1070B LEU* 2.9 35.8 + - + +
1071B ALA 3.9 4.3 - - - +
1072B LYS 3.1 0.4 - - - -
1073B SER* 1.3 79.2 + - - +
1075B GLY* 1.3 61.3 + - - +
1076B VAL* 3.4 2.6 + - + -
1502B VAL* 3.0 32.3 + - - +
1503B VAL* 2.9 37.1 + - + +
1505B ASP* 3.0 35.2 + - - +
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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