Contacts of the helix formed by residues 1032 - 1037 (chain B) in PDB entry 1M8W
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 HIS1032 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998B PHE* 3.5 57.1 - + + +
1028B GLU* 3.3 23.6 - - + -
1029B LEU 3.0 2.6 + - - -
1031B GLN* 1.3 99.7 + - + +
1033B THR* 1.3 65.5 + - - +
1034B GLU* 3.0 4.6 + - - -
1035B GLN* 3.0 23.3 + - - +
1036B LEU* 3.0 28.3 + - + +
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Residues in contact with THR1033 (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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1029B LEU 3.1 14.5 + - - -
1030B HIS* 3.6 16.2 + - - -
1031B GLN 3.8 1.0 - - - -
1032B HIS* 1.3 74.9 - - - +
1034B GLU* 1.3 63.8 + - - +
1036B LEU* 3.1 7.5 + - - -
1037B VAL* 2.9 47.3 + - + +
1046B ILE* 4.5 5.4 - - + +
1060B LYS 5.3 0.2 - - - -
1061B ILE* 4.2 28.2 + - + +
1064B GLU* 3.6 36.8 - - + +
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Residues in contact with GLU1034 (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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1032B HIS 3.0 1.6 + - - -
1033B THR* 1.3 81.3 - - - +
1035B GLN* 1.3 82.0 + - + +
1037B VAL* 3.4 11.4 - - - +
1038B GLN* 3.2 32.7 + - - +
1064B GLU* 4.7 14.9 + - + +
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Residues in contact with GLN1035 (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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998B PHE* 3.5 34.9 - - + -
1031B GLN 5.3 1.2 + - - -
1032B HIS* 3.0 25.8 + - - +
1034B GLU* 1.3 103.5 + - + +
1036B LEU* 1.3 65.3 + - - +
1038B GLN* 3.3 8.1 + - - +
1039B ASP* 3.1 21.2 + - - +
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Residues in contact with LEU1036 (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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998B PHE* 3.6 26.7 - - + -
1001B SER* 3.6 24.2 - - - -
1002B THR* 4.0 8.1 - - + -
1029B LEU* 3.6 28.9 - - + +
1032B HIS* 3.0 38.0 + - + +
1033B THR 3.1 3.3 + - - +
1035B GLN* 1.3 72.7 - - - +
1037B VAL* 1.3 65.7 + - - +
1038B GLN 3.0 3.6 + - - -
1039B ASP* 3.0 8.2 + - - -
1042B GLY* 3.0 11.6 - - - +
1043B ASN 2.9 21.3 + - - -
1046B ILE* 3.7 25.6 - - + -
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Residues in contact with VAL1037 (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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1033B THR* 2.9 32.4 + - + +
1034B GLU* 3.4 17.5 - - - +
1036B LEU* 1.3 74.8 - - - +
1038B GLN* 1.3 70.2 + - + +
1043B ASN* 3.5 13.3 - - - +
1046B ILE* 3.9 21.3 - - + -
1061B ILE* 5.2 0.2 - - + -
1065B ILE* 4.6 7.0 - - + -
1072B LEU* 4.4 20.6 - - + -
1078B ALA* 3.2 26.2 + - + -
1081B VAL* 4.0 24.9 - - + +
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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