Contacts of the helix formed by residues 1063 - 1078 (chain U) in PDB entry 5MQF
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 GLU1063 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062U GLU* 3.8 24.7 - - - +
1064U ALA* 3.8 29.2 - - - +
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Residues in contact with ALA1064 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063U GLU* 3.8 28.9 - - - +
1065U ALA* 3.8 26.7 - - - +
1095U GLY* 4.6 11.0 - - - +
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Residues in contact with ALA1065 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064U ALA* 3.8 25.8 - - - +
1066U GLN* 3.8 28.7 - - - +
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Residues in contact with GLN1066 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065U ALA* 3.8 25.8 - - - +
1067U ILE* 3.8 29.4 - - - +
1102U PRO* 4.5 18.6 - - - -
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Residues in contact with ILE1067 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066U GLN* 3.8 29.2 - - - +
1068U LEU* 3.8 29.8 - - - +
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Residues in contact with LEU1068 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067U ILE* 3.8 28.9 - - - +
1069U GLU* 3.8 29.4 - - - +
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Residues in contact with GLU1069 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068U LEU* 3.8 26.5 - - - +
1070U ILE* 3.8 29.6 - - - +
1118U SER* 4.6 7.2 - - - +
1119U LEU* 4.5 22.2 - - - +
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Residues in contact with ILE1070 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069U GLU* 3.8 28.7 - - - +
1071U GLU* 3.8 26.2 - - - +
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Residues in contact with GLU1071 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070U ILE* 3.8 25.8 - - - +
1072U THR* 3.8 28.9 - - - +
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Residues in contact with THR1072 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071U GLU* 3.8 28.9 - - - +
1073U PHE* 3.8 26.2 - - - +
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Residues in contact with PHE1073 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072U THR* 3.8 29.6 - - - +
1074U ILE* 3.8 27.6 - - - +
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Residues in contact with ILE1074 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073U PHE* 3.8 29.4 - - - +
1075U PRO* 3.8 26.5 - - - -
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Residues in contact with PRO1075 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074U ILE* 3.8 25.6 - - - -
1076U LEU* 3.8 28.5 - - - -
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Residues in contact with LEU1076 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075U PRO* 3.8 24.9 - - - -
1077U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU1077 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076U LEU* 3.8 28.5 - - - +
1078U LEU* 3.8 28.3 - - - +
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Residues in contact with LEU1078 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077U LEU* 3.8 28.5 - - - +
1079U GLN* 3.8 25.6 - - - +
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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