Contacts of the helix formed by residues 1010 - 1020 (chain r) in PDB entry 6FF7
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 SER1010 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2077A ALA 5.4 0.2 - - - -
2080A ALA* 3.5 31.4 - - - -
2081A ALA 5.5 0.7 - - - -
1008r THR 3.5 4.2 + - - -
1009r LEU* 1.3 75.3 - - - +
1011r GLU* 1.3 61.5 + - - +
1012r ILE* 3.9 17.0 - - - -
1013r GLU* 3.2 9.1 + - - +
1014r LEU* 2.8 26.7 + - - +
1110r LYS* 6.0 1.1 - - - -
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Residues in contact with GLU1011 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010r SER* 1.3 69.7 - - - +
1012r ILE* 1.3 66.5 + - - +
1014r LEU* 3.0 19.1 + - - +
1015r PHE* 3.0 17.0 + - - +
1046r ILE* 5.4 10.8 - - + +
1110r LYS* 5.5 12.2 - - + +
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Residues in contact with ILE1012 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077A ALA* 3.7 25.8 - - + +
2078A ILE* 4.9 7.4 - - + -
1010r SER* 3.9 9.4 - - - -
1011r GLU* 1.3 78.2 - - - +
1013r GLU* 1.3 60.3 + - - +
1015r PHE* 4.0 5.0 + - - +
1016r ARG* 3.9 13.3 + - - +
1046r ILE* 5.3 7.6 - - - +
1047r PRO* 4.1 26.0 - - + +
1048r VAL* 5.7 0.7 - - - -
1050r GLU* 5.8 3.3 - - - +
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Residues in contact with GLU1013 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009r LEU* 4.7 9.4 - - + -
1010r SER* 3.2 17.7 + - - +
1011r GLU 3.1 0.4 - - - -
1012r ILE* 1.3 78.8 - - + +
1014r LEU* 1.3 67.4 + - - +
1015r PHE 3.2 1.8 - - - -
1016r ARG* 3.0 9.3 + - + +
1017r VAL* 3.0 22.4 + - - +
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Residues in contact with LEU1014 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009r LEU* 4.9 7.8 - - + +
1010r SER 2.8 18.4 + - - +
1011r GLU* 3.0 13.2 + - - +
1013r GLU* 1.3 72.1 - - - +
1015r PHE* 1.3 64.4 + - - +
1017r VAL* 3.2 8.2 + - - +
1018r PHE* 2.9 21.1 + - - +
1110r LYS* 5.8 7.0 - - + -
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Residues in contact with PHE1015 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011r GLU 3.0 14.3 + - - +
1012r ILE* 4.1 5.4 - - - +
1014r LEU* 1.3 77.1 - - - +
1016r ARG* 1.3 56.4 + - - +
1018r PHE* 3.0 11.6 + - - +
1019r SER* 2.9 27.1 + - - -
1046r ILE* 5.8 7.4 - - + -
1060r ASN* 4.9 17.8 - - + +
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Residues in contact with ARG1016 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012r ILE 3.9 7.4 + - - +
1013r GLU* 3.0 14.5 + - - +
1015r PHE* 1.3 76.2 - - - +
1017r VAL* 1.3 59.4 + - - +
1019r SER* 2.8 26.2 + - - -
1020r LEU* 3.0 13.4 + - - +
1050r GLU* 5.9 7.0 - - + -
1056r SER* 5.5 5.2 - - - -
1060r ASN* 5.6 2.6 - - - +
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Residues in contact with VAL1017 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000r THR* 6.1 0.5 - - - -
1001r TYR* 6.2 2.5 - - - -
1004r LEU* 4.5 23.3 - - + -
1005r LEU* 5.7 2.5 - - + +
1013r GLU 3.0 12.2 + - - +
1014r LEU* 3.5 11.0 - - - +
1016r ARG* 1.3 75.7 - - - +
1018r PHE* 1.3 63.6 + - - +
1020r LEU* 3.2 19.2 + - - +
1021r SER* 3.8 3.8 + - - -
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Residues in contact with PHE1018 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014r LEU 2.9 12.0 + - - +
1015r PHE* 3.1 14.6 - - - +
1017r VAL* 1.3 76.5 - - - +
1019r SER* 1.3 62.6 + - - +
1020r LEU 3.1 1.2 + - - -
1021r SER* 3.1 22.2 + - - -
1091r LEU* 5.9 6.4 - - + +
1092r MET* 6.4 2.7 - - + -
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Residues in contact with SER1019 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015r PHE 2.9 11.1 + - - -
1016r ARG* 2.8 16.6 + - - -
1018r PHE* 1.3 76.2 - - - +
1020r LEU* 1.3 57.6 + - - +
1021r SER* 3.2 5.4 + - - +
1024r PHE* 4.7 10.4 - - - +
1055r PRO 5.7 0.7 - - - -
1056r SER* 3.6 38.9 - - - -
1059r ILE* 4.3 17.4 - - - +
1060r ASN* 4.5 6.1 - - - -
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Residues in contact with LEU1020 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000r THR* 4.4 17.8 - - - -
1004r LEU* 6.4 2.0 - - + -
1016r ARG 3.0 9.7 + - - +
1017r VAL* 3.7 13.9 - - - +
1018r PHE 3.0 1.0 - - - -
1019r SER* 1.3 78.4 - - - +
1021r SER* 1.3 65.3 + - - +
1022r SER* 3.3 3.8 + - - -
1056r SER* 6.3 0.9 - - - -
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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