Contacts of the helix formed by residues 1093 - 1100 (chain G) in PDB entry 1F66
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 ASP1093 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064G GLU* 5.6 2.5 - - - +
1068G LEU* 4.2 18.3 - - + +
1089G ALA 3.4 13.9 + - - +
1090G ILE 3.2 3.6 + - - +
1091G ARG 4.7 0.7 - - - -
1092G GLY* 1.3 77.5 - - - +
1094G GLU* 1.3 67.0 + - - +
1095G GLU* 3.1 12.8 + - - +
1096G LEU* 2.8 36.7 + - + +
1097G ASP* 2.9 27.2 + - - +
1503H LEU* 5.7 0.9 - - - +
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Residues in contact with GLU1094 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092G GLY 4.1 2.2 + - - -
1093G ASP* 1.3 73.9 + - - +
1095G GLU* 1.3 74.0 + - + +
1097G ASP* 3.6 6.8 - - - +
1098G SER* 3.1 25.3 + - - -
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Residues in contact with GLU1095 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093G ASP* 3.1 9.7 + - - +
1094G GLU* 1.3 88.5 - - + +
1096G LEU* 1.3 61.1 + - - +
1098G SER* 3.3 7.6 + - - -
1099G LEU* 3.0 22.7 + - - +
1500H PRO* 3.7 23.5 - - + +
1501H GLY* 4.0 2.6 + - - -
1502H GLU* 2.9 45.0 + - - +
1503H LEU* 3.1 28.0 + - + +
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Residues in contact with LEU1096 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061G LEU* 4.9 4.5 - - + -
1064G GLU* 4.5 16.2 - - + -
1065G VAL* 4.2 31.9 - - + -
1068G LEU* 3.6 31.9 - - + -
1089G ALA* 4.4 6.1 - - + +
1090G ILE* 4.1 23.1 - - + +
1093G ASP* 2.8 21.4 + - + +
1095G GLU* 1.3 69.0 - - - +
1097G ASP* 1.3 66.9 + - - +
1099G LEU* 3.0 10.9 + - + +
1100G ILE* 2.7 37.3 + - + +
1462H PHE* 5.6 0.4 - - + -
1503H LEU* 4.1 18.8 - - + -
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Residues in contact with ASP1097 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G ILE* 3.4 14.2 + - - +
1091G ARG* 2.6 61.0 + - - +
1093G ASP 2.9 20.3 + - - +
1094G GLU* 3.6 7.1 - - - +
1096G LEU* 1.3 77.8 - - - +
1098G SER* 1.3 64.7 + - - +
1100G ILE 3.5 3.8 - - - +
1101G LYS* 3.4 13.7 - - - -
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Residues in contact with SER1098 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094G GLU* 3.1 16.8 + - - -
1095G GLU* 3.4 6.5 - - - -
1097G ASP* 1.3 83.1 + - - +
1099G LEU* 1.3 61.0 + - - +
1101G LYS* 3.5 25.3 + - - +
1500H PRO* 3.7 17.4 - - - +
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Residues in contact with LEU1099 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061G LEU* 4.0 31.6 - - + -
1095G GLU 3.0 15.4 + - - +
1096G LEU* 3.0 13.0 + - + +
1098G SER* 1.3 77.2 + - - +
1100G ILE* 1.3 67.0 + - + +
1101G LYS* 3.7 3.2 + - - +
1462H PHE* 4.7 7.4 - - + -
1466H VAL* 5.2 4.7 - - + -
1469H ARG* 3.1 48.5 + - - +
1498H LEU* 3.8 12.3 - - + +
1499H LEU* 3.5 28.0 - - + -
1500H PRO* 4.3 9.2 - - + -
1503H LEU* 4.1 10.3 - - + -
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Residues in contact with ILE1100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 4.0 24.7 - - + +
1065G VAL* 4.5 3.1 - - + -
1090G ILE* 3.5 42.8 - - + -
1091G ARG* 2.9 35.0 + - - +
1096G LEU* 2.7 31.6 + - + +
1097G ASP 3.8 3.4 - - - -
1098G SER 3.5 0.4 - - - -
1099G LEU* 1.3 78.9 - - + +
1101G LYS* 1.3 57.3 + - - +
1102G ALA 4.2 5.2 - - - +
1104G ILE* 4.5 5.2 - - + -
1462H PHE* 3.6 38.4 - - + -
1469H ARG* 4.5 3.6 - - - +
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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