Contacts of the helix formed by residues 1012 - 1021 (chain C) in PDB entry 5IFE
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 PRO1012 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006C MET 6.0 0.7 - - - +
1009C MET* 3.5 11.0 - - + +
1010C THR 3.1 12.3 - - - +
1011C PRO* 1.3 83.7 - - + +
1013C ILE* 1.3 54.4 + - - +
1014C LYS* 4.3 8.7 - - + +
1015C ASP* 2.7 35.6 + - + +
1016C LEU 2.6 31.0 + - - -
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Residues in contact with ILE1013 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001C VAL* 6.0 0.9 - - + -
1006C MET* 3.6 38.3 + - - +
1009C MET* 5.0 11.2 - - + +
1011C PRO 3.5 0.6 + - - +
1012C PRO* 1.3 70.9 - - - +
1014C LYS* 1.3 62.9 + - - +
1016C LEU* 4.0 10.3 - - + -
1017C LEU* 2.9 26.5 + - + +
1042C ILE* 3.6 41.3 - - + -
1046C GLY* 4.1 9.0 - - - +
1049C TYR* 3.5 37.1 - - + -
1050C VAL* 3.7 17.3 - - + +
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Residues in contact with LYS1014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012C PRO* 3.1 7.1 - - + +
1013C ILE* 1.3 78.1 - - - +
1015C ASP* 1.3 65.5 + - - +
1018C PRO* 3.2 21.0 - - - +
1048C GLU 5.7 0.4 + - - -
1049C TYR* 3.1 37.3 + - + +
1050C VAL* 5.3 3.0 - - - +
1051C SER* 5.7 2.6 - - - +
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Residues in contact with ASP1015 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979C TYR* 3.8 18.1 + - + +
1011C PRO* 5.1 1.3 - - + -
1012C PRO* 2.7 44.2 + - + +
1014C LYS* 1.3 82.3 - - - +
1016C LEU* 1.3 62.8 + - - +
1017C LEU 3.5 0.4 - - - -
1018C PRO* 3.5 12.9 - - - +
1019C ARG* 3.6 12.8 + - - +
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Residues in contact with LEU1016 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979C TYR* 3.8 28.5 - - + -
982C LEU* 4.8 0.7 - - + -
997C LEU* 4.4 19.1 - - + -
1001C VAL* 4.6 10.5 - - + -
1009C MET* 4.0 25.1 - - + -
1011C PRO* 4.0 11.9 - - + +
1012C PRO 2.6 18.1 + - - +
1013C ILE* 4.0 10.1 - - + -
1015C ASP* 1.3 73.9 - - - +
1017C LEU* 1.3 64.3 + - - +
1019C ARG* 3.2 6.6 + - - +
1020C LEU* 3.1 43.8 + - + +
1038C LEU* 5.0 4.5 - - + -
1042C ILE* 3.7 20.4 - - + -
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Residues in contact with LEU1017 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013C ILE* 2.9 17.7 + - + +
1016C LEU* 1.3 77.5 - - - +
1018C PRO* 1.3 67.2 - - + +
1020C LEU* 2.7 30.5 + - + +
1021C THR* 2.9 19.5 + - + +
1039C VAL* 5.0 6.5 - - + -
1042C ILE* 4.0 11.6 - - + +
1050C VAL* 3.6 31.9 - - + -
1054C GLU* 3.9 11.0 - - + -
1055C TRP* 3.4 40.6 - - + -
1058C ILE* 3.6 22.4 - - + -
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Residues in contact with PRO1018 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013C ILE 3.9 0.4 - - - +
1014C LYS* 3.2 27.6 - - - +
1015C ASP* 3.5 11.9 - - - +
1017C LEU* 1.3 97.8 - - + +
1019C ARG* 1.3 55.1 + - - +
1021C THR* 2.9 27.2 + - + +
1022C PRO* 3.2 8.8 - - - +
1050C VAL* 6.0 0.2 - - + -
1054C GLU* 4.6 12.3 - - - +
1057C ARG* 4.3 10.3 - - - +
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Residues in contact with ARG1019 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979C TYR* 3.6 36.4 + - + +
982C LEU* 3.1 51.9 + - + +
983C GLY* 3.4 10.3 - - - +
1015C ASP 3.7 4.9 - - - +
1016C LEU 3.2 9.4 + - - +
1017C LEU 3.1 0.8 - - - -
1018C PRO* 1.3 81.4 - - - +
1020C LEU* 1.3 58.7 + - - +
1022C PRO* 3.2 20.5 - - - +
1023C ILE* 3.4 17.6 - - - +
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Residues in contact with LEU1020 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982C LEU* 3.7 24.0 - - + -
994C LEU* 3.7 22.0 - - + -
1016C LEU* 3.1 22.6 + - + +
1017C LEU* 2.7 16.6 + - + +
1019C ARG* 1.3 72.0 - - - +
1021C THR* 1.3 63.6 + - - +
1022C PRO 3.4 0.2 - - - -
1023C ILE* 3.2 14.5 + - + -
1024C LEU* 3.9 2.8 + - - +
1035C CYS* 3.5 20.9 - - - -
1038C LEU* 3.6 35.2 - - + -
1039C VAL* 4.4 19.7 - - + +
1042C ILE* 3.8 20.4 - - + -
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Residues in contact with THR1021 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C LEU* 3.2 16.8 - - + +
1018C PRO* 2.9 17.1 + - + -
1020C LEU* 1.3 77.7 - - - +
1022C PRO* 1.3 61.7 - - - +
1023C ILE 3.5 0.3 + - - -
1024C LEU* 3.6 26.3 + - - +
1039C VAL* 5.9 1.8 - - + -
1057C ARG* 3.4 36.3 + - - +
1058C ILE* 3.6 33.0 - - + -
1061C GLU* 4.0 11.8 - - - +
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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