Contacts of the helix formed by residues 1108 - 1115 (chain F) in PDB entry 6C3P
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 PRO1108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510F LYS* 4.4 9.2 - - - +
1106F LEU 3.7 3.6 - - - +
1107F ALA* 1.3 87.3 - - + +
1109F MET* 1.3 65.1 + - - +
1110F ARG* 3.4 12.2 + - + +
1111F PHE* 3.4 14.9 + - + +
1112F PHE* 3.0 19.6 + - - -
1321F GLU* 4.1 31.9 - - + +
1322F ALA 4.5 6.5 - - - +
1323F GLU* 4.5 12.8 - - + -
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Residues in contact with MET1109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F ILE* 4.4 4.7 - - + +
507F LYS* 3.5 43.5 - - + +
510F LYS* 3.5 27.6 - - + +
1108F PRO* 1.3 73.1 - - - +
1110F ARG* 1.3 65.7 + - - +
1111F PHE 3.2 0.2 - - - -
1112F PHE* 3.3 17.4 + - + -
1113F GLU* 2.9 33.8 + - + +
1394F MET* 3.6 38.8 - - + +
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Residues in contact with ARG1110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108F PRO* 3.3 10.4 - - + +
1109F MET* 1.3 77.9 - - - +
1111F PHE* 1.3 55.9 + - - +
1113F GLU* 3.8 13.4 + - - +
1114F THR* 2.5 76.5 + - - +
1353F TYR* 4.3 22.4 - - - +
1354F ASP* 3.9 34.0 - - + +
1357F LEU* 5.0 6.5 - - - +
2001F ADP 4.4 16.3 + - - -
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Residues in contact with PHE1111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104F ILE* 5.1 7.9 - - + -
1107F ALA* 4.3 22.0 - - + -
1108F PRO* 3.4 16.2 + - + +
1109F MET 3.2 0.6 - - - -
1110F ARG* 1.3 80.6 - - - +
1112F PHE* 1.3 70.0 + + - +
1114F THR* 3.1 3.5 + - - -
1115F THR* 2.6 72.1 + - + -
1120F ILE* 3.9 35.7 - - + -
1317F LEU* 5.1 11.4 - - + -
1321F GLU* 6.4 1.1 - - + -
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Residues in contact with PHE1112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503F LEU* 3.7 27.6 - - + -
506F ILE* 3.7 33.9 - - + -
510F LYS* 4.9 4.0 - - + -
1104F ILE* 3.5 28.9 - - + -
1105F ILE* 4.3 7.4 - - - -
1107F ALA* 3.1 30.3 - - + -
1108F PRO 3.0 22.2 - - - -
1109F MET* 3.3 22.5 + - + +
1111F PHE* 1.3 85.3 - + - +
1113F GLU* 1.3 59.3 + - - +
1115F THR* 2.9 22.8 - - - +
1117F LEU* 4.7 18.9 - - + +
1120F ILE* 5.8 4.0 - - + -
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Residues in contact with GLU1113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827F ILE* 5.0 6.2 - - - +
828F ASN* 4.7 15.1 - - - +
1109F MET* 2.9 27.2 + - + +
1110F ARG* 4.0 17.6 + - - +
1112F PHE* 1.3 76.8 - - - +
1114F THR* 1.3 61.0 + - - +
1115F THR 4.7 0.2 - - - +
2001F ADP 4.6 15.3 - - - +
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Residues in contact with THR1114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827F ILE* 4.6 14.9 - - + +
1110F ARG* 2.5 54.5 + - - +
1111F PHE* 3.7 3.4 - - - -
1113F GLU* 1.3 79.6 - - - +
1115F THR* 1.3 67.4 + - - +
1116F PRO* 3.6 7.1 - - - +
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Residues in contact with THR1115 (chain F).
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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1111F PHE* 2.6 61.0 + - + -
1112F PHE* 2.9 20.5 - - - +
1113F GLU 4.5 0.5 - - - +
1114F THR* 1.3 75.2 - - - +
1116F PRO* 1.3 85.8 - - + +
1117F LEU* 3.7 3.3 + - - +
1119F SER* 4.9 4.5 - - - -
1120F ILE* 4.3 13.4 - - + +
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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