Contacts of the helix formed by residues 1100 - 1105 (chain C) in PDB entry 1FBV
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 LYS1100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A LYS* 5.6 2.5 - - - +
2005A SO4 3.4 37.8 + - - -
1006C ARG* 5.7 0.2 - - - +
1010C GLU* 3.4 21.8 - - - +
1013C GLU* 3.9 17.3 + - - +
1098C ALA 4.2 8.1 - - - +
1099C THR* 1.3 74.7 - - - +
1101C THR* 1.3 69.2 + - - +
1102C ASP* 2.8 20.3 + - + +
1103C GLN* 2.9 20.4 + - + +
1104C VAL* 3.6 8.6 + - - +
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Residues in contact with THR1101 (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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1010C GLU* 2.7 26.5 + - + +
1014C ILE* 4.3 5.9 - - - +
1035C TRP* 3.6 19.3 - - - -
1055C ILE* 5.5 1.3 - - - -
1057C PHE* 3.2 34.5 - - + -
1061C TYR* 3.2 22.4 - - + +
1066C PRO* 5.3 3.8 - - + -
1099C THR 3.8 2.4 + - - -
1100C LYS* 1.3 69.1 - - - +
1102C ASP* 1.3 68.5 + - - +
1104C VAL* 2.6 39.6 + - - +
1105C ILE* 3.2 9.1 + - - +
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Residues in contact with ASP1102 (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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1010C GLU* 4.0 1.9 + - - +
1013C GLU* 5.2 8.7 - - + -
1014C ILE* 3.6 23.0 - - + +
1017C CYS* 5.2 6.5 - - - +
1019C MET* 3.0 31.7 - - - +
1100C LYS* 2.8 18.8 + - + +
1101C THR* 1.3 83.7 + - - +
1103C GLN* 1.3 69.3 + - - +
1104C VAL 3.1 2.9 + - - -
1105C ILE* 3.3 20.4 + - - +
1106C GLN* 4.0 6.7 + - - +
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Residues in contact with GLN1103 (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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1089C VAL* 5.5 7.5 - - + +
1099C THR* 4.6 18.0 - - - +
1100C LYS* 2.9 17.1 + - + +
1102C ASP* 1.3 82.5 - - - +
1104C VAL* 1.3 61.7 + - + +
1106C GLN* 3.7 24.6 + - - +
1107C SER* 3.5 19.1 + - - -
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Residues in contact with VAL1104 (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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1055C ILE* 5.9 2.0 - - + -
1066C PRO* 5.5 6.3 - - + -
1068C ILE* 4.1 5.8 - - + -
1087C LEU* 4.2 2.3 - - - +
1089C VAL* 4.5 14.8 - - + +
1090C ILE* 3.3 39.9 - - + -
1095C TRP* 5.2 5.2 - - + -
1099C THR* 5.1 9.2 - - - +
1100C LYS 3.8 10.3 - - - +
1101C THR* 2.6 41.1 + - - +
1103C GLN* 1.3 71.6 - - + +
1105C ILE* 1.3 62.8 + - + +
1106C GLN 2.6 17.5 + - - -
1107C SER* 2.8 17.9 + - - +
1108C LEU* 3.0 13.6 + - - +
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Residues in contact with ILE1105 (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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1014C ILE* 5.6 6.1 - - + -
1019C MET* 4.1 14.8 - - - +
1022C PHE* 3.6 51.5 - - + +
1035C TRP* 5.3 2.2 - - + -
1039C ILE* 4.9 7.0 - - + -
1053C ILE* 5.6 0.9 - - + -
1055C ILE* 3.2 35.0 - - + -
1068C ILE* 4.5 8.7 - - + -
1101C THR* 3.2 11.1 + - - +
1102C ASP* 3.3 9.4 + - - +
1104C VAL* 1.3 90.1 - - + +
1106C GLN* 1.3 60.1 + - - +
1108C LEU* 4.3 15.0 - - + -
1109C ILE* 4.4 10.1 - - + +
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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