Contacts of the helix formed by residues 86 - 93 (chain J) in PDB entry 1FQV
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 PRO 86 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64J HIS* 6.0 1.3 - - - +
65J HIS* 5.2 4.5 - - - +
85J ILE* 1.3 95.2 - - + +
87J VAL* 1.3 63.6 + - - +
88J TRP* 3.3 3.8 - - + +
89J ASP* 3.9 31.0 - - - +
90J GLN* 2.9 22.0 + - - +
118J VAL* 5.0 4.3 - - + -
245M VAL* 5.9 7.2 - - + -
269M ARG* 5.7 6.5 - - + +
271M ASP* 5.1 11.4 - - + +
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Residues in contact with VAL 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J PRO* 1.3 72.9 - - - +
88J TRP* 1.3 59.8 + - - +
90J GLN* 3.1 16.5 + - + +
91J GLU* 2.9 29.6 + - + +
271M ASP* 5.3 0.6 + - - -
295M GLU* 4.3 1.8 - - + +
296M THR* 3.0 55.4 + - + +
298M THR* 4.0 8.5 - - + -
323M ASN* 3.7 37.7 - - + +
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Residues in contact with TRP 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J GLN* 3.8 33.6 + - + -
61J TRP* 3.9 15.3 - + - -
64J HIS* 3.3 62.2 + + + +
65J HIS* 3.8 6.5 - + - -
86J PRO* 3.3 3.4 - - + +
87J VAL* 1.3 78.9 - - - +
89J ASP* 1.3 78.9 + - - +
91J GLU* 2.8 34.0 + - + +
92J PHE* 2.6 53.9 + + + +
269M ARG* 6.0 3.8 - - + -
296M THR* 4.6 8.8 - - + +
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Residues in contact with ASP 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J TRP* 3.5 14.6 + - - +
64J HIS* 4.1 1.2 - - - -
65J HIS* 3.0 40.4 + - - -
85J ILE* 3.8 19.7 - - + -
86J PRO* 3.5 20.2 + - + +
87J VAL 3.4 0.4 - - - -
88J TRP* 1.3 83.8 - - - +
90J GLN* 1.3 56.1 + - - +
92J PHE* 3.6 8.3 - - - -
93J LEU* 2.8 38.2 + - + +
118J VAL* 3.6 20.9 - - + +
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Residues in contact with GLN 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ILE* 2.8 36.1 + - + +
86J PRO 2.9 19.2 + - - +
87J VAL* 3.3 16.1 - - + +
88J TRP 3.1 0.2 - - - -
89J ASP* 1.3 75.8 - - - +
91J GLU* 1.3 65.9 + - - +
93J LEU* 3.3 5.5 + - - +
94J LYS* 3.1 23.9 + - - +
323M ASN* 5.1 8.7 + - - -
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Residues in contact with GLU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J GLN* 5.3 1.2 - - - +
87J VAL* 2.9 13.7 + - + +
88J TRP* 2.8 59.0 + - + +
90J GLN* 1.3 75.7 - - - +
92J PHE* 1.3 85.5 + - - +
94J LYS* 3.0 26.2 + - - +
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Residues in contact with PHE 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J LYS* 3.1 83.9 + - + +
60J GLN* 3.4 28.0 - - + -
61J TRP* 3.5 32.5 - + + -
88J TRP* 2.6 38.9 + + + +
89J ASP* 3.3 9.0 - - - +
90J GLN 3.1 0.2 - - - -
91J GLU* 1.3 86.5 + - - +
93J LEU* 1.3 89.9 + - + +
94J LYS 3.2 3.3 + - - -
95J VAL* 3.6 5.7 - - - +
103J LEU* 4.4 4.0 - - + -
115J LEU* 4.2 5.2 - - + -
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ILE* 5.6 0.9 - - + -
89J ASP* 2.8 26.4 + - + +
90J GLN* 3.3 5.8 + - - +
92J PHE* 1.3 99.2 - - + +
94J LYS* 1.3 55.7 + - - +
95J VAL* 3.1 21.0 + - - +
100J LEU* 4.4 6.9 - - + +
103J LEU* 3.7 21.5 - - + -
115J LEU* 4.9 0.9 - - + -
118J VAL* 3.7 27.8 - - + +
119J THR* 4.1 14.8 - - + -
122J THR* 3.0 44.9 - - + +
126J MET* 5.3 4.7 - - - +
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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