Contacts of the helix formed by residues 86 - 93 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245K VAL* 6.4 2.0 - - + -
269K ARG* 5.9 3.8 - - + +
271K ASP* 4.9 12.6 - - + +
296K THR* 6.4 0.4 - - - -
64P HIS* 6.0 0.9 - - - +
65P HIS* 5.1 3.8 - - - +
85P ILE* 1.3 91.7 - - + +
87P VAL* 1.3 61.5 + - - +
88P TRP* 3.4 3.6 - - + +
89P ASP* 3.3 30.5 + - - +
90P GLN* 2.9 30.5 + - - +
118P VAL* 4.9 4.9 - - + -
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Residues in contact with VAL 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271K ASP* 5.1 0.4 + - - -
295K GLU* 4.1 4.3 - - + +
296K THR* 3.0 40.6 + - + +
298K THR* 3.7 9.9 - - + -
323K ASN* 3.1 48.9 - - + +
85P ILE 5.4 0.7 - - - +
86P PRO* 1.3 73.0 - - - +
88P TRP* 1.3 54.0 + - - +
90P GLN* 2.9 14.5 + - + +
91P GLU* 2.7 38.6 + - + +
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Residues in contact with TRP 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K ARG* 6.5 0.4 - - + -
296K THR* 4.6 12.6 - - + +
60P GLN* 3.9 25.4 + - + -
61P TRP* 3.7 35.2 - + - -
64P HIS* 3.1 71.4 + + + +
86P PRO* 4.5 2.0 - - + +
87P VAL* 1.3 79.4 - - - +
89P ASP* 1.3 62.0 + - - +
91P GLU* 2.5 47.1 + - + +
92P PHE* 2.7 37.0 + + + +
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Residues in contact with ASP 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P TRP* 3.2 13.0 + - + +
64P HIS* 4.1 1.2 + - - -
65P HIS* 2.9 39.5 + - - -
85P ILE* 3.8 13.2 - - + -
86P PRO* 3.3 33.3 + - - +
87P VAL 3.2 0.2 - - - -
88P TRP* 1.3 83.8 - - - +
90P GLN* 1.3 62.4 + - - +
92P PHE* 3.4 3.8 - - - +
93P LEU* 2.8 36.1 + - + +
118P VAL* 3.9 15.3 - - + +
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Residues in contact with GLN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323K ASN* 5.1 7.9 + - - +
348K TYR* 6.0 6.7 - - - -
85P ILE* 3.1 36.9 + - + +
86P PRO 2.9 18.0 + - - +
87P VAL* 2.9 15.2 + - - +
89P ASP* 1.3 73.3 - - - +
91P GLU* 1.3 67.4 + - - +
93P LEU* 3.1 6.6 + - - +
94P LYS* 3.0 23.3 + - - +
122P THR* 6.0 1.1 - - - -
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Residues in contact with GLU 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P GLN* 5.2 2.1 - - - +
87P VAL* 2.7 17.9 + - + +
88P TRP* 2.5 58.0 + - + +
90P GLN* 1.3 71.4 - - - +
92P PHE* 1.3 85.7 + - - +
94P LYS* 2.9 27.3 + - - +
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Residues in contact with PHE 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LYS* 3.2 76.6 + - + +
58P VAL* 5.2 0.2 - - - -
60P GLN* 3.5 23.3 - - - -
61P TRP* 3.4 34.8 - + + -
88P TRP* 2.7 40.1 + + + +
89P ASP* 3.4 4.3 - - - +
91P GLU* 1.3 90.9 + - - +
93P LEU* 1.3 92.7 + - + +
94P LYS 3.4 1.9 + - - -
95P VAL* 3.7 6.6 - - - +
103P LEU* 4.3 5.8 - - + -
115P LEU* 4.1 5.6 - - + -
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Residues in contact with LEU 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P ILE* 5.9 1.1 - - + -
89P ASP* 2.8 25.0 + - + +
90P GLN* 3.1 6.3 + - - +
92P PHE* 1.3 103.2 - - + +
94P LYS* 1.3 59.7 + - - +
95P VAL* 2.8 19.3 + - + +
100P LEU* 4.5 8.4 - - + +
103P LEU* 3.7 21.1 - - + -
115P LEU* 5.0 0.2 - - + -
118P VAL* 4.0 15.7 - - + +
119P THR* 4.0 30.1 - - + -
122P THR* 3.4 39.0 - - + +
126P 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