Contacts of the helix formed by residues 113 - 119 (chain B) in PDB entry 1PV7
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 TYR 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B PHE* 2.7 52.1 - + - -
59B PHE* 3.9 31.1 - + - -
83B MET* 3.9 15.0 - - + -
90B PHE* 6.0 0.4 - - + -
109B VAL* 3.7 12.9 - - + +
110B GLY* 5.0 7.4 - - - +
111B GLY 3.0 3.5 + - - -
112B ILE* 1.3 97.1 - - - +
114B LEU* 1.3 60.3 + - - +
115B GLY 2.6 4.0 - - - +
116B PHE* 2.6 42.5 + + + +
117B CYS* 3.1 1.0 - - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 6.3 0.4 - - + -
83B MET* 3.0 42.8 - - + +
84B LEU* 4.6 5.6 - - + +
86B MET* 3.8 15.5 - - + +
87B PHE* 3.5 29.6 - - + -
90B PHE* 3.0 67.3 - - + -
91B PHE* 4.6 1.3 - - + -
111B GLY 4.0 2.0 + - - -
113B TYR* 1.3 77.7 - - - +
115B GLY* 1.3 58.7 + - - +
117B CYS* 3.1 31.3 - - - +
118B PHE* 5.0 4.2 - - + -
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.8 30.0 + - - -
52B ILE* 5.2 5.3 - - - +
90B PHE* 4.4 2.6 - - - -
91B PHE* 5.9 0.7 - - - -
95B PHE* 5.7 1.3 - - - -
111B GLY 3.5 14.4 + - - -
112B ILE* 4.2 9.6 - - - +
113B TYR 2.6 5.8 - - - +
114B LEU* 1.3 80.4 - - - +
116B PHE* 1.3 60.0 + - - -
117B CYS 3.2 0.8 + - - -
118B PHE* 3.7 10.5 + - - +
119B ASN* 4.7 3.5 + - - +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 6.4 0.4 - - - -
55B PHE* 4.8 7.4 - - + +
59B PHE* 3.5 48.5 - + + -
63B PHE* 4.3 22.7 - + - -
76B LEU* 6.2 1.3 - - + -
79B ILE* 5.3 10.3 - - + -
80B ILE* 5.3 8.7 - - + -
83B MET* 4.2 13.2 - - - -
112B ILE* 3.9 8.7 - - - +
113B TYR* 2.6 39.9 + - + +
115B GLY* 1.3 68.1 - - - -
117B CYS* 1.3 75.1 + - - +
118B PHE 2.7 17.1 + - - -
119B ASN* 3.1 17.2 + - + +
120B ALA* 3.5 28.1 + - + -
121B GLY* 4.0 3.1 + - - -
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Residues in contact with CYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 2.8 20.8 + - - -
79B ILE 5.2 1.1 - - - -
80B ILE* 4.7 8.2 - - + +
83B MET* 3.7 21.5 - - - -
84B LEU* 3.4 25.6 - - + +
113B TYR 3.1 16.8 - - - -
114B LEU* 3.1 21.5 - - - +
115B GLY 3.2 0.8 - - - -
116B PHE* 1.3 100.6 - - - +
118B PHE* 1.3 63.6 + - - +
119B ASN 3.8 0.4 - - - -
121B GLY* 4.1 5.6 - - - +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.5 35.9 - + - -
22B ILE* 3.1 50.3 - - + -
23B MET* 3.6 41.4 - - + +
26B TYR* 3.7 42.8 - + + -
84B LEU* 3.7 18.4 - - + -
87B PHE* 4.4 7.2 - + - -
114B LEU* 5.0 5.2 - - + -
115B GLY 3.7 8.4 + - - +
116B PHE 2.7 4.0 + - - -
117B CYS* 1.3 87.4 - - - +
119B ASN* 1.3 57.5 + - - +
122B ALA* 4.3 6.0 - - - +
1F YIO 5.2 2.9 + - - -
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.8 13.1 - - + +
55B PHE 5.8 0.2 - - - +
56B SER* 2.8 42.8 + - - -
60B GLN* 3.4 11.7 + - - -
115B GLY 4.7 2.2 + - - +
116B PHE* 3.1 10.4 + - - +
118B PHE* 1.3 79.2 - - - +
120B ALA* 1.3 56.6 + - + +
122B ALA* 3.6 3.3 - - - +
123B PRO* 2.8 32.2 - - - +
359B GLN* 5.1 2.9 + - - +
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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