Contacts of the helix formed by residues 81 - 89 (chain O) in PDB entry 1VF5
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 LEU 81 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129N VAL* 3.8 24.0 - - + -
133N VAL* 3.4 28.7 - - + -
1304N TDS 3.3 37.7 - - + +
77O PRO* 4.5 9.2 - - + -
78O GLU* 3.0 27.6 + - + +
80O TYR* 1.3 85.7 - - - +
82O TYR* 1.3 54.5 + - - +
83O PRO* 3.7 0.4 - - - -
84O VAL* 4.1 13.9 - - + +
85O PHE* 2.7 40.2 + - - +
1201O CLA 5.0 7.4 - - + -
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Residues in contact with TYR 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O LEU* 4.2 18.0 + - - +
77O PRO* 3.0 34.5 + - + -
78O GLU 3.2 8.1 - - - -
79O TRP* 3.0 61.8 + + - +
81O LEU* 1.3 77.4 - - - +
83O PRO* 1.3 67.7 - - + +
84O VAL 3.1 0.9 - - - -
85O PHE* 2.9 6.6 + + + -
86O GLN* 2.5 37.0 + - - +
143O LEU 4.0 2.5 - - - -
144O GLY* 3.8 12.1 - - - -
145O ILE* 4.0 17.9 - - - +
146O GLY* 6.1 2.7 - - - -
149O LEU* 5.9 5.4 - - + -
1R MET* 4.5 2.3 - - - +
8R TYR* 3.7 18.6 - + - -
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Residues in contact with PRO 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O TRP 4.2 2.0 - - - +
80O TYR* 3.8 11.9 - - - +
82O TYR* 1.3 96.7 - - + +
84O VAL* 1.3 67.0 + - - +
86O GLN* 3.3 2.6 + - - +
87O ILE* 3.1 24.1 + - - +
140O THR* 3.6 24.7 - - + +
143O LEU* 3.7 17.9 - - + +
144O GLY* 4.0 4.9 - - - -
1201O CLA 3.2 49.6 - - + +
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Residues in contact with VAL 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304N TDS 5.7 4.9 - - + -
80O TYR 4.2 8.3 - - - +
81O LEU* 4.1 14.4 - - + +
83O PRO* 1.3 75.4 - - + +
85O PHE* 1.3 55.2 + - - +
87O ILE* 3.1 4.0 + - + +
88O LEU* 2.8 44.1 + - + +
101O MET* 3.3 41.7 - - + -
1201O CLA 2.8 58.7 - - + +
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Residues in contact with PHE 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 5.9 4.3 - - + -
129D HIS* 5.8 4.3 - - - -
150N ILE* 4.9 14.4 - - + -
1304N TDS 4.0 23.6 - - + -
74O GLU 4.9 4.0 - - - -
75O ILE* 4.2 36.1 - - + -
77O PRO* 4.4 7.4 - - + -
81O LEU 2.7 24.6 + - - +
82O TYR* 3.5 6.5 - + - +
84O VAL* 1.3 72.7 - - - +
86O GLN* 1.3 64.2 + - - +
87O ILE 2.9 5.9 + - - -
88O LEU* 3.9 9.9 - - + +
89O ARG* 3.0 59.6 + - + +
145O ILE 4.6 8.5 - - - -
146O GLY* 4.6 1.8 - - - -
147O ALA* 4.5 15.3 - - - -
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Residues in contact with GLN 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TYR 2.5 14.3 + - - +
83O PRO 3.6 2.5 - - - +
85O PHE* 1.3 73.8 - - - +
87O ILE* 1.3 57.9 + - - +
89O ARG* 3.3 28.0 + - - +
90O SER* 3.1 26.6 + - - -
142O TRP* 4.1 1.8 + - - -
143O LEU* 2.7 51.1 + - + +
145O ILE* 3.1 41.2 - - - +
152O ASP* 3.7 28.3 - - - +
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Residues in contact with ILE 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O PRO 3.1 8.5 + - - +
84O VAL* 3.1 10.5 + - + +
85O PHE 2.9 1.4 - - - -
86O GLN* 1.3 75.2 - - - +
88O LEU* 1.3 66.7 + - + +
89O ARG 3.0 1.3 - - - -
90O SER* 2.6 31.2 + - - -
91O LEU* 3.3 31.1 + - + +
97O GLY* 4.5 7.0 - - - +
100O LEU* 4.5 11.2 - - + +
101O MET* 5.3 7.4 - - - +
104O VAL* 5.5 0.4 - - + -
143O LEU* 3.3 29.6 - - + -
1201O CLA 3.6 42.6 - - + -
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Residues in contact with LEU 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 5.1 9.7 - - + +
154N VAL* 4.2 11.7 - - + -
1304N TDS 3.7 41.1 - - + -
84O VAL* 2.8 34.0 + - + +
85O PHE* 3.9 8.3 - - + +
87O ILE* 1.3 83.9 - - + +
89O ARG* 1.3 60.9 + - - +
91O LEU* 3.4 15.1 - - - +
93O ASN* 4.5 11.1 + - - +
97O GLY* 4.3 15.7 - - - +
98O VAL* 5.3 1.1 - - + +
101O MET* 3.6 36.6 - - + -
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Residues in contact with ARG 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 4.3 22.4 - - + +
129D HIS* 4.8 12.0 - - + -
85O PHE* 3.0 45.8 + - + +
86O GLN* 3.3 26.8 + - - +
87O ILE 2.8 0.8 + - - -
88O LEU* 1.3 76.4 - - + +
90O SER* 1.3 69.4 + - - +
91O LEU 4.4 1.1 - - - +
92O PRO* 5.7 0.5 - - - +
93O ASN* 5.7 1.8 + - - +
145O ILE* 3.9 6.7 - - - +
146O GLY* 3.2 33.7 + - - +
147O ALA* 3.5 8.6 - - - +
148O ALA* 3.0 28.9 - - - +
149O LEU 4.4 1.0 - - - +
151O LEU* 4.7 10.6 - - - +
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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