Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 1VRR
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 ASP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A THR* 3.4 5.7 + - + +
84A ALA* 1.3 76.5 - - - +
86A PRO* 1.3 73.8 - - - +
87A LYS* 2.7 26.7 + - - +
88A LEU* 3.4 20.1 + - + +
89A ILE* 3.2 23.6 + - - +
109A LYS* 3.6 30.7 + - + +
5B GLU* 5.4 1.3 - - - -
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Residues in contact with PRO 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA 3.4 8.3 - - - +
85A ASP* 1.3 88.9 - - - +
87A LYS* 1.3 66.4 + - + +
89A ILE* 3.1 15.1 + - + +
90A ARG* 2.9 31.7 + - + +
5B GLU* 5.6 2.2 - - - +
7B TYR* 4.2 26.5 - - + -
177B TYR* 5.8 0.4 - - - +
181B LEU* 4.5 6.1 - - + -
185B ILE* 4.2 23.5 - - + +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 2.7 20.5 + - - +
86A PRO* 1.3 76.3 - - + +
88A LEU* 1.3 62.0 + - - +
90A ARG* 3.5 22.2 + - - +
91A GLU* 3.2 21.3 + - - +
189B ARG* 5.6 5.7 - - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 3.5 12.3 - - + -
85A ASP* 3.4 23.8 + - + +
86A PRO 3.2 0.4 - - - -
87A LYS* 1.3 75.9 - - - +
89A ILE* 1.3 66.5 + - - +
91A GLU* 3.2 10.4 + - + +
92A THR* 3.1 26.8 - - + +
103A VAL* 4.8 7.6 - - + +
104A ILE* 3.4 45.1 - - + +
107A ALA* 4.2 18.8 - - + -
109A LYS* 3.7 24.2 - - + +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR 5.5 0.4 - - - +
82A VAL* 5.2 0.7 - - - -
83A THR* 3.1 38.4 - - + +
85A ASP 3.2 13.7 - - - +
86A PRO* 3.1 8.9 + - + +
88A LEU* 1.3 77.4 - - - +
90A ARG* 1.3 62.1 + - - +
92A THR* 3.0 21.3 + - - +
93A LEU* 3.1 17.8 - - + +
178B GLU 4.9 0.4 - - - +
181B LEU* 3.8 19.7 - - + -
182B TYR* 3.3 49.8 - - + +
185B ILE* 3.8 20.2 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 2.9 21.3 + - - +
87A LYS* 3.7 25.8 - - - +
89A ILE* 1.3 76.9 - - - +
91A GLU* 1.3 59.7 + - - +
92A THR 3.2 1.1 + - - -
93A LEU* 3.7 26.4 + - + +
94A SER 5.2 0.5 + - - -
7B TYR* 5.3 0.2 + - - -
185B ILE* 3.3 37.6 + - + +
188B GLY* 4.0 13.3 + - - -
189B ARG* 3.5 42.9 - - - +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LYS 3.2 13.2 + - - +
88A LEU* 3.7 8.1 - - + +
89A ILE 3.2 1.2 - - - -
90A ARG* 1.3 79.1 - - - +
92A THR* 1.3 63.2 + - + +
93A LEU 3.6 0.2 - - - -
94A SER* 5.0 4.2 + - - -
95A LEU* 4.1 13.7 - - - +
103A VAL* 5.4 8.6 - - + +
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Residues in contact with THR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR 4.8 7.4 + - - -
88A LEU* 3.1 16.9 + - + +
89A ILE* 3.0 17.9 + - - +
91A GLU* 1.3 82.8 - - + +
93A LEU* 1.3 56.9 + - - +
94A SER 3.3 3.6 + - - -
95A LEU* 3.4 12.2 + - + -
100A GLN* 2.7 50.1 + - - +
103A VAL* 4.3 22.7 - - + -
104A ILE* 4.1 25.3 - - + +
182B TYR* 5.4 1.7 - - - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 3.1 15.3 - - + +
90A ARG* 3.7 28.9 + - + +
91A GLU 3.6 1.4 - - - -
92A THR* 1.3 78.0 - - - +
94A SER* 1.3 60.3 + - - +
95A LEU 3.8 1.4 + - - +
100A GLN* 4.1 8.8 + - - +
182B TYR* 3.7 33.3 + - + +
185B ILE* 4.3 18.4 - - + +
186B ARG* 4.1 22.7 - - + +
188B GLY 6.1 0.4 - - - +
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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