Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 1VI7
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 GLY 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL 4.5 2.0 - - - -
72A PHE* 3.7 29.9 - - - +
73A SER 4.2 7.9 - - - -
74A ASP* 3.0 14.4 + - - -
81A THR 3.7 1.4 - - - +
82A ALA* 1.3 80.5 - - - +
84A LYS* 1.4 67.1 + - - +
85A PRO* 3.4 0.8 - - - +
86A MET* 3.4 8.4 + - - +
87A LEU* 3.2 15.4 + - - +
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Residues in contact with LYS 84 (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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72A PHE* 4.1 32.4 - - + -
74A ASP* 4.9 0.4 + - - -
80A GLY* 4.9 12.2 + - - +
83A GLY* 1.4 69.1 - - - +
85A PRO* 1.3 77.4 - - + +
87A LEU* 2.7 26.5 + - + +
88A ALA* 3.0 14.2 + - - +
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Residues in contact with PRO 85 (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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80A GLY 3.6 20.2 - - - +
81A THR 4.0 16.8 - - - +
82A ALA 4.5 0.2 - - - +
83A GLY 3.5 6.5 - - - +
84A LYS* 1.3 96.2 - - + +
86A MET* 1.3 60.4 + - - +
88A ALA* 3.2 14.7 + - + +
89A GLN* 3.5 16.3 + - - +
117A VAL* 4.1 22.9 - - + +
120A TYR* 5.0 1.6 - - + -
121A GLY* 3.9 24.1 - - - +
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS* 3.5 13.7 - - + +
57A VAL* 4.0 17.5 - - - +
58A ALA* 3.4 18.6 - - + -
82A ALA 2.7 28.7 + - - +
83A GLY 3.4 8.9 + - - +
84A LYS 3.2 0.8 - - - -
85A PRO* 1.3 75.3 - - - +
87A LEU* 1.3 66.2 + - - +
89A GLN* 3.4 5.5 + - - +
90A LEU* 3.4 21.8 + - - +
100A ALA 4.6 4.0 - - - +
102A VAL* 3.3 23.1 - - + -
120A TYR* 3.2 38.6 - - + +
121A GLY* 4.0 5.1 - - - -
124A VAL* 3.2 26.0 - - + +
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Residues in contact with LEU 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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58A ALA* 4.1 8.5 - - + -
59A TRP 3.3 30.1 - - - +
60A VAL* 4.8 3.6 - - + -
70A LEU* 4.3 15.0 - - + -
71A GLY 4.0 11.9 - - - +
72A PHE* 4.7 10.8 - - + -
83A GLY 3.2 12.7 + - - +
84A LYS* 2.7 23.8 + - + +
86A MET* 1.3 71.8 - - - +
88A ALA* 1.3 59.6 + - + +
90A LEU* 2.8 10.3 + - + +
91A MET* 2.7 61.6 + - + +
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Residues in contact with ALA 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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84A LYS 3.0 9.9 + - - +
85A PRO* 3.2 10.7 + - + +
87A LEU* 1.3 81.2 - - + +
89A GLN* 1.3 57.5 + - - +
91A MET* 3.4 10.5 + - - +
92A GLY* 2.7 29.1 + - - -
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Residues in contact with GLN 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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85A PRO 3.8 12.4 + - - +
86A MET 3.4 8.0 + - - +
87A LEU 3.2 0.4 - - - -
88A ALA* 1.3 77.0 + - - +
90A LEU* 1.3 67.1 + - - +
92A GLY* 2.7 13.7 + - - -
93A SER* 2.7 15.6 + - - -
121A GLY* 3.5 25.0 + - - +
124A VAL* 3.9 4.3 - - + -
125A ASN* 2.6 40.6 + - - +
128A LEU* 3.8 20.1 - - + +
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Residues in contact with LEU 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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29A LEU* 5.2 0.9 - - + -
58A ALA* 3.8 36.6 - - + +
59A TRP* 3.9 11.9 - - - +
60A VAL* 4.9 12.1 - - + -
65A ASP* 4.2 4.4 - - - +
86A MET 3.4 15.3 - - - +
87A LEU* 2.8 9.5 + - + +
89A GLN* 1.3 72.8 - - - +
91A MET* 1.3 65.7 + - - +
93A SER* 2.7 21.9 + - - +
94A GLY 3.5 4.9 + - - -
95A VAL 4.4 4.8 + - - +
98A ILE* 4.4 28.9 - - + +
100A ALA* 4.3 12.8 - - + -
124A VAL* 3.5 22.9 - - + -
128A LEU* 4.3 15.0 - - + -
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Residues in contact with MET 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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60A VAL* 4.5 5.8 - - + -
65A ASP* 2.9 49.4 - - + +
70A LEU* 3.9 24.7 - - + -
87A LEU* 2.7 48.0 + - + +
88A ALA* 3.7 7.4 - - - +
90A LEU* 1.3 78.9 - - - +
92A GLY* 1.3 61.7 + - - +
94A GLY* 3.6 6.8 + - - -
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Residues in contact with GLY 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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88A ALA 2.7 13.9 + - - -
89A GLN* 2.7 13.8 + - - -
91A MET* 1.3 72.6 - - - +
93A SER* 1.3 61.1 + - - +
94A GLY* 3.4 0.9 + - - -
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Residues in contact with SER 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 GLN 2.7 15.8 + - - -
90A LEU* 2.7 27.4 + - - +
92A GLY* 1.3 73.8 - - - +
94A GLY* 1.3 61.1 + - - +
95A VAL* 4.1 24.5 + - - +
98A ILE* 5.7 0.5 - - - +
128A LEU* 4.3 23.5 - - - +
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Residues in contact with GLY 94 (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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7A TRP* 5.7 0.2 - - - +
8A LEU* 4.6 15.2 + - - +
64A PRO* 4.9 12.7 - - - +
65A ASP* 4.8 8.5 - - - -
90A LEU 3.5 4.8 + - - -
91A MET 3.6 6.4 + - - -
92A GLY 3.4 3.9 - - - -
93A SER* 1.3 80.9 + - - +
95A VAL* 1.3 63.1 + - - +
96A GLY 4.2 0.7 - - - -
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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