Contacts of the helix formed by residues 101 - 113 (chain C) in PDB entry 1VBF
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 ASN 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.1 6.4 - - - +
51C ILE* 3.5 28.4 - - + +
99C GLU* 2.6 19.8 + - - +
100C ILE* 1.3 78.9 - - + +
102C GLU* 1.3 58.3 + - - +
103C LYS* 2.7 39.3 + - - +
104C MSE 3.0 17.2 + - + -
105C TYR* 2.9 26.8 + - - +
122C LEU* 4.3 0.2 - - - -
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ILE 3.7 3.8 + - - -
101C ASN* 1.3 71.6 + - - +
103C LYS* 1.3 58.3 + - + +
105C TYR* 2.9 8.5 + - + +
106C ASN* 2.7 55.4 + - - +
122C LEU* 3.9 29.3 - - + +
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.1 25.1 - - + -
101C ASN* 2.7 15.7 + - - +
102C GLU* 1.3 74.1 - - + +
104C MSE 1.3 60.6 + - - +
106C ASN* 3.5 10.6 + - - +
107C TYR* 3.1 24.3 + - - +
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Residues in contact with MSE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 3.7 30.5 - - + -
48C LEU* 3.4 21.1 - - + -
51C ILE* 3.4 35.7 - - + -
52C ASN 4.8 6.7 - - - +
53C THR* 5.5 1.1 - - + +
80C GLY* 3.1 44.5 - - - +
81C ILE* 3.9 6.7 - - + +
99C GLU* 3.8 20.0 - - + +
101C ASN* 3.0 15.1 + - + +
103C LYS* 1.3 77.4 - - - +
105C TYR* 1.3 64.3 + - - +
107C TYR* 3.5 8.6 + - - +
108C ALA* 3.1 25.3 + - - +
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C THR* 5.8 1.3 - - + -
99C GLU* 4.4 14.4 - - + -
101C ASN 2.9 16.2 + - - +
102C GLU* 3.0 15.0 - - + +
104C MSE 1.3 79.3 - - - +
106C ASN* 1.3 69.8 + - - +
108C ALA* 3.4 3.4 + - - +
109C SER* 2.8 48.4 + - - -
120C LEU* 3.9 27.7 + - + +
121C ILE 3.9 9.4 - - - -
122C LEU* 3.7 53.2 + - + +
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Residues in contact with ASN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLU* 2.7 38.7 + - - +
103C LYS* 3.8 8.9 - - - +
105C TYR* 1.3 82.6 - - - +
107C TYR* 1.3 68.1 + - - +
109C SER* 2.9 18.3 + - - -
110C LYS* 3.3 12.1 + - - +
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE 2.5 30.7 + - - -
29C LEU 3.3 18.9 + - - -
30C PRO* 3.4 19.7 - - + +
47C ILE* 5.2 6.1 - - + -
80C GLY 4.9 0.4 - - - -
81C ILE* 3.8 27.4 - - + -
103C LYS 3.1 16.1 + - - +
104C MSE 3.7 11.9 - - - +
106C ASN* 1.3 79.8 - - - +
108C ALA* 1.3 61.2 + - - +
110C LYS* 2.9 54.4 + - - +
111C LEU* 3.5 14.4 - - + +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C THR* 3.8 21.5 - - + -
80C GLY 3.3 26.5 - - - +
81C ILE 4.1 11.7 - - - -
82C GLY* 4.3 1.6 - - - +
104C MSE 3.1 10.8 + - - +
105C TYR* 3.9 3.6 - - - +
106C ASN 3.0 0.6 - - - -
107C TYR* 1.3 79.9 - - - +
109C SER* 1.3 63.3 + - - +
110C LYS 3.3 0.7 - - - -
111C LEU* 3.3 2.8 + - - +
112C LEU* 3.1 28.0 + - + +
120C LEU* 4.4 3.1 - - + -
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C TYR* 2.8 41.3 + - - -
106C ASN* 2.9 12.2 + - - -
108C ALA* 1.3 77.7 - - - +
110C LYS* 1.3 59.0 + - - +
112C LEU 3.4 0.7 + - - -
113C SER* 2.8 27.9 + - - -
120C LEU* 3.9 17.7 - - - +
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU* 5.8 0.2 - - - -
106C ASN 3.3 6.0 + - - +
107C TYR* 2.9 57.4 + - - +
109C SER* 1.3 78.6 - - - +
111C LEU* 1.3 87.2 + - + +
112C LEU 3.3 0.2 + - - -
113C SER* 3.3 19.6 + - - -
114C TYR* 5.0 5.0 - - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.6 19.1 - - + +
28C PHE* 3.8 34.4 - - + +
81C ILE 3.8 13.2 - - - +
107C TYR* 3.5 28.7 - - + +
108C ALA 3.3 7.2 + - - +
110C LYS* 1.3 111.6 - - + +
112C LEU* 1.3 64.2 + - + +
113C SER 3.6 0.4 - - - -
114C TYR* 5.2 1.3 + - - -
115C TYR* 4.6 6.1 - - - -
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 4.2 10.3 - - + -
79C THR* 4.3 3.8 - - + -
82C GLY* 3.7 33.9 - - - +
85C THR* 4.1 13.2 - - + -
86C ALA* 4.2 3.6 - - + +
108C ALA 3.1 16.9 + - - +
109C SER 3.8 1.6 - - - +
110C LYS 3.2 0.2 - - - -
111C LEU* 1.3 81.3 - - + +
113C SER* 1.3 64.6 + - - +
114C TYR 3.2 3.1 - - - -
115C TYR* 3.1 34.2 + - + +
118C ILE* 4.1 24.3 - - + +
120C LEU* 3.7 39.9 - - + -
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 2.9 39.3 + - - +
132B GLU* 3.5 23.0 + - - -
109C SER 2.8 21.5 + - - -
110C LYS* 3.3 14.7 + - - -
111C LEU 3.6 0.2 - - - -
112C LEU* 1.3 77.2 - - - +
114C TYR* 1.3 80.0 + - - +
115C TYR 3.2 6.5 + - - +
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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