Contacts of the helix formed by residues 102 - 114 (chain C) in PDB entry 3VBB
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 GLN 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C ASP* 3.4 30.6 - - + +
78C GLU 4.0 7.1 + - - +
79C SER 2.3 36.7 - - - +
80C VAL* 4.9 2.9 - - - +
81C PRO* 4.2 16.0 - - + +
98C LEU* 3.1 44.5 - - + +
101C SER* 1.3 74.2 + - - +
103C ILE* 1.3 59.2 + - - +
104C LYS 3.0 2.0 - - - -
105C LYS* 2.8 27.6 + - + +
106C VAL* 3.0 15.9 + - + +
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Residues in contact with ILE 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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60C CYS* 3.8 35.2 - - - +
63C THR* 4.3 13.2 - - + -
64C ILE* 4.0 15.0 - - + +
95C LEU* 3.5 41.1 - - + +
97C ASN 4.7 0.2 - - - +
98C LEU* 4.2 11.9 - - + -
99C LYS 3.1 27.1 - - - +
100C VAL* 4.2 7.2 - - - +
101C SER 3.4 0.6 - - - -
102C GLN* 1.3 74.7 - - - +
104C LYS* 1.3 59.6 + - - +
106C VAL* 3.7 9.4 - - + -
107C ARG* 2.9 28.6 + - + +
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Residues in contact with LYS 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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64C ILE* 4.6 13.1 - - + +
68C MET* 4.7 16.1 - - - +
100C VAL* 4.0 17.1 + - - +
101C SER* 3.5 17.8 + - - +
103C ILE* 1.3 80.1 - - - +
105C LYS* 1.3 60.5 + - - +
106C VAL 3.3 0.7 + - - -
107C ARG* 3.4 5.3 + - - +
108C LEU* 3.3 20.4 + - - +
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Residues in contact with LYS 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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78C GLU 5.6 3.1 - - - +
80C VAL* 3.6 24.2 - - + +
101C SER 5.4 0.2 - - - +
102C GLN* 2.8 17.9 + - + +
104C LYS* 1.3 79.2 - - - +
106C VAL* 1.3 60.2 - - - +
108C LEU* 3.5 12.8 - - - +
109C LEU* 3.5 23.4 + - - +
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Residues in contact with VAL 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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60C CYS* 3.9 16.4 - - - -
80C VAL* 3.4 30.3 - - + -
81C PRO* 5.1 2.7 - - + -
84C VAL* 4.6 9.4 - - + -
85C LEU* 4.6 13.0 - - + -
90C LEU* 4.5 20.2 - - + -
95C LEU* 5.8 5.4 - - + -
102C GLN* 3.0 11.8 + - + +
103C ILE* 3.7 12.8 - - + +
104C LYS 3.1 0.2 - - - -
105C LYS* 1.3 74.4 - - - +
107C ARG* 1.3 67.9 + - - +
108C LEU 3.0 2.0 - - - -
109C LEU* 3.0 18.1 + - + +
110C ILE* 3.2 15.0 + - + +
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Residues in contact with ARG 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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57C LYS* 4.1 15.5 - - + +
60C CYS* 3.3 27.4 - - + -
61C SER* 5.3 4.5 - - - +
64C ILE* 6.4 1.6 - - + -
103C ILE* 2.9 16.9 + - + +
104C LYS* 3.4 6.3 + - - +
106C VAL* 1.3 73.4 - - - +
108C LEU* 1.3 61.0 + - - +
110C ILE* 3.5 5.9 + - - +
111C ASP* 3.2 23.7 + - - +
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Residues in contact with LEU 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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104C LYS 3.3 11.4 + - - +
105C LYS* 3.5 15.9 - - - +
106C VAL 3.0 0.6 - - - -
107C ARG* 1.3 79.1 - - - +
109C LEU* 1.3 60.9 + - + +
111C ASP* 3.6 4.8 + - + +
112C GLU* 3.1 40.9 + - - +
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Residues in contact with LEU 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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80C VAL* 4.3 21.8 - - + -
85C LEU* 4.2 29.2 - - + -
105C LYS 3.5 13.6 + - - +
106C VAL* 3.0 11.0 + - - +
108C LEU* 1.3 81.3 - - + +
110C ILE* 1.3 64.4 + - + +
112C GLU* 3.7 16.1 + - + +
113C ALA* 3.3 19.8 + - - +
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Residues in contact with ILE 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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53C LEU* 3.5 40.8 - - + +
56C LEU* 3.6 38.4 - - + +
57C LYS* 4.1 15.7 - - + +
60C CYS* 4.4 13.5 - - - -
90C LEU* 4.2 18.8 - - + -
106C VAL* 3.2 15.6 + - + +
107C ARG* 3.8 7.2 - - - +
108C LEU 3.3 0.2 - - - -
109C LEU* 1.3 75.0 - - + +
111C ASP* 1.3 62.1 + - - +
113C ALA* 2.8 24.8 + - - +
114C ILE* 3.1 8.4 + - + +
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Residues in contact with ASP 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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57C LYS* 2.5 38.4 + - - +
107C ARG 3.2 11.8 + - - +
108C LEU* 4.2 5.4 - - + +
110C ILE* 1.3 78.6 - - - +
112C GLU* 1.3 62.4 + - - +
113C ALA 3.2 0.7 + - - -
114C ILE* 3.2 25.7 + - - +
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Residues in contact with GLU 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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108C LEU* 3.1 37.2 + - - +
109C LEU* 3.8 16.5 - - + +
110C ILE 3.2 0.2 - - - -
111C ASP* 1.3 76.9 - - - +
113C ALA* 1.3 59.2 + - - +
114C ILE 4.4 2.9 - - - +
115C LEU* 6.0 1.0 - - - +
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Residues in contact with ALA 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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49C ARG* 5.8 2.3 - - - -
53C LEU* 3.6 26.7 - - + +
109C LEU 3.3 10.6 + - - +
110C ILE* 2.8 14.0 + - - +
112C GLU* 1.3 79.6 - - - +
114C ILE* 1.3 61.1 + - - -
115C LEU* 3.3 14.9 + - - +
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Residues in contact with ILE 114 (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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50C ALA* 4.6 9.4 - - + -
53C LEU* 3.7 22.7 - - + -
54C ASN* 3.3 46.0 - - - +
57C LYS* 4.0 25.6 - - - +
110C ILE* 3.1 11.8 + - + +
111C ASP* 3.2 18.0 + - - +
112C GLU 4.4 2.9 - - - +
113C ALA* 1.3 74.7 - - - +
115C LEU* 1.3 70.9 + - - +
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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