Contacts of the helix formed by residues 74 - 86 (chain C) in PDB entry 3VTW
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 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C HIS 3.5 3.9 + - - +
73C VAL* 1.3 79.6 - - - +
75C MET* 1.3 68.9 + - - +
76C SER* 2.8 41.8 + - - -
77C GLU* 2.9 49.8 + - - +
78C LEU* 3.1 10.1 + - - +
107C SER* 3.4 25.1 + - - +
108C THR 3.2 19.1 - - - +
109C PRO* 4.0 2.7 - - + -
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Residues in contact with MET 75 (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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74C ASN* 1.3 75.3 - - - +
76C SER* 1.3 64.4 + - - +
78C LEU* 2.9 21.5 + - + +
79C ILE* 2.9 23.9 + - + +
96C LEU* 4.9 5.6 - - - -
98C VAL* 5.0 1.6 - - - -
103C MET* 3.7 35.4 - - - +
104C VAL 4.9 2.2 - - - +
106C VAL* 4.3 17.0 - - + -
107C SER 4.7 2.5 - - - +
108C THR 3.4 8.3 + - - +
110C ILE* 3.5 50.7 - - + +
113C VAL* 4.1 17.7 - - + -
126C MET* 4.4 16.2 - - + -
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Residues in contact with SER 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASN* 2.8 21.9 + - - -
75C MET* 1.3 75.7 - - - +
77C GLU* 1.3 62.0 + - - +
79C ILE* 3.8 12.4 - - - +
80C LYS* 3.1 24.8 + - - +
104C VAL 5.1 7.1 + - - -
105C SER* 6.0 2.2 - - - -
106C VAL 5.9 0.7 - - - -
107C SER* 4.9 10.1 - - - +
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Residues in contact with GLU 77 (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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72C HIS* 4.3 2.8 + - - +
73C VAL* 3.5 18.8 - - + +
74C ASN* 2.9 51.1 + - - +
76C SER* 1.3 80.5 - - - +
78C LEU* 1.3 61.1 + - - +
80C LYS* 3.4 8.6 + - + +
81C ILE* 3.0 38.8 + - + +
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Residues in contact with LEU 78 (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 VAL* 5.0 2.5 - - + -
50C ILE* 4.4 7.2 - - + -
67C PHE* 6.0 1.6 - - + -
69C VAL* 4.1 25.4 - - + -
73C VAL* 4.5 5.6 - - + +
74C ASN 3.1 10.3 + - - +
75C MET* 2.9 16.5 + - + +
77C GLU* 1.3 75.7 - - - +
79C ILE* 1.3 54.0 + - - +
81C ILE* 3.1 16.5 + - + +
82C ILE* 2.8 58.7 + - + +
96C LEU* 4.8 5.6 - - + -
110C ILE* 3.5 32.8 - - + -
126C MET* 4.0 20.2 - - + -
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Residues in contact with ILE 79 (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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75C MET* 2.9 22.3 + - + +
76C SER* 3.8 7.6 - - - +
78C LEU* 1.3 72.1 - - - +
80C LYS* 1.3 61.5 + - - +
82C ILE* 3.2 5.7 + - - +
83C ARG* 2.8 47.6 + - - +
94C PHE* 4.0 18.8 - - + -
96C LEU* 3.8 33.9 - - + +
103C MET* 4.4 5.2 - - + -
104C VAL* 4.0 35.4 - - - +
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Residues in contact with LYS 80 (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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76C SER 3.1 16.2 + - - +
77C GLU* 3.7 11.4 - - + +
78C LEU 3.3 0.4 - - - -
79C ILE* 1.3 76.5 - - - +
81C ILE* 1.3 62.8 + - + +
83C ARG* 3.6 7.8 - - - +
84C ARG* 2.9 41.8 + - + +
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Residues in contact with ILE 81 (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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73C VAL* 5.1 9.0 - - + -
77C GLU* 3.0 26.7 + - + +
78C LEU* 3.1 16.1 + - + +
80C LYS* 1.3 85.3 - - + +
82C ILE* 1.3 65.4 + - + +
84C ARG* 3.6 7.2 - - + +
85C ARG* 2.9 40.6 + - + +
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Residues in contact with ILE 82 (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 ILE* 3.6 38.1 - - + -
62C LEU* 4.4 20.9 - - + -
67C PHE* 5.0 5.4 - - + -
78C LEU* 2.8 35.8 + - + +
79C ILE* 3.9 3.8 - - - +
81C ILE* 1.3 77.0 - - + +
83C ARG* 1.3 68.1 + - - +
85C ARG* 3.2 12.8 + - - +
86C LEU* 3.0 37.4 + - + +
94C PHE* 3.6 24.7 - - + -
96C LEU* 5.2 6.5 - - + -
128C TYR* 4.8 2.2 - - + -
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Residues in contact with ARG 83 (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 ILE* 2.8 33.1 + - - +
80C LYS* 3.6 7.2 - - - +
82C ILE* 1.3 73.0 - - - +
84C ARG* 1.3 62.5 + - - +
86C LEU* 3.4 1.3 + - - -
87C GLN 3.1 16.3 + - - -
88C LEU* 3.2 29.6 + - + +
89C ASN 3.1 21.4 + - - -
90C ALA* 3.0 31.9 + - - +
92C GLN 3.1 16.7 + - - -
94C PHE* 3.3 50.3 + - + +
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Residues in contact with ARG 84 (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 LYS* 2.9 34.9 + - + +
81C ILE* 3.6 7.6 - - + +
83C ARG* 1.3 71.3 - - - +
85C ARG* 1.4 62.7 + - + +
87C GLN* 2.9 27.5 + - - +
88C LEU 5.9 0.4 - - - -
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Residues in contact with ARG 85 (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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62C LEU* 3.8 17.7 - - + +
63C ASP* 2.8 44.7 + - - +
64C LYS* 4.9 7.0 - - - +
67C PHE* 4.0 30.5 - - - -
81C ILE* 2.9 33.3 + - + +
82C ILE* 3.2 10.0 + - - +
84C ARG* 1.4 78.6 - - + +
86C LEU* 1.3 60.1 + - - +
87C GLN* 3.2 11.2 + - - +
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Residues in contact with LEU 86 (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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59C LEU* 5.3 0.7 - - + -
60C PRO* 3.7 24.9 - - + +
61C VAL 3.9 4.5 - - - +
62C LEU* 3.6 41.5 - - + +
82C ILE* 3.0 29.5 + - + +
83C ARG 4.0 1.1 - - - +
85C ARG* 1.3 74.0 - - - +
87C GLN* 1.3 71.4 + - - +
88C LEU* 3.3 24.8 + - + +
94C PHE* 4.1 11.2 - - + -
128C TYR* 3.6 35.7 - - + +
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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