Contacts of the helix formed by residues 73 - 86 (chain C) in PDB entry 3VJR
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 LEU 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C THR* 3.3 22.6 + - + +
70C PHE* 2.9 15.7 + - + +
72C ASN* 1.3 95.2 - - - +
74C SER* 1.3 65.1 + - - +
75C GLY 3.1 3.1 - - - -
76C LYS* 3.1 42.2 + - + +
122C ASP* 3.1 11.2 - - - +
126C LYS* 4.5 13.7 - - - +
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Residues in contact with SER 74 (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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12C LEU* 3.8 13.0 - - - +
13C ALA 4.7 2.3 + - - -
67C PRO* 4.4 10.5 - - - +
69C THR* 3.6 10.7 + - - -
70C PHE 4.1 0.9 + - - -
71C MET* 2.8 37.1 + - - -
72C ASN 3.6 0.2 - - - -
73C LEU* 1.3 77.4 - - - +
75C GLY* 1.3 62.4 + - - +
77C ALA* 3.1 7.3 + - - +
78C VAL* 3.0 22.9 + - - +
119C GLY 4.0 4.7 - - - -
122C ASP* 3.4 1.2 + - - -
123C ILE* 4.0 23.1 - - - -
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Residues in contact with GLY 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 SER* 1.3 76.2 - - - +
76C LYS* 1.3 57.1 + - - +
78C VAL* 4.4 1.6 - - - -
79C ALA* 2.6 38.3 + - - +
122C ASP* 2.9 21.5 + - - -
123C ILE* 3.8 14.9 - - - +
126C LYS* 3.6 19.9 - - - +
127C LEU* 6.3 0.4 - - - -
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Residues in contact with LYS 76 (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 PHE* 3.8 46.8 - - + -
69C THR* 4.1 14.3 - - + +
73C LEU* 3.1 35.2 + - + +
75C GLY* 1.3 75.0 - - - +
77C ALA* 1.3 57.2 + - - +
79C ALA* 4.2 4.2 - - - +
80C ALA* 3.1 30.5 + - - +
122C ASP* 3.9 2.4 + - - -
126C LYS* 4.0 12.5 - - + +
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Residues in contact with ALA 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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48C PHE 3.3 26.9 - - - +
49C PHE* 3.5 20.3 - - + +
65C LEU* 3.7 13.7 - - + +
67C PRO* 3.7 22.0 - - + -
69C THR* 4.7 2.2 - - + -
73C LEU 3.9 1.2 + - - -
74C SER 3.1 9.9 + - - +
76C LYS* 1.3 77.5 - - - +
78C VAL* 1.3 64.5 - - - +
80C ALA* 3.4 0.9 + - - +
81C MET* 3.2 18.0 + - - +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.4 7.3 - - + +
10C VAL* 3.8 33.2 - - + -
65C LEU* 4.0 6.5 - - + -
67C PRO* 5.1 0.9 - - + -
74C SER 3.0 19.1 + - - +
75C GLY* 3.9 3.4 - - - +
77C ALA* 1.3 75.8 - - - +
79C ALA* 1.3 57.5 + - - +
80C ALA 3.3 0.2 + - - -
81C MET* 3.3 2.9 + - - +
82C ALA* 3.0 31.0 + - - +
92C ILE* 4.1 21.3 - - + -
94C VAL* 5.4 0.7 - - + -
123C ILE* 3.8 31.9 - - + -
127C LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 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 GLY 2.6 21.4 + - - +
76C LYS* 4.2 4.0 - - - +
78C VAL* 1.3 73.6 - - - +
80C ALA* 1.3 57.2 + - - +
82C ALA* 4.0 1.9 - - - +
83C SER* 2.9 34.2 + - - -
126C LYS* 3.6 29.2 - - + +
127C LEU* 4.3 9.6 - - + +
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Residues in contact with ALA 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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47C LYS 3.8 21.8 - - - +
48C PHE* 4.0 11.5 - - + -
49C PHE* 4.3 6.7 - - + -
76C LYS 3.1 21.0 + - - +
77C ALA 3.8 4.3 - - - +
78C VAL 3.2 0.2 - - - -
79C ALA* 1.3 77.8 - - - +
81C MET* 1.3 56.5 + - - +
83C SER* 3.7 3.6 - - - -
84C PHE* 3.0 29.5 + - - +
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Residues in contact with MET 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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8C LEU* 4.0 14.6 - - + -
48C PHE* 3.4 32.8 - - + -
52C THR* 3.5 34.8 - - + -
63C ARG* 3.8 27.6 - - + +
64C LEU 4.8 0.2 - - - +
65C LEU* 3.7 24.0 - - + -
77C ALA 3.2 12.7 + - - +
78C VAL 4.0 2.0 - - - +
80C ALA* 1.3 75.6 - - - +
82C ALA* 1.3 59.9 + - - +
84C PHE 3.4 0.5 + - - -
85C PHE* 3.0 63.1 + - + +
87C ILE* 4.9 1.3 - - - -
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Residues in contact with ALA 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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8C LEU* 4.5 2.4 - - + +
78C VAL 3.0 19.0 + - - +
79C ALA* 4.0 4.5 - - - +
81C MET* 1.3 76.4 - - - +
83C SER* 1.3 57.2 + - - +
86C ARG* 2.8 11.4 + - - -
87C ILE* 2.8 54.3 + - + +
92C ILE* 4.0 20.6 - - + -
127C LEU* 4.8 5.8 - - + -
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Residues in contact with SER 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 ALA 2.9 21.6 + - - -
80C ALA* 3.7 5.2 - - - -
82C ALA* 1.3 73.8 - - - +
84C PHE* 1.3 67.4 + - - +
86C ARG* 3.2 17.3 + - - +
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Residues in contact with PHE 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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47C LYS* 3.9 24.7 - - - -
48C PHE* 3.6 22.9 - + + -
80C ALA 3.0 18.7 + - - +
81C MET 3.9 1.6 - - - +
83C SER* 1.3 75.9 - - - +
85C PHE* 1.3 96.5 + + - +
86C ARG* 3.5 20.6 + - - -
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Residues in contact with PHE 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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7C LYS* 5.8 2.4 + - - +
48C PHE* 4.0 13.2 - + - -
63C ARG* 3.4 57.2 - - - -
81C MET* 3.0 46.9 + - + +
84C PHE* 1.3 108.9 - + - +
86C ARG* 1.3 81.2 + - - +
87C ILE* 3.4 21.6 - - + +
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Residues in contact with ARG 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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7C LYS* 4.9 8.3 + - - -
82C ALA 2.8 9.3 + - - -
83C SER* 3.2 11.7 + - - +
84C PHE 3.5 19.1 + - - +
85C PHE* 1.3 90.9 + - - +
87C ILE* 1.3 58.4 + - - +
88C ASN* 4.0 6.2 + - - +
91C GLU* 4.5 2.6 - - - +
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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