Contacts of the helix formed by residues 75 - 85 (chain C) in PDB entry 6VVT
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 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C TRP 3.6 11.4 - - - -
55C LEU 4.1 3.6 - - - -
57C GLY* 4.4 5.6 - - - -
61C TRP* 3.7 13.9 - - - -
62C ARG* 5.9 0.6 - - - +
73C PRO 4.2 0.4 + - - -
74C VAL* 1.3 78.2 - - - +
76C GLY* 1.3 57.7 + - - -
77C LEU* 3.3 4.7 - - - -
78C GLU* 3.5 12.2 - - - +
79C GLU* 2.4 37.2 + - - +
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Residues in contact with GLY 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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54C TRP* 3.2 17.8 + - - -
55C LEU* 3.1 19.9 + - - -
74C VAL 3.9 0.6 + - - -
75C GLY* 1.3 70.4 - - - +
77C LEU* 1.3 57.8 + - - +
79C GLU* 3.4 2.3 + - - +
80C VAL* 2.9 32.7 + - - +
377C GLN* 3.0 27.8 + - - -
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Residues in contact with LEU 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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55C LEU* 2.8 51.6 - - + +
56C VAL* 3.5 22.9 - - + +
57C GLY* 5.0 0.2 - - - -
75C GLY* 4.2 3.6 - - - -
76C GLY* 1.3 72.6 - - - +
78C GLU* 1.3 76.7 + - + +
80C VAL* 3.1 9.5 + - - +
81C LEU* 3.0 37.5 + - + +
101C PRO* 5.0 11.9 - - + -
103C PHE* 4.7 14.6 - - + -
124C LEU* 6.1 3.8 - - + -
148C PHE* 4.8 13.9 - - + -
380C ILE* 5.3 11.0 - - + -
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Residues in contact with GLU 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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74C VAL* 3.4 9.4 - - + +
75C GLY* 3.0 24.1 + - - +
77C LEU* 1.3 86.6 - - + +
79C GLU* 1.3 57.0 + - - +
81C LEU* 3.5 9.2 + - - +
82C ALA* 3.0 27.2 + - - +
101C PRO* 5.3 7.1 - - + +
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Residues in contact with GLU 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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54C TRP* 6.0 2.0 - - + -
74C VAL* 3.1 21.4 - - + +
75C GLY 2.4 31.6 + - - +
76C GLY* 3.7 6.1 - - - +
78C GLU* 1.3 64.5 - - - +
80C VAL* 1.3 65.7 + - - +
82C ALA* 3.4 6.1 + - - +
83C GLU* 3.3 24.3 + - - +
377C GLN* 5.1 6.3 - - - +
381C ARG* 5.0 4.1 + - - +
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Residues in contact with VAL 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 GLY 2.9 23.8 + - - +
77C LEU* 3.1 10.5 + - - +
79C GLU* 1.3 77.5 - - - +
81C LEU* 1.3 58.7 + - + +
83C GLU* 3.0 26.7 - - + +
84C LEU* 3.1 11.4 + - + +
377C GLN* 3.6 30.5 - - + +
380C ILE* 4.3 10.3 - - + -
381C ARG* 4.4 20.6 - - + +
384C LEU* 3.2 35.4 - - + -
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Residues in contact with LEU 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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77C LEU* 3.0 33.5 + - + +
78C GLU* 4.0 5.4 - - - +
80C VAL* 1.3 74.6 - - + +
82C ALA* 1.3 58.3 + - - +
84C LEU* 4.2 5.2 - - + -
85C SER* 2.6 39.5 + - - -
98C PHE* 3.9 35.7 - - + +
99C SER* 4.8 3.8 - - - -
101C PRO* 3.9 32.5 - - + -
126C VAL* 5.7 7.0 - - + -
384C LEU* 3.5 29.6 - - + -
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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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74C VAL* 5.0 6.1 - - + -
78C GLU 3.0 17.8 + - - +
79C GLU* 3.6 10.5 - - - +
80C VAL 3.3 0.4 - - - -
81C LEU* 1.3 75.7 - - - +
83C GLU* 1.3 56.8 + - - +
85C SER* 3.0 27.9 + - - +
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Residues in contact with GLU 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 GLU 3.3 9.8 + - - +
80C VAL* 3.0 23.2 - - - +
82C ALA* 1.3 79.9 - - - +
84C LEU* 1.3 67.9 + - - +
85C SER 4.3 2.3 - - - +
86C PRO 5.2 0.3 - - - +
381C ARG* 2.3 52.7 + - - +
385C SER* 5.8 0.2 + - - -
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Residues in contact with LEU 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 VAL* 3.1 18.4 + - + +
81C LEU* 3.0 11.3 + - + +
83C GLU* 1.3 88.1 - - - +
85C SER* 1.3 51.8 + - - +
86C PRO 2.5 24.3 - - - +
87C ILE* 3.5 15.9 - - + -
98C PHE* 4.6 22.4 - - + -
384C LEU* 4.9 20.2 - - + +
385C SER* 4.7 22.4 - - - +
388C GLU* 4.9 16.4 - - + -
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Residues in contact with SER 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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81C LEU 2.6 28.3 + - - -
82C ALA* 3.0 19.4 + - - +
83C GLU 4.3 2.2 - - - +
84C LEU* 1.3 72.8 - - - +
86C PRO* 1.3 68.2 - - - +
87C ILE 3.9 0.7 - - - +
98C PHE* 3.6 29.4 + - - +
99C SER* 5.5 2.1 - - - -
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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