Contacts of the helix formed by residues 74 - 86 (chain C) in PDB entry 6GL7
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 ALA 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 5.3 11.0 - - + +
63C CYS* 3.6 18.4 - - + -
73C LEU* 1.3 74.3 - - - +
75C ASN* 1.3 52.2 + - - +
77C GLU* 3.1 7.4 + - - +
78C CYS* 2.7 40.0 + - - -
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Residues in contact with ASN 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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63C CYS* 3.7 20.3 - - - +
73C LEU* 3.2 10.5 - - + +
74C ALA* 1.3 77.8 - - - +
76C LYS* 1.3 57.6 + - - +
78C CYS* 3.9 1.4 - - - +
79C GLN* 2.9 30.1 + - - +
114C LEU* 5.2 2.1 - - - +
115C GLY 5.5 2.3 - - - +
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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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73C LEU* 3.1 24.5 + - + +
75C ASN* 1.3 78.7 - - - +
77C GLU* 1.3 71.3 + - + +
79C GLN* 3.4 6.5 + - - +
80C ALA* 3.0 25.6 + - - +
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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
----------------------------------------------------------
56C ARG* 2.9 29.1 + - - +
59C THR* 3.6 15.6 - - + +
73C LEU 3.3 10.7 + - - +
74C ALA* 3.1 9.9 + - - +
76C LYS* 1.3 89.1 - - - +
78C CYS* 1.3 60.9 + - - +
80C ALA* 3.2 7.7 + - - +
81C ALA* 2.8 28.4 + - - +
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Residues in contact with CYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 3.2 36.3 - - - -
60C LEU* 3.1 13.3 - - + +
62C GLN* 4.5 1.1 - - - -
63C CYS* 2.1 49.4 - - - -
74C ALA* 2.7 19.6 + - - +
75C ASN* 3.9 3.4 - - - +
77C GLU* 1.3 72.8 - - - +
79C GLN* 1.3 61.3 + - - +
81C ALA* 3.1 0.7 + - - -
82C LEU* 3.0 19.1 + - - +
114C LEU* 3.4 20.2 - - + +
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Residues in contact with GLN 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 ASN 2.9 19.5 + - - +
76C LYS* 3.6 6.5 - - - +
77C GLU 3.3 0.2 - - - -
78C CYS* 1.3 76.4 - - - +
80C ALA* 1.3 62.2 + - - +
82C LEU* 3.2 23.1 + - - +
83C GLU* 3.2 33.7 + - - +
114C LEU* 3.1 24.8 - - + +
79F ARG* 4.1 20.3 - - - +
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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
----------------------------------------------------------
56C ARG* 4.2 19.5 - - - +
76C LYS* 3.0 14.6 + - + +
77C GLU* 3.5 12.1 - - - +
79C GLN* 1.3 75.8 - - - +
81C ALA* 1.3 57.4 + - - +
83C GLU* 3.1 11.3 + - - +
84C VAL* 2.9 35.8 + - + +
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Residues in contact with ALA 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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56C ARG* 3.4 45.7 - - + +
59C THR* 3.9 7.2 - - + -
60C LEU* 3.7 11.0 - - + -
77C GLU 2.8 17.0 + - - +
78C CYS 3.1 9.2 + - - +
80C ALA* 1.3 73.0 - - - +
82C LEU* 1.3 57.2 + - - +
85C LEU* 2.8 37.6 + - - +
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Residues in contact with LEU 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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60C LEU* 4.1 6.6 - - + +
78C CYS 3.0 12.3 + - - +
79C GLN* 3.5 26.2 - - - +
80C ALA 3.2 0.2 - - - -
81C ALA* 1.3 78.1 - - - +
83C GLU* 1.3 59.0 + - + +
85C LEU* 3.7 1.7 - - + -
86C GLN* 2.7 38.7 + - + +
91C TYR* 5.5 9.6 - - + -
112C ILE* 3.6 24.0 - - + +
113C HIS* 5.0 1.3 - - - -
114C LEU* 3.8 31.2 - - + +
79F ARG* 6.2 1.6 - - - +
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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 GLN* 3.2 25.0 + - - +
80C ALA* 3.1 12.5 + - - +
82C LEU* 1.3 79.5 - - + +
84C VAL* 1.3 62.7 + - + +
86C GLN* 3.5 25.0 - - - +
87C GLU* 4.2 8.1 + - - +
79F ARG* 3.2 34.1 + - - +
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Residues in contact with VAL 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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52C ASN* 4.3 25.6 - - + +
53C CYS* 5.2 3.9 - - - +
56C ARG* 4.0 33.4 - - + +
80C ALA* 2.9 21.0 + - + +
81C ALA 4.0 2.5 - - - +
83C GLU* 1.3 76.7 - - + +
85C LEU* 1.3 67.1 + - + +
87C GLU* 3.2 19.6 + - - +
88C SER* 4.2 2.1 + - - -
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Residues in contact with LEU 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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44C ASN* 6.1 1.3 - - - +
53C CYS* 3.7 46.7 - - + +
56C ARG* 3.7 24.0 - - + +
57C TYR* 3.8 10.1 - - + +
60C LEU* 3.4 30.5 - - + -
81C ALA 2.8 20.1 + - - +
82C LEU* 4.1 3.6 - - + +
84C VAL* 1.3 68.5 - - + +
86C GLN* 1.3 60.1 + - - +
87C GLU 3.0 2.5 - - - -
88C SER* 2.7 38.1 + - - +
91C TYR* 3.8 5.6 - - - +
112C ILE* 3.9 24.7 - - + +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 2.7 26.5 + - + +
83C GLU* 3.5 21.0 - - - +
84C VAL 3.1 0.4 - - - -
85C LEU* 1.3 73.0 - - - +
87C GLU* 1.3 69.3 + - - +
88C SER 4.2 0.2 - - - +
91C TYR* 2.9 73.4 + - + +
79F ARG* 5.2 9.6 + - - +
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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