Contacts of the helix formed by residues 63 - 75 (chain Y) in PDB entry 5GAG
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 63 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59Y ILE 2.6 21.5 + - - +
60Y ASP* 3.6 5.0 + - - -
61Y LYS 3.4 3.0 + - - -
62Y LYS* 1.3 79.0 - - - +
64Y ILE* 1.3 65.6 + - - -
65Y ASP 3.3 3.2 + - - -
66Y THR* 3.6 5.6 + - - -
67Y VAL* 3.7 10.7 + - - +
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Residues in contact with ILE 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y PHE* 4.0 27.6 - - + -
39Y TRP 4.4 6.5 - - - +
40Y VAL* 4.1 34.5 - - + -
41Y GLU 5.2 1.3 - - - +
47Y VAL* 6.2 0.9 - - + -
49Y LEU* 4.8 8.1 - - + -
59Y ILE* 3.7 37.1 + - + +
63Y GLY* 1.3 73.9 - - - -
65Y ASP* 1.3 75.7 + - - +
67Y VAL* 3.4 7.6 + - + +
68Y LEU* 2.9 33.0 + - + +
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Residues in contact with ASP 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Y VAL* 3.5 19.6 - - - +
41Y GLU* 5.1 1.8 + - - +
42Y SER* 3.7 21.9 + - - -
43Y GLU* 5.7 0.2 - - - +
63Y GLY 3.3 1.4 - - - -
64Y ILE* 1.3 90.0 - - - +
66Y THR* 1.3 60.7 + - - +
68Y LEU* 3.5 7.3 + - - +
69Y ALA* 2.9 28.1 + - - +
72Y ARG* 4.2 2.6 + - - -
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Residues in contact with THR 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Y LYS* 2.6 48.6 + - + +
63Y GLY 3.7 1.2 - - - -
65Y ASP* 1.3 75.5 - - - +
67Y VAL* 1.3 65.5 + - - +
69Y ALA* 3.0 18.9 + - + +
70Y GLU* 3.0 36.8 + - + +
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Residues in contact with VAL 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL* 3.6 31.2 - - + -
49Y LEU* 4.9 2.9 - - + -
58Y VAL* 4.8 8.1 - - + +
59Y ILE* 3.8 32.1 - - + +
62Y LYS* 4.7 12.1 - - + -
63Y GLY 3.7 13.0 - - - +
64Y ILE* 3.4 13.9 + - + +
65Y ASP 3.4 0.4 - - - -
66Y THR* 1.3 80.0 - - - +
68Y LEU* 1.3 62.6 + - + +
70Y GLU* 3.1 11.6 + - - +
71Y LEU* 2.9 34.0 + - + +
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Residues in contact with LEU 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y VAL* 4.5 9.0 - - + -
43Y GLU* 4.1 20.4 - - - +
47Y VAL* 4.4 17.5 - - + -
49Y LEU* 5.0 7.9 - - + -
64Y ILE* 2.9 27.2 + - + +
65Y ASP* 3.7 7.0 - - - +
66Y THR 3.3 0.2 - - - -
67Y VAL* 1.3 82.8 - - + +
69Y ALA* 1.3 57.7 + - - +
71Y LEU* 3.2 13.5 + - + +
72Y ARG* 3.0 46.0 + - - +
78Y TYR* 3.7 48.9 - - + -
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Residues in contact with ALA 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Y ASP 2.9 15.4 + - - +
66Y THR* 3.0 16.3 + - + +
68Y LEU* 1.3 77.2 - - - +
70Y GLU* 1.3 57.9 + - + +
72Y ARG* 3.3 19.9 + - - +
73Y ALA* 2.9 25.9 + - - +
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Residues in contact with GLU 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Y LYS* 3.5 17.6 - - - -
66Y THR* 3.0 36.6 + - + +
67Y VAL* 3.6 8.3 - - - +
69Y ALA* 1.3 76.6 - - + +
71Y LEU* 1.3 60.8 + - - +
73Y ALA* 3.6 11.7 - - + +
74Y ARG* 3.2 38.1 + - - +
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Residues in contact with LEU 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLN* 3.2 48.0 - - + +
7Y VAL* 4.6 5.8 - - + -
49Y LEU* 4.4 6.5 - - + -
67Y VAL* 2.9 20.1 + - + +
68Y LEU* 3.2 19.5 + - + +
70Y GLU* 1.3 77.3 - - - +
72Y ARG* 1.3 60.7 + - - +
74Y ARG* 3.7 10.4 + - - +
75Y GLY 3.3 2.6 + - - -
76Y GLU* 2.8 51.4 + - - +
78Y TYR* 3.5 37.9 - - + -
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Residues in contact with ARG 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Y GLU* 4.6 8.8 + - - -
65Y ASP* 4.2 2.6 + - - +
68Y LEU* 3.0 43.2 + - - +
69Y ALA* 3.3 19.4 + - - +
71Y LEU* 1.3 76.4 - - - +
73Y ALA* 1.3 63.1 + - - +
75Y GLY* 3.1 14.2 + - - +
76Y GLU 4.3 3.4 - - - +
77Y LYS* 4.5 10.5 - - + +
78Y TYR* 3.1 40.3 + - + -
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Residues in contact with ALA 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Y ALA 2.9 22.2 + - - +
70Y GLU* 3.6 13.2 - - + +
72Y ARG* 1.3 76.6 - - - +
74Y ARG* 1.3 62.0 + - - +
75Y GLY* 3.1 1.7 + - - -
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Residues in contact with ARG 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y CYS 4.7 3.4 + - - -
6Y GLN* 2.9 26.8 + - - +
7Y VAL 3.1 22.6 + - - -
8Y THR 5.1 2.3 + - - -
9Y GLY* 4.8 8.1 - - - -
70Y GLU* 3.2 27.8 + - - +
71Y LEU* 3.8 11.2 - - - +
72Y ARG 3.4 0.2 - - - -
73Y ALA* 1.3 78.1 - - - +
75Y GLY* 1.3 56.6 + - - +
76Y GLU* 3.3 24.2 + - + +
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Residues in contact with GLY 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A U 4.9 8.1 + - - -
71Y LEU 3.3 1.0 + - - -
72Y ARG* 3.1 14.8 + - - -
73Y ALA 3.1 4.9 - - - -
74Y ARG* 1.3 78.5 - - - +
76Y GLU* 1.3 62.1 + - - +
77Y LYS* 3.8 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