Contacts of the helix formed by residues 53 - 63 (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 ALA 53 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A C 3.4 28.9 + - - +
399A U 6.1 0.2 - - - +
2090A A 3.5 16.2 - - + +
2091A C 4.8 12.8 - - - +
32Y ASN* 3.4 13.6 + - - +
34Y HIS* 5.1 4.8 - - + -
51Y VAL 3.9 0.6 + - - -
52Y SER* 1.3 71.9 - - - +
54Y LYS* 1.3 62.7 + - - +
56Y MET* 3.0 13.1 + - - +
57Y ARG* 2.9 27.7 + - + +
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Residues in contact with LYS 54 (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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372A G 2.7 31.1 + - - +
373A U 3.0 30.3 + - - -
397A U 5.1 6.7 - - + +
398A C 4.4 21.6 + - + +
399A U 4.6 15.3 - - + -
400A G 5.1 0.2 - - - -
8Y THR* 4.8 7.6 - - + +
10Y LYS* 3.9 34.8 - - + +
52Y SER* 4.2 4.7 - - - +
53Y ALA* 1.3 77.5 - - - +
55Y GLY* 1.3 56.1 + - - +
57Y ARG* 3.2 11.4 + - - +
58Y VAL* 3.0 33.9 + - + +
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Residues in contact with GLY 55 (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* 4.5 1.8 - - - -
7Y VAL* 3.9 23.8 - - - +
8Y THR* 4.0 8.0 - - - +
51Y VAL* 4.8 2.0 - - - -
52Y SER* 2.7 25.6 + - - -
54Y LYS* 1.3 76.2 - - - +
56Y MET* 1.3 55.0 + - - -
58Y VAL* 3.4 4.0 + - - +
59Y ILE* 3.0 34.2 + - - +
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Residues in contact with MET 56 (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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2091A C 3.5 42.8 - - - +
27H ARG* 3.6 35.7 - - - +
34Y HIS* 5.1 4.7 - - + -
36Y HIS* 3.5 29.4 - - + -
38Y PHE* 3.7 23.3 - - + -
51Y VAL* 4.2 12.7 - - + +
52Y SER 2.8 10.0 + - - +
53Y ALA* 3.0 13.2 + - - +
55Y GLY* 1.3 74.6 - - - +
57Y ARG* 1.3 66.1 + - + +
59Y ILE* 3.2 9.7 + - - +
60Y ASP* 3.0 27.5 + - - +
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Residues in contact with ARG 57 (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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372A G 3.9 33.2 + - + +
399A U 3.7 40.5 + - - +
400A G 2.9 62.8 + - - -
2091A C 6.1 1.8 - - - +
27H ARG* 5.3 2.2 - - - +
53Y ALA 2.9 15.9 + - - +
54Y LYS* 3.4 11.5 - - + +
56Y MET* 1.3 77.1 - - + +
58Y VAL* 1.3 62.6 + - - +
60Y ASP* 2.9 13.7 + - - +
61Y LYS* 2.9 21.8 + - - +
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Residues in contact with VAL 58 (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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372A G 4.0 40.6 - - + +
7Y VAL* 4.2 15.3 - - + -
8Y THR* 4.2 14.8 - - + -
54Y LYS* 3.0 24.3 + - - +
55Y GLY* 3.4 9.0 - - - +
57Y ARG* 1.3 75.4 - - - +
59Y ILE* 1.3 64.2 + - - +
61Y LYS* 3.2 3.5 + - - +
62Y LYS* 2.9 46.4 + - + +
67Y VAL* 4.9 3.6 - - + -
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Residues in contact with ILE 59 (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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7Y VAL* 4.1 17.9 - - + -
38Y PHE* 3.4 44.0 - - + -
49Y LEU* 4.5 2.2 - - + -
51Y VAL* 4.4 4.3 - - + -
55Y GLY 3.0 19.1 + - - +
56Y MET* 3.3 9.4 - - - +
58Y VAL* 1.3 75.3 - - - +
60Y ASP* 1.3 62.4 + - - +
63Y GLY* 2.6 35.0 + - - -
64Y ILE* 3.7 34.3 - - + +
67Y VAL* 3.8 24.2 - - + -
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Residues in contact with ASP 60 (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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1H MET* 4.2 21.0 - - + +
23H ALA* 5.0 0.9 - - - +
27H ARG* 2.4 47.8 + - - +
38H PRO* 5.7 5.2 - - - +
38Y PHE* 5.5 0.5 - - - -
56Y MET 3.0 15.4 + - - +
57Y ARG* 2.9 14.0 + - - +
59Y ILE* 1.3 86.5 - - - +
61Y LYS* 1.3 62.7 + - - +
63Y GLY* 3.6 6.1 + - - -
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Residues in contact with LYS 61 (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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371A A 2.8 46.1 + - - +
372A G 3.1 80.2 + - + +
40H THR* 5.9 2.9 - - - +
57Y ARG 2.9 11.2 + - - +
58Y VAL* 3.2 7.2 + - - +
60Y ASP* 1.3 78.6 - - - +
62Y LYS* 1.3 61.9 + - + +
63Y GLY 3.7 0.2 + - - -
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Residues in contact with LYS 62 (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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371A A 5.3 1.6 + - - -
372A G 3.4 42.4 + - - +
58Y VAL* 2.9 35.9 + - + +
59Y ILE 4.5 0.2 - - - +
61Y LYS* 1.3 76.6 - - + +
63Y GLY* 1.3 61.2 + - - +
66Y THR* 2.6 42.3 + - + +
67Y VAL* 4.7 6.3 - - + -
70Y GLU* 3.5 26.9 + - - +
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Residues in contact with GLY 63 (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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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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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