Contacts of the helix formed by residues 59 - 71 (chain O) 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 SER 59 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57O THR* 6.0 0.2 - - - -
58O ASP* 1.3 80.6 + - - +
60O VAL* 1.3 64.3 + - - +
61O ALA* 3.2 21.7 - - - +
62O ASN* 3.0 23.3 + - - +
63O ARG* 3.0 25.0 + - - +
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Residues in contact with VAL 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1454A C 3.9 22.7 - - - +
1455A G 3.8 34.5 - - + +
2851A A 4.2 7.6 - - - +
2852A G 4.9 11.2 - - - +
59O SER* 1.3 73.2 - - - +
61O ALA* 1.3 64.6 + - - +
63O ARG* 3.3 7.5 + - - +
64O ARG* 2.9 56.9 + - - +
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Residues in contact with ALA 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2850A A 4.1 28.7 - - + +
2851A A 4.5 19.5 + - + +
59O SER* 3.2 11.9 - - - +
60O VAL* 1.3 80.4 - - - +
62O ASN* 1.3 62.2 + - - +
64O ARG* 3.9 3.4 - - - +
65O LEU* 3.0 30.2 + - - +
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Residues in contact with ASN 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2870A C 5.0 6.9 + - - -
54O LEU* 3.3 32.3 - - + +
57O THR* 3.4 40.9 + - - +
58O ASP 4.0 0.4 - - - -
59O SER* 3.0 29.8 + - - +
61O ALA* 1.3 77.0 - - - +
63O ARG* 1.3 67.1 + - - +
65O LEU* 3.2 5.8 + - - +
66O ALA* 2.9 20.8 + - - +
80O PHE* 3.5 12.2 - - + -
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Residues in contact with ARG 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453A A 4.1 15.2 + - - -
1454A C 3.7 66.1 + - + +
58O ASP* 3.3 30.8 + - - +
59O SER 3.0 19.2 + - - +
60O VAL* 3.5 9.4 - - - +
62O ASN* 1.3 78.4 - - - +
64O ARG* 1.3 65.2 + - - +
66O ALA* 3.2 3.3 + - - +
67O PHE* 2.9 22.2 + - - +
76O VAL* 4.3 7.5 + - - +
77O ALA* 4.1 19.0 - - - +
80O PHE* 3.6 28.7 - - + +
81O ASN* 3.2 24.7 + - - +
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Residues in contact with ARG 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1454A C 3.5 25.5 + - - +
1455A G 3.4 37.4 + - - -
2705A A 3.7 14.5 + - - -
2706A A 3.0 42.9 + - - +
2707A U 4.9 2.1 + - - +
2851A A 3.0 34.6 + - - -
2852A G 3.3 17.1 + - - -
60O VAL* 2.9 29.2 + - - +
61O ALA* 3.9 3.6 - - - +
63O ARG* 1.3 75.3 - - - +
65O LEU* 1.3 63.6 + - - +
67O PHE* 3.0 11.9 + - - +
68O ALA* 2.9 22.7 + - - +
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Residues in contact with LEU 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2870A C 4.3 29.6 - - - +
2871A U 6.0 0.2 - - - +
54O LEU* 4.1 23.6 - - + -
61O ALA 3.0 19.0 + - - +
62O ASN* 3.5 9.0 - - - +
63O ARG 3.1 0.2 - - - -
64O ARG* 1.3 76.9 - - - +
66O ALA* 1.3 62.4 - - - +
68O ALA* 3.0 13.4 + - + +
69O ARG* 3.0 54.1 + - - +
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Residues in contact with ALA 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O LEU* 5.3 4.7 - - + +
54O LEU* 3.8 17.6 - - + +
55O ALA* 6.3 0.2 - - + -
62O ASN 2.9 16.5 + - - +
63O ARG 3.6 3.8 - - - +
65O LEU* 1.3 76.1 - - - +
67O PHE* 1.3 58.2 + - - +
69O ARG* 3.0 9.1 + - - +
70O THR* 2.9 33.1 + - + +
76O VAL* 4.1 8.1 - - + -
79O LEU* 5.2 11.4 - - + -
80O PHE* 3.9 18.4 - - + -
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Residues in contact with PHE 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1454A C 3.5 19.5 - - - +
2701A U 3.7 30.3 - - - -
2706A A 5.7 2.2 - + - -
2707A U 4.4 6.3 - - + -
63O ARG 2.9 12.8 + - - +
64O ARG* 3.0 9.6 + - - +
66O ALA* 1.3 76.6 - - - +
68O ALA* 1.3 58.6 + - - +
70O THR* 4.0 0.7 - - - -
71O ARG* 2.6 76.2 + - - -
72O ASP* 3.7 31.4 - - - -
73O ASN* 3.5 29.2 - - - -
76O VAL* 3.9 10.5 - - + +
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Residues in contact with ALA 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2707A U 3.2 40.4 - - - +
2708A G 3.7 22.7 - - - +
22O ARG* 4.6 4.2 + - - -
64O ARG 2.9 10.9 + - - +
65O LEU* 3.3 16.2 - - + +
67O PHE* 1.3 79.3 - - - +
69O ARG* 1.3 64.4 + - - +
71O ARG* 4.1 5.9 - - - +
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Residues in contact with ARG 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2692A G 5.1 8.3 + - - -
2870A C 3.7 8.1 + - - -
2871A U 2.7 29.5 + - - -
22O ARG* 3.2 29.7 + - - +
50O PRO* 6.2 1.8 - - - +
51O LEU* 3.8 29.3 - - + +
54O LEU* 4.4 7.3 - - - +
65O LEU* 3.0 53.4 + - - +
66O ALA* 3.0 10.5 + - - +
68O ALA* 1.3 80.4 - - - +
70O THR* 1.3 57.8 + - + +
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Residues in contact with THR 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O ARG* 3.2 24.7 - - - +
25O ALA* 5.7 5.2 - - + -
26O GLY* 5.9 3.1 - - - +
51O LEU* 3.7 29.4 - - + -
66O ALA* 2.9 20.1 + - - +
67O PHE 4.0 0.3 + - - -
69O ARG* 1.3 72.1 - - - +
71O ARG* 1.3 72.7 + - - +
72O ASP* 3.2 22.4 + - - +
75O ILE* 3.9 26.0 - - + +
76O VAL* 3.7 7.1 - - + +
79O LEU* 5.1 4.0 - - + -
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Residues in contact with ARG 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2700A A 4.0 13.9 + - - -
2701A U 3.7 25.3 + - - -
2707A U 3.1 35.0 + - - -
2708A G 3.2 46.2 + - - +
22O ARG* 3.7 19.3 - - - +
67O PHE* 2.6 60.1 + - - +
68O ALA* 4.1 5.6 - - - +
70O THR* 1.3 78.0 + - - +
72O ASP* 1.3 56.7 - - - +
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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