Contacts of the helix formed by residues 72 - 82 (chain O) in PDB entry 5GAH
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 ASP 72 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1294A U 6.2 0.6 - - - +
1453A A 5.2 0.3 + - - -
30O ARG* 3.1 27.7 + - - -
67O PHE* 3.5 6.7 - - - -
70O THR* 3.1 10.3 + - - +
71O ARG* 1.3 80.7 - - - +
73O ASN* 1.3 78.2 + - - +
74O GLU* 2.8 24.5 + - - +
75O ILE* 3.8 16.3 + - + +
76O VAL* 3.1 31.4 + - - +
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Residues in contact with ASN 73 (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 3.1 34.4 + - + +
1454A C 3.7 28.6 + - - -
2701A U 3.4 25.3 + - - -
2702A G 5.0 2.6 + - - -
67O PHE* 3.8 12.7 - - - -
72O ASP* 1.3 78.8 + - - +
74O GLU* 1.3 58.7 + - - +
75O ILE 3.3 0.2 - - - -
76O VAL* 3.1 8.7 - - + +
77O ALA* 2.9 32.7 + - - +
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Residues in contact with GLU 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453A A 3.2 36.3 - - - +
30O ARG* 3.4 31.8 + - - +
72O ASP* 2.8 15.2 + - - +
73O ASN* 1.3 77.4 - - - +
75O ILE* 1.3 64.5 + - - +
77O ALA* 4.0 1.8 - - - +
78O LYS* 3.0 30.0 + - - +
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Residues in contact with ILE 75 (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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26O GLY* 3.7 35.7 - - - +
29O VAL* 4.2 13.8 - - + +
30O ARG* 3.8 41.7 - - + +
70O THR* 3.3 36.1 - - + +
72O ASP* 3.7 15.7 + - + +
73O ASN 3.3 0.4 - - - -
74O GLU* 1.3 83.7 - - - +
76O VAL* 1.3 63.7 + - + +
78O LYS* 3.5 5.6 + - + +
79O LEU* 2.9 35.5 + - + +
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453A A 4.9 6.5 - - - +
1454A C 5.0 10.1 - - + -
63O ARG* 4.4 11.2 - - - +
66O ALA* 3.9 10.8 - - + -
67O PHE* 3.6 36.3 - - + +
70O THR* 3.9 6.7 - - + +
72O ASP 3.1 17.3 + - - +
73O ASN* 3.1 23.8 - - + +
75O ILE* 1.3 75.3 - - + +
77O ALA* 1.3 69.6 + - + +
79O LEU* 2.9 19.2 + - + +
80O PHE* 3.0 26.0 + - + -
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Residues in contact with ALA 77 (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 3.9 37.5 - - + +
63O ARG* 3.7 15.0 - - - +
73O ASN 2.9 19.8 + - - +
74O GLU 4.1 2.5 - - - +
76O VAL* 1.3 76.1 - - - +
78O LYS* 1.3 63.5 + - - +
81O ASN* 3.0 37.4 + - - +
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Residues in contact with LYS 78 (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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29O VAL* 2.7 38.7 + - + +
30O ARG* 2.9 23.6 + - - +
32O GLU* 3.7 20.1 + - - +
74O GLU* 3.0 20.4 + - - +
75O ILE* 3.7 7.9 - - + +
77O ALA* 1.3 77.4 - - - +
79O LEU* 1.3 64.4 + - - +
81O ASN* 5.2 0.2 - - - -
82O GLU* 3.0 62.7 + - + +
83O LEU* 3.6 8.5 + - + -
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Residues in contact with LEU 79 (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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29O VAL* 4.3 13.2 - - + -
51O LEU* 4.1 39.0 - - + +
52O ILE* 4.5 15.3 - - + -
55O ALA* 3.6 17.6 - - + +
66O ALA* 4.8 11.4 - - + -
70O THR* 5.2 0.7 - - + -
75O ILE* 2.9 25.9 + - + +
76O VAL* 3.2 10.8 - - - +
78O LYS* 1.3 76.3 - - - +
80O PHE* 1.3 64.1 + - + +
83O LEU* 3.2 35.2 + - + +
84O GLY 2.8 26.2 + - - -
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Residues in contact with PHE 80 (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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54O LEU 4.4 1.1 - - - -
55O ALA* 3.4 42.0 - - + +
57O THR 3.9 15.7 - - - -
58O ASP* 3.8 27.7 - - + +
62O ASN* 3.7 30.1 - - + -
63O ARG* 3.5 46.0 - - - +
66O ALA* 4.2 16.8 - - + -
76O VAL* 3.0 24.2 + - + -
79O LEU* 1.3 83.0 - - + +
81O ASN* 1.3 62.1 + - - +
82O GLU 3.4 1.1 - - - -
84O GLY* 4.5 1.0 - - - +
85O PRO* 3.3 18.4 - - - +
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Residues in contact with ASN 81 (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 5.7 2.2 + - - -
58O ASP* 5.4 0.3 - - - +
63O ARG* 3.6 24.2 + - - +
77O ALA* 3.0 28.6 + - - +
78O LYS* 4.5 0.7 - - - +
80O PHE* 1.3 78.7 - - - +
82O GLU* 1.3 65.4 + - + +
85O PRO* 4.0 12.8 - - - +
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Residues in contact with GLU 82 (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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32O GLU* 4.4 6.8 - - - +
78O LYS* 3.0 49.6 + - - +
80O PHE 3.4 0.6 - - - -
81O ASN* 1.3 87.8 - - + +
83O LEU* 1.3 69.0 + - + +
84O GLY 3.3 1.1 - - - -
85O PRO* 3.7 5.2 - - - +
86O ARG* 3.0 34.9 + - - +
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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