Contacts of the helix formed by residues 76 - 82 (chain A) in PDB entry 4D0G
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.2 15.5 - - + -
67A THR* 5.3 1.8 - - + +
70A LEU* 5.7 3.1 - - + -
74A ARG* 4.0 29.2 - - + +
75A ALA* 1.3 74.3 - - - +
77A THR* 1.3 67.1 + - - +
78A ARG 3.4 0.9 - - - -
79A SER* 3.4 7.5 + - - -
80A TYR* 3.0 24.9 + - + +
622C ASP* 3.1 33.4 + - - +
625C LEU* 3.6 26.2 - - + -
626C VAL* 3.8 9.9 - - - +
629C MET* 4.3 10.9 - - - +
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.6 12.5 - - + +
72A ARG 4.1 1.7 + - - -
73A PHE* 3.9 21.4 - - + -
74A ARG* 2.8 46.0 + - - +
75A ALA 3.2 0.4 - - - -
76A VAL* 1.3 80.2 - - - +
78A ARG* 1.3 67.2 + - - +
80A TYR* 3.1 15.1 + - - +
81A TYR* 3.3 21.7 + - + -
112A LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 4.7 14.7 - - + -
74A ARG 4.5 0.6 + - - -
75A ALA 4.3 5.2 + - - +
76A VAL 3.4 0.2 - - - -
77A THR* 1.3 83.0 - - - +
79A SER* 1.3 59.6 + - - +
81A TYR* 3.4 2.9 + - - +
82A ARG* 3.0 65.4 + - + +
112A LEU* 4.8 18.1 - - + +
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.1 17.0 + - - -
75A ALA 5.0 2.2 + - - -
76A VAL* 3.4 13.2 + - - -
77A THR 3.4 0.2 - - - -
78A ARG* 1.3 80.5 - - - +
80A TYR* 1.3 62.2 + - - +
82A ARG* 3.5 22.4 + - - +
626C VAL* 4.9 8.9 - - - +
629C MET* 3.4 31.7 - - - +
630C GLU* 5.6 9.0 - - - -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.0 20.3 + - - +
15A ILE* 3.3 36.1 - - + +
16A ILE 2.8 23.9 + - - -
17A ILE* 4.1 15.0 - - + -
46A VAL* 4.3 17.0 - - + -
65A TRP* 2.8 42.4 + - + -
66A ASP* 3.8 8.6 - - - -
67A THR* 3.7 31.5 + - + -
70A LEU* 5.3 5.4 - - + -
76A VAL* 3.0 23.4 + - + +
77A THR* 3.1 8.0 + - - +
79A SER* 1.3 76.1 + - - +
81A TYR* 1.3 73.7 + + - +
629C MET* 4.0 8.5 - - + -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.3 32.3 - - + -
17A ILE* 3.7 25.5 - - + +
70A LEU* 4.5 12.0 - - + +
77A THR* 3.3 23.9 + - + -
78A ARG 4.0 4.0 - - - +
80A TYR* 1.3 90.6 - + + +
82A ARG* 1.3 66.1 + - - +
83A GLY 3.5 0.7 - - - -
84A ALA* 3.1 22.1 + - - +
105A TRP* 3.9 17.2 - - - -
108A ASP* 4.2 9.6 + - + +
109A ALA* 3.7 23.1 - - + -
112A LEU* 3.4 47.3 - - + +
113A THR* 3.6 17.9 - - + +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.7 0.7 - - - +
78A ARG* 3.0 53.2 + - + +
79A SER* 3.5 24.0 + - - +
80A TYR 3.2 3.0 - - - -
81A TYR* 1.3 77.7 - - - +
83A GLY* 1.3 61.2 + - - +
84A ALA 3.5 1.9 + - - -
112A LEU 4.4 9.4 - - - +
113A THR* 5.0 4.7 - - - -
114A ASN* 5.0 9.0 + - - +
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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