Contacts of the helix formed by residues 80 - 89 (chain N) in PDB entry 4ADV
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 ARG 80 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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973A G 3.7 5.3 + - - -
974A A 3.4 20.4 + - - +
1202A U 6.1 0.4 - - - -
51J VAL* 3.5 27.6 - - + +
52J LEU* 3.1 48.2 - - + +
53J ILE 5.3 0.2 - - - -
54J SER 2.9 20.6 + - - -
55J PRO* 3.1 13.1 - - - +
56J HIS 2.8 28.1 - - - +
57J VAL 5.2 0.4 + - - -
68N ARG* 3.7 21.2 - - - +
70N HIS 4.6 0.9 - - - +
71N GLY* 3.1 25.7 + - - -
73N LEU* 4.3 0.8 - - - +
79N SER* 1.3 67.6 - - - +
81N ILE* 1.3 64.4 + - + +
83N VAL* 2.6 37.4 + - - +
84N ARG 2.9 7.3 + - - -
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Residues in contact with ILE 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A C 4.4 12.6 - - - +
1202A U 3.2 52.0 - - + +
51J VAL* 4.5 0.6 - - - +
52J LEU 4.7 1.5 + - - +
53J ILE 3.7 22.4 - - - +
55J PRO* 4.6 12.1 - - + -
68N ARG* 4.9 6.5 - - - +
79N SER* 3.0 25.1 - - - +
80N ARG* 1.3 92.7 - - + +
82N LYS* 1.3 71.2 + - + +
84N ARG* 3.0 19.4 - - - +
85N GLU* 2.7 35.8 + - + +
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Residues in contact with LYS 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A U 4.4 15.9 - - - +
1203A C 5.6 7.5 + - - -
63N CYS* 3.7 11.7 - - - -
65N GLN* 3.6 38.6 - - + +
66N THR* 4.2 10.1 - - + +
78N LEU* 3.6 22.8 - - + +
79N SER 2.8 13.4 + - - +
80N ARG 2.8 4.2 + - - -
81N ILE* 1.3 81.7 - - + +
83N VAL* 1.3 61.6 + - - +
85N GLU* 3.3 33.5 + - + +
86N ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J VAL* 4.9 9.6 - - + -
65J TYR* 4.9 12.6 - - + -
73N LEU* 3.6 26.7 - - + -
76N PHE* 3.4 38.8 - - + -
78N LEU* 3.5 28.3 - - + -
80N ARG* 2.6 21.8 + - - +
82N LYS* 1.3 73.5 - - - +
84N ARG* 1.3 56.5 + - - +
87N ALA* 2.8 35.4 + - + +
92N ILE* 3.5 9.0 - - + +
95N LEU* 5.2 0.7 - - + -
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Residues in contact with ARG 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A C 3.5 18.6 + - - -
1060A U 2.6 28.9 + - - -
3C LYS 5.2 3.4 + - - -
4C VAL* 6.2 0.6 - - - +
5C HIS* 6.0 2.4 - - - +
51J VAL* 5.2 4.2 - - + +
52J LEU 5.3 0.2 - - - -
53J ILE* 3.2 43.0 + - - +
63J ASP* 3.4 24.5 + - - +
65J TYR* 3.6 22.8 + - + +
80N ARG 2.9 6.0 + - - +
81N ILE* 3.0 30.3 - - - +
83N VAL* 1.3 77.3 - - - +
85N GLU* 1.3 64.2 + - + +
87N ALA* 3.4 2.4 - - - +
88N MET* 3.1 35.8 + - + +
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Residues in contact with GLU 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A G 4.3 14.5 + - - -
1059A C 6.2 4.3 - - - -
1202A U 5.7 0.5 - - - +
81N ILE* 2.7 22.5 + - + +
82N LYS* 3.3 29.8 + - + +
84N ARG* 1.3 72.9 - - + +
86N ALA* 1.3 68.4 + - - +
87N ALA 2.9 0.9 + - - -
88N MET* 2.9 7.2 + - - -
89N ARG* 2.8 61.1 + - - +
91N GLU* 5.4 0.9 - - - +
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Residues in contact with ALA 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.6 1.1 - - + -
65N GLN* 5.2 5.4 - - - +
78N LEU* 4.0 11.7 - - + -
82N LYS 2.9 19.4 + - - +
85N GLU* 1.3 73.0 - - - +
87N ALA* 1.3 58.6 + - - +
89N ARG 3.7 0.2 + - - -
90N GLY 3.3 0.9 + - - -
91N GLU* 2.7 56.5 + - + +
92N ILE* 3.2 26.9 + - + -
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Residues in contact with ALA 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.0 15.8 - - - +
65J TYR* 4.5 13.9 - - + -
83N VAL* 2.8 22.9 + - + +
84N ARG 3.4 4.5 - - - +
85N GLU 2.9 1.0 + - - -
86N ALA* 1.3 74.1 - - - +
88N MET* 1.3 74.3 + - + +
90N GLY* 2.8 18.0 + - - -
92N ILE* 3.3 15.4 - - + +
95N LEU* 4.2 18.4 - - + +
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Residues in contact with MET 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 5.6 0.9 - - - -
5C HIS* 3.3 58.5 + - + +
7C ASN* 4.2 3.5 - - - +
8C GLY* 3.6 32.3 + - - +
9C ILE 4.4 0.9 - - - -
11C LEU* 3.8 7.1 - - + +
65J TYR* 3.8 32.8 - - + +
84N ARG* 3.1 23.3 + - + +
85N GLU* 2.9 9.7 + - - +
87N ALA* 1.3 87.1 - - + +
89N ARG* 1.3 59.4 + - + +
90N GLY 3.0 4.0 + - - -
95N LEU 5.4 1.6 - - - +
97N LYS* 5.0 18.8 - - + +
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Residues in contact with ARG 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C HIS* 4.8 11.5 - - + +
7C ASN* 6.3 0.4 - - - +
11C LEU* 5.1 0.9 - - - -
18C ASN* 3.2 18.3 + - - +
184C ASN* 5.6 6.5 - - - +
185C THR* 4.6 19.0 + - - -
85N GLU* 2.8 45.1 + - - +
88N MET* 1.3 76.5 - - + +
90N GLY* 1.3 56.1 - - - +
91N GLU* 2.8 41.5 + - + -
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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