Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 1A7A
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 ASN 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.3 0.9 - - - +
10A ALA* 3.3 29.9 + - + +
11A ASP 5.3 1.5 + - - +
14A LEU* 3.7 20.1 - - + +
85A GLN* 1.3 71.8 - - - +
87A HIS* 1.3 53.4 + - - +
89A ALA* 2.8 9.3 + - - +
90A ALA* 2.6 35.9 + - - +
102A TRP* 3.4 5.9 - - - -
103A LYS* 3.0 43.5 + - - +
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Residues in contact with HIS 87 (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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14A LEU* 3.5 27.2 - - + +
17A TRP* 3.5 72.0 + + + -
18A GLY* 3.2 14.0 - - - -
21A ALA* 3.8 20.4 - - + +
58A VAL* 3.9 10.1 - - + +
85A GLN* 4.1 25.1 - - + -
86A ASN* 1.3 74.8 + - - +
88A ALA* 1.3 61.6 + - - +
90A ALA* 3.8 1.0 - - - +
91A ALA 2.9 23.0 + - - -
351A MSE 5.2 11.7 - - + -
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Residues in contact with ALA 88 (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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18A GLY* 4.7 1.1 - - - -
22A LEU* 4.4 7.9 - - + -
56A MSE 3.5 3.3 - - - +
57A THR* 3.7 7.6 - - - +
58A VAL* 3.4 46.0 - - + +
61A ALA* 4.4 2.4 - - + +
85A GLN* 3.2 10.9 + - + +
86A ASN 3.1 0.4 - - - -
87A HIS* 1.3 79.3 - - - +
89A ALA* 1.3 69.1 + - - +
91A ALA* 3.7 6.0 - - - +
92A ILE* 3.3 26.7 + - - +
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Residues in contact with ALA 89 (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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9A VAL* 4.0 14.4 - - + +
56A MSE 3.6 25.7 - - + +
84A THR* 4.0 9.9 - - + -
85A GLN 2.9 12.6 + - - +
86A ASN* 2.8 14.7 + - - +
88A ALA* 1.3 78.6 - - - +
90A ALA* 1.3 63.6 + - - +
92A ILE* 3.3 3.8 + - - +
93A ALA* 3.1 19.2 + - - +
99A VAL* 4.1 4.0 - - + +
101A ALA 4.1 13.0 - - - +
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Residues in contact with ALA 90 (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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9A VAL* 4.3 6.4 - - + +
11A ASP 3.5 24.7 - - - +
12A ILE* 3.8 11.4 - - - +
14A LEU* 4.1 2.2 - - + -
15A ALA* 3.7 20.2 - - - +
86A ASN 2.6 18.1 + - - +
87A HIS 3.8 1.8 - - - +
89A ALA* 1.3 71.5 - - - +
91A ALA* 1.3 66.8 + - - +
93A ALA* 2.8 8.9 + - - +
94A LYS* 2.8 24.6 + - - +
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Residues in contact with ALA 91 (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 ALA* 3.9 13.2 - - - +
18A GLY* 3.8 22.9 - - - -
19A ARG* 4.0 14.5 + - + +
22A LEU* 4.1 17.5 - - + -
87A HIS 2.9 21.4 + - - +
88A ALA 3.7 5.6 - - - +
90A ALA* 1.3 74.2 - - - +
92A ILE* 1.3 63.0 + - - +
94A LYS* 3.3 5.1 + - - +
95A ALA* 3.0 19.5 + - - +
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Residues in contact with ILE 92 (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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22A LEU* 4.7 0.7 - - + -
56A MSE 3.2 32.3 - - + -
61A ALA* 3.7 36.8 - - + +
64A ILE* 4.2 12.1 - - + -
65A GLU* 3.9 23.6 - - + +
88A ALA 3.3 5.6 + - - +
89A ALA 3.3 2.1 + - - +
90A ALA 3.1 0.4 - - - -
91A ALA* 1.3 77.3 - - + +
93A ALA* 1.3 65.7 + - - +
95A ALA* 3.0 18.2 + - + +
97A ILE* 3.3 32.7 + - + -
99A VAL* 3.1 21.5 - - + -
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Residues in contact with ALA 93 (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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7A TYR* 3.9 39.1 - - + -
9A VAL* 3.9 11.4 - - + -
12A ILE* 3.7 15.0 - - + -
89A ALA 3.1 12.3 + - - +
90A ALA 2.8 12.5 + - - +
92A ILE* 1.3 71.1 - - - +
94A LYS* 1.3 59.8 + - - +
96A GLY* 2.8 24.1 + - - -
97A ILE 3.7 11.6 + - - +
99A VAL* 3.9 1.8 - - + +
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Residues in contact with LYS 94 (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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7A TYR* 5.9 0.2 - - - -
12A ILE* 3.6 17.4 - - + +
15A ALA* 3.6 25.9 - - + +
16A ALA* 5.7 3.4 - - - +
19A ARG* 6.2 3.8 - - + +
90A ALA 2.8 13.9 + - - +
91A ALA* 3.6 9.4 - - - +
93A ALA* 1.3 74.1 - - - +
95A ALA* 1.3 56.8 + - - +
96A GLY* 3.0 4.6 + - - -
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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