Contacts of the strand formed by residues 82 - 87 (chain A) in PDB entry 1GO1
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 ALA 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 2.9 31.5 + - - +
20A ALA* 4.4 5.3 - - - +
23A SER* 3.5 9.9 - - - +
35A ILE* 5.3 0.2 - - + -
36A ILE 3.5 6.1 - - - +
37A VAL* 3.9 13.5 - - + -
38A ALA 4.8 0.2 - - - +
45A ILE* 4.8 2.0 - - + -
49A ILE* 3.5 32.8 - - + -
70A LEU* 5.1 0.9 - - - -
80A VAL* 3.7 6.6 - - - +
81A SER* 1.4 80.8 - - - +
83A LEU* 1.4 60.3 + - - +
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Residues in contact with LEU 83 (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 LEU* 4.1 9.4 - - + -
16A ILE* 3.9 18.2 - - + -
17A VAL 3.4 10.5 - - - +
18A MET* 4.2 9.9 - - + -
23A SER* 3.6 4.9 - - - -
35A ILE* 3.6 2.9 - - - +
36A ILE* 2.9 58.2 + - + +
70A LEU* 3.8 28.9 - - + -
74A LEU* 3.8 30.1 - - + -
80A VAL* 4.5 2.0 - - + -
82A ALA* 1.4 74.8 - - - +
84A ALA* 1.4 56.3 + - - +
85A VAL* 3.6 26.0 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.9 0.2 - - - -
17A VAL* 2.9 48.2 + - + +
23A SER* 3.6 13.8 + - - +
26A TYR* 4.3 18.2 - - + -
32A ALA* 4.3 11.0 - - + -
34A LEU 4.0 3.1 - - - -
35A ILE* 4.1 18.2 - - + -
83A LEU* 1.4 72.0 - - - +
85A VAL* 1.4 63.5 + - - +
86A VAL* 3.5 3.6 + - - +
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Residues in contact with VAL 85 (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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10A ALA* 4.7 1.3 - - + -
15A LYS 4.0 5.8 - - - +
16A ILE* 3.6 24.9 - - + -
32A ALA* 3.8 1.8 - - - +
33A LYS* 2.8 29.7 + - - +
34A LEU* 2.7 31.7 + - + +
36A ILE* 4.2 13.2 - - + -
83A LEU* 3.6 25.1 - - + -
84A ALA* 1.4 69.1 - - - +
86A VAL* 1.4 54.9 + - - +
87A ASP 4.1 17.0 - - - +
88A PRO* 4.3 4.0 - - + -
93A ILE* 4.0 28.7 - - + -
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Residues in contact with VAL 86 (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 LYS* 3.4 27.6 + - + +
17A VAL* 3.8 18.8 - - + -
26A TYR* 3.6 32.1 - - + -
31A GLY 3.5 17.5 - - - +
32A ALA* 4.3 1.7 - - - +
33A LYS* 3.6 27.9 + - - +
84A ALA 4.0 2.9 - - - +
85A VAL* 1.4 71.9 - - - +
87A ASP* 1.4 64.0 + - + +
88A PRO 4.3 0.2 - - - -
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Residues in contact with ASP 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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10A ALA* 4.2 1.9 - - - +
13A THR 5.2 0.3 - - - +
14A GLY* 3.4 15.0 - - - -
15A LYS* 3.3 35.8 + - + +
85A VAL* 4.1 5.8 - - - +
86A VAL* 1.4 82.9 - - + +
88A PRO* 1.4 70.1 - - - +
89A GLY* 4.1 9.8 + - - -
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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