Contacts of the strand formed by residues 35 - 41 (chain D) in PDB entry 1O94
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 LYS 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D SER 3.3 7.0 + - - +
2D LYS* 3.3 21.7 - - + +
3D ILE* 2.8 24.8 + - - -
33D GLU 3.8 3.5 + - - +
34D ASP* 1.3 74.9 - - - +
36D VAL* 1.3 63.0 + - - +
37D VAL 3.9 0.2 - - - -
58D ASP* 3.3 19.1 - - + +
59D GLU* 5.0 8.5 - - + +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.3 15.0 - - + +
5D VAL* 4.3 5.6 - - + -
22D ILE* 4.9 3.6 - - + -
25D ALA* 3.9 37.9 - - + +
26D ASN* 3.9 22.7 - - - +
29D LYS* 5.8 4.5 - - + -
34D ASP 5.5 1.8 - - - +
35D LYS* 1.3 72.2 - - - +
37D VAL* 1.3 60.1 + - - +
38D VAL* 4.2 21.5 + - + -
56D GLY 3.5 19.3 - - - +
57D VAL* 4.3 0.3 - - - -
58D ASP* 3.1 31.9 + - - +
59D GLU* 3.4 6.2 + - - +
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 4.5 17.5 - - + -
3D ILE 2.8 16.6 + - - +
4D LEU* 3.3 26.3 - - + +
5D VAL* 2.7 32.4 + - - +
35D LYS 3.8 0.4 + - - -
36D VAL* 1.3 73.2 - - - +
38D VAL* 1.3 61.8 + - - +
39D ALA* 5.4 0.2 - - + -
59D GLU* 3.3 20.9 - - + +
61D VAL* 3.8 30.1 - - + -
86D HIS* 4.0 28.5 - - + +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 3.3 17.9 - - + +
7D ALA* 4.0 17.0 - - + -
22D ILE* 3.8 26.5 - - + -
36D VAL* 4.1 8.0 - - + -
37D VAL* 1.3 78.1 - - - +
39D ALA* 1.3 70.9 + - - +
52D LEU* 4.1 12.3 - - + -
57D VAL* 3.8 26.7 - - + -
59D GLU 2.8 6.3 + - - -
60D LEU* 3.3 17.3 - - + +
61D VAL 2.9 25.3 + - - -
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.3 4.9 - - + -
5D VAL 2.9 7.5 + - - +
6D ILE* 3.7 12.6 - - + +
7D ALA* 2.8 31.5 + - - +
37D VAL* 5.4 0.2 - - + -
38D VAL* 1.3 78.2 - - - +
40D VAL* 1.3 59.8 + - - +
41D ILE* 4.3 2.9 - - + -
61D VAL* 3.1 11.9 - - + +
63D VAL* 4.8 2.9 - - + -
82D LEU* 3.5 37.7 - - + -
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 4.4 7.4 - - + -
9D HIS* 3.5 25.8 - - + -
14D LEU* 5.0 2.0 - - + -
39D ALA* 1.3 74.9 - - - +
41D ILE* 1.3 64.0 + - - +
45D ALA* 3.6 28.0 - - + +
48D PHE* 3.9 16.8 - - + -
52D LEU* 3.7 24.7 - - + -
60D LEU* 4.3 4.7 - - + -
61D VAL 3.1 3.3 + - - +
62D VAL* 3.6 20.3 - - + -
63D VAL 3.0 24.1 + - - +
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.2 11.0 - - + -
7D ALA 5.4 2.4 + - - -
9D HIS* 2.7 29.2 + - - -
39D ALA* 5.0 0.2 - - + -
40D VAL* 1.3 81.5 - - - +
42D GLY* 1.3 58.0 + - - +
45D ALA* 3.9 1.1 - - - -
63D VAL* 3.3 24.9 - - + +
64D LYS 5.8 0.2 - - - -
65D GLY 5.6 1.8 - - - +
68D ILE 4.4 0.3 - - - +
74D VAL* 4.2 9.9 - - + -
75D PHE* 3.7 52.5 - - + -
78D SER* 3.9 26.7 - - - +
79D VAL* 3.8 28.5 - - + -
82D LEU* 4.6 8.3 - - + -
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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