Contacts of the strand formed by residues 59 - 64 (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 GLU 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D LYS* 3.2 32.4 + - - -
35D LYS* 5.0 6.2 - - + +
36D VAL 3.4 2.6 + - - +
37D VAL* 3.3 16.2 - - + +
38D VAL 2.8 31.4 + - - -
57D VAL* 3.5 7.6 - - - +
58D ASP* 1.3 88.1 - - + +
60D LEU* 1.3 57.0 + - - +
61D VAL* 4.0 3.6 - - + +
86D HIS* 4.0 18.1 - - - -
169D PRO* 4.4 0.2 - - - -
170D VAL* 3.5 20.2 - - + +
172D SER* 5.3 3.0 + - - +
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Residues in contact with LEU 60 (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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38D VAL* 3.3 22.4 - - + +
40D VAL* 4.3 7.4 - - + -
49D VAL* 3.6 50.0 - - + +
52D LEU* 3.7 46.7 - - + +
53D SER* 4.6 1.3 - - - +
57D VAL* 4.6 2.5 - - + -
59D GLU* 1.3 72.2 - - - +
61D VAL* 1.3 68.9 + - - +
62D VAL* 3.8 2.6 + - + -
169D PRO* 4.2 9.8 - - + +
170D VAL 3.1 6.8 + - - -
171D VAL* 3.2 14.4 - - + +
172D SER 2.8 27.2 + - - +
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Residues in contact with VAL 61 (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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37D VAL* 3.8 16.4 - - + -
38D VAL 2.9 8.7 + - - +
39D ALA* 3.1 25.2 - - + +
40D VAL* 3.1 5.9 + - - +
59D GLU* 5.1 4.0 - - + +
60D LEU* 1.3 73.4 - - - +
62D VAL* 1.3 72.5 + - - +
63D VAL* 4.2 1.6 - - + -
82D LEU* 4.0 22.7 - - + -
86D HIS* 3.8 27.8 - - + +
172D SER* 3.4 21.8 - - - +
174D VAL* 4.0 22.9 - - + -
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Residues in contact with VAL 62 (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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40D VAL* 3.6 18.6 - - + -
42D GLY 5.1 0.4 - - - +
45D ALA* 3.7 14.6 - - + +
46D ASP* 3.6 24.5 - - + +
49D VAL* 3.7 31.0 - - + -
60D LEU* 4.7 4.7 - - + -
61D VAL* 1.3 72.8 - - - +
63D VAL* 1.3 65.4 + - - +
64D LYS* 4.9 4.3 - - + +
171D VAL* 4.8 1.6 - - + -
172D SER 2.8 16.6 + - - +
173D ASN* 3.3 22.8 - - - +
174D VAL* 2.8 29.3 + - - +
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Residues in contact with VAL 63 (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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39D ALA* 4.8 0.4 - - + -
40D VAL 3.0 7.8 + - - +
41D ILE* 3.3 17.9 - - + +
42D GLY 2.9 26.9 + - - +
61D VAL* 4.2 9.9 - - + +
62D VAL* 1.3 75.3 - - - +
64D LYS* 1.3 59.9 + - - +
78D SER* 3.6 26.2 - - - +
82D LEU* 4.1 28.7 - - + -
174D VAL* 3.4 27.6 - - + -
175D ASP 4.5 0.4 - - - +
176D ALA* 4.0 17.9 - - + +
177D PRO* 5.7 0.2 - - + -
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Residues in contact with LYS 64 (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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41D ILE* 5.8 0.4 - - - -
42D GLY 3.4 13.7 - - - +
43D SER* 4.2 14.1 - - - +
62D VAL* 4.2 5.5 - - + +
63D VAL* 1.3 73.1 - - - +
65D GLY* 1.3 55.9 + - - +
174D VAL 3.1 12.6 + - - +
175D ASP* 3.6 15.0 - - - +
176D ALA* 2.6 32.6 + - - +
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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