Contacts of the strand formed by residues 130 - 135 (chain D) in PDB entry 2IDK
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 PHE 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D ARG* 3.5 32.1 - - - +
60D VAL 3.9 3.8 - - - -
61D LEU* 3.5 35.2 - - + -
82D THR* 3.2 35.0 - - + -
124D VAL* 6.1 1.3 - - + -
125D PRO 5.1 5.4 - - - -
126D ALA* 3.9 13.7 - - + -
129D GLY* 1.3 76.7 - - - -
131D ASP* 1.3 68.2 + - - +
132D ALA* 3.3 14.7 + - - +
133D VAL* 4.3 4.5 - - + -
163D MET* 2.8 45.6 + - + +
164D VAL* 4.0 4.5 - - - +
165D ARG* 3.0 24.0 + - - +
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Residues in contact with ASP 131 (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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56D GLY 5.0 1.1 - - - -
57D CYS* 3.6 25.0 - - - -
58D HIS* 2.5 17.1 + - - +
59D ARG* 2.5 45.1 + - - +
130D PHE* 1.3 72.3 - - - +
132D ALA* 1.3 59.9 + - - +
165D ARG* 3.3 33.0 + - - +
168D GLY* 3.3 6.2 - - - -
169D LEU* 2.8 24.4 + - - +
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Residues in contact with ALA 132 (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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52D LEU* 3.8 29.6 - - + -
57D CYS* 3.8 14.8 - - + -
59D ARG 3.3 2.4 + - - -
60D VAL* 3.4 12.2 - - + +
61D LEU 3.0 23.4 + - - -
130D PHE* 3.8 2.5 - - - +
131D ASP* 1.3 81.7 - - - +
133D VAL* 1.3 68.2 + - - +
134D ILE* 4.2 1.3 - - + -
169D LEU* 3.1 14.1 - - + +
171D VAL* 5.6 1.1 - - + -
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Residues in contact with VAL 133 (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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61D LEU* 3.4 7.4 - - + +
63D VAL* 3.8 27.6 - - + -
130D PHE* 4.3 5.6 - - + -
132D ALA* 1.3 77.9 - - - +
134D ILE* 1.3 66.7 + - - +
160D ILE* 4.1 11.9 - - + +
163D MET* 4.0 24.7 - - + +
164D VAL* 3.4 24.2 - - + -
169D LEU 2.8 8.7 + - - -
170D LEU* 3.3 25.3 - - + +
171D VAL* 2.8 27.4 + - - +
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Residues in contact with ILE 134 (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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48D LEU* 4.5 17.5 - - + -
52D LEU* 4.8 8.1 - - + -
60D VAL* 4.3 13.9 - - + -
61D LEU 3.0 8.8 + - - +
62D ASP* 3.5 37.1 - - + +
63D VAL* 3.1 28.0 + - - +
70D ASP* 4.5 15.0 - - + +
74D LEU* 4.1 22.9 - - + -
132D ALA* 4.2 0.4 - - + -
133D VAL* 1.3 79.8 - - - +
135D CYS* 1.3 61.8 + - - +
136D LEU* 4.0 15.9 - - + +
171D VAL* 3.5 21.1 - - + +
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Residues in contact with CYS 135 (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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62D ASP* 5.0 0.4 - - - -
63D VAL* 3.6 16.4 - - + -
64D ALA* 4.0 12.1 - - - -
117D TRP* 3.8 29.6 - - - -
134D ILE* 1.3 73.8 - - - +
136D LEU* 1.3 61.5 + - - +
139D SER* 4.6 1.0 + - - -
140D PHE* 4.3 14.4 - - - -
160D ILE* 4.7 4.3 - - + -
170D LEU* 5.5 4.0 - - + -
171D VAL 2.9 7.4 + - - +
172D ILE* 3.3 30.7 - - + +
173D ASP* 3.1 24.9 + - - +
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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