Contacts of the strand formed by residues 59 - 62 (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 ARG 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D HIS* 1.3 80.2 - - + +
60D VAL* 1.3 61.2 + - - +
80D SER* 3.4 25.3 + - - +
82D THR* 4.8 4.6 - - + +
126D ALA* 6.2 1.0 - - - +
128D ASP* 3.2 14.2 + - - -
129D GLY 2.7 29.3 + - - -
130D PHE* 3.5 33.9 - - + +
131D ASP* 2.5 51.9 + - - +
132D ALA 3.3 3.3 + - - +
165D ARG* 5.4 1.6 - - - +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 4.0 13.5 - - + -
57D CYS* 4.8 3.4 - - + -
58D HIS 4.0 10.3 - - - +
59D ARG* 1.3 77.9 - - - +
61D LEU* 1.3 69.8 + - - +
62D ASP* 4.0 1.2 + - + +
74D LEU* 3.8 24.0 - - + -
79D PHE* 4.0 20.2 - - + -
80D SER 2.7 14.4 + - - +
81D VAL* 3.6 6.7 - - + +
82D THR* 3.0 27.4 + - - +
130D PHE* 3.9 3.6 - - - -
132D ALA* 3.4 18.2 - - + +
134D ILE* 4.3 17.7 - - + -
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Residues in contact with LEU 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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60D VAL* 1.3 74.8 - - - +
62D ASP* 1.3 65.3 + - - +
63D VAL* 3.4 27.4 + - + -
82D THR* 3.2 30.3 - - - +
84D VAL* 4.5 13.0 - - + -
120D LEU* 5.1 1.3 - - + -
124D VAL* 5.1 5.2 - - + -
130D PHE* 3.5 25.3 - - + -
132D ALA 3.0 9.1 + - - +
133D VAL* 3.4 5.9 - - + +
134D ILE* 3.0 24.6 + - - +
163D MET* 3.5 45.5 - - + -
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Residues in contact with ASP 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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60D VAL* 4.0 2.3 + - + +
61D LEU* 1.3 73.2 - - - +
63D VAL* 1.3 57.3 + - - +
64D ALA* 3.2 20.7 + - - +
65D CYS* 4.0 15.6 - - - +
70D ASP* 4.3 5.5 + - - +
71D SER* 2.8 35.4 + - - +
74D LEU* 6.1 0.2 - - + -
81D VAL* 5.1 3.8 - - + -
82D THR 2.9 8.5 + - - +
83D SER* 3.6 6.9 - - - +
84D VAL* 2.8 31.9 + - - +
134D ILE* 3.5 34.0 - - + +
135D CYS* 5.0 0.7 - - - -
136D LEU 5.4 1.0 + - - -
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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