Contacts of the strand formed by residues 256 - 260 (chain A) in PDB entry 2IDZ
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 ASP 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ASN* 3.1 6.9 + - - +
187A ASN* 2.9 19.4 - - - +
188A LEU 2.8 24.8 + - - -
253A THR* 3.6 20.2 - - + +
254A THR 2.9 7.6 + - - +
255A GLY* 1.3 78.7 - - - +
257A ILE* 1.3 82.9 + - - +
258A ILE* 5.7 0.7 - - - -
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Residues in contact with ILE 257 (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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148A ASP* 3.7 7.4 - - - +
169A GLU* 3.4 42.2 - - + +
172A ASN* 4.8 2.2 - - - +
173A ARG* 4.3 11.7 - - - +
188A LEU* 3.2 12.1 - - + +
190A ALA* 3.6 28.0 - - + +
255A GLY 5.3 1.1 - - - +
256A ASP* 1.3 94.9 + - - +
258A ILE* 1.3 69.8 + - - +
259A TYR* 3.5 45.4 - - + +
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Residues in contact with ILE 258 (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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187A ASN* 5.3 0.9 - - + -
188A LEU 2.8 9.6 + - - +
189A VAL* 3.2 5.2 - - - +
190A ALA 2.8 27.1 + - - -
241A THR* 3.5 25.6 - - + -
245A LEU* 3.7 35.7 - - + -
250A LEU* 4.8 13.5 - - + -
253A THR* 4.3 20.9 - - + +
256A ASP* 5.7 0.7 - - - -
257A ILE* 1.3 79.7 - - - +
259A TYR* 1.3 65.9 + - - +
260A ALA 3.5 1.0 + - - -
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Residues in contact with TYR 259 (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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150A ASP* 4.0 25.4 + - + -
169A GLU* 4.7 1.4 + - - -
190A ALA* 3.4 26.5 - - + -
257A ILE* 3.5 47.7 - - + +
258A ILE* 1.3 78.4 - - - +
260A ALA* 1.3 60.6 + - - +
261A ASP* 3.3 13.8 + - + +
262A GLY 5.1 0.3 + - - -
263A GLY* 5.3 1.0 + - - -
265A HIS* 3.1 57.7 - + + +
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Residues in contact with ALA 260 (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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189A VAL* 3.7 21.5 - - + -
190A ALA 2.8 7.7 + - - -
191A ALA* 3.4 2.8 - - - +
192A GLY 3.1 7.8 + - - -
230A TRP* 3.0 22.5 - - - -
237A PRO* 4.4 2.0 - - + +
238A VAL* 4.1 13.7 - - + +
241A THR* 3.4 28.5 - - + +
258A ILE 3.5 1.8 + - - -
259A TYR* 1.3 69.8 - - - +
261A ASP* 1.3 57.4 + - - +
262A GLY 3.7 1.8 - - - +
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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