Contacts of the strand formed by residues 221 - 224 (chain A) in PDB entry 2HU2
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 CYS 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ILE* 4.4 7.4 - - - -
128A LEU* 5.3 0.2 - - - -
129A TYR* 3.6 29.6 - - + +
165A THR 3.2 5.4 + - - +
166A LEU* 3.4 27.7 - - + +
167A GLY 2.8 31.7 + - - -
187A PHE* 4.9 0.4 - - + -
220A ASP* 1.3 79.9 - - - +
222A VAL* 1.3 59.8 + - - +
249A PHE* 3.6 23.1 - - + +
251A VAL* 4.2 20.6 - - - -
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Residues in contact with VAL 222 (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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167A GLY 3.5 2.9 - - - -
169A ILE* 3.8 28.0 - - + -
215A LEU* 4.1 11.2 - - + -
216A LEU* 4.5 12.8 - - + +
219A SER* 3.9 24.2 - - - +
221A CYS* 1.3 75.7 - - - +
223A THR* 1.3 65.1 + - - +
224A LEU* 5.3 0.7 - - + -
236A ILE* 5.2 2.7 - - + -
244A MET* 3.8 21.5 - - + -
248A ALA* 5.3 0.4 - - + -
249A PHE 2.9 13.1 + - - +
250A LEU* 3.5 19.8 - - + +
251A VAL* 2.8 28.1 + - - +
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Residues in contact with THR 223 (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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121A THR* 3.6 14.3 - - - +
125A ILE* 4.9 1.8 - - + -
166A LEU* 4.1 21.1 - - + -
167A GLY 2.8 19.7 + - - +
168A ILE* 3.5 15.6 - - + -
169A ILE* 3.0 27.5 + - - +
178A VAL* 4.5 4.0 - - + -
222A VAL* 1.3 76.7 - - - +
224A LEU* 1.3 64.2 + - - +
225A HIS* 2.9 34.0 + - + +
251A VAL* 3.4 18.0 + - - +
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Residues in contact with LEU 224 (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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169A ILE* 3.8 34.8 - - + -
222A VAL* 5.3 0.2 - - + -
223A THR* 1.3 74.0 + - - +
225A HIS* 1.3 73.7 + - - +
226A CYS* 4.2 9.6 - - - -
235A LEU* 4.1 17.0 - - + -
236A ILE* 4.3 10.5 - - + -
250A LEU* 4.6 9.4 - - + -
251A VAL 3.0 10.3 + - - +
252A ASN* 3.5 33.4 - - + +
253A THR 4.0 3.3 + - - -
254A ALA* 3.4 21.4 + - + +
258A LEU* 4.6 9.0 - - + -
259A VAL* 3.7 26.2 - - + -
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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