Contacts of the strand formed by residues 210 - 216 (chain C) in PDB entry 2HU4
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 ILE 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TYR* 4.3 3.8 - - - +
129A CYS* 5.7 0.7 - - - -
412A GLN* 3.5 67.1 - - + +
413A THR* 3.8 25.6 - - + +
419A ARG* 5.1 1.3 - - - +
206C LYS* 4.0 1.8 - - - -
207C TYR* 3.0 36.7 + - + +
208C ASN* 4.2 11.2 - - + +
209C GLY* 1.3 84.0 - - - +
211C ILE* 1.3 69.4 + - - +
212C THR* 3.2 9.5 + - + +
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.8 23.8 - - + +
99A VAL 3.9 10.1 - - - +
100A TYR* 4.0 25.3 - - + -
413A THR* 5.5 2.6 - - - +
419A ARG* 2.8 38.7 + - - +
447A CYS* 4.1 12.3 - - + -
449A VAL* 3.7 21.3 - - + -
204C VAL* 3.7 27.1 - - + -
205C LEU 3.3 12.3 - - - +
206C LYS* 3.9 5.1 - - + +
209C GLY 4.3 0.2 + - - -
210C ILE* 1.3 73.6 - - - +
212C THR* 1.3 62.9 + - - +
213C ASP* 3.8 15.7 - - - +
214C THR* 5.0 0.2 - - - +
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A THR* 6.5 0.9 - - + -
415A LEU* 6.5 0.2 - - + -
419A ARG* 5.3 2.2 - - - +
205C LEU 2.8 13.7 + - - -
207C TYR* 3.6 22.9 + - + -
210C ILE* 3.5 18.4 - - + +
211C ILE* 1.3 74.4 - - - +
213C ASP* 1.3 65.7 + - - +
259C LYS 3.6 12.8 - - - +
260C GLY* 2.9 28.8 + - - +
261C LYS* 3.0 28.5 + - - +
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Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A VAL* 6.3 0.2 - - - -
451A SER* 3.7 14.8 + - - -
204C VAL* 4.0 0.2 - - - -
205C LEU* 3.1 32.7 + - + +
211C ILE* 3.8 9.8 - - - +
212C THR* 1.3 83.0 + - - +
214C THR* 1.3 91.5 + - - +
260C GLY 3.5 14.4 - - - +
261C LYS* 3.7 10.7 - - - +
262C VAL* 3.0 36.8 + - - +
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 4.3 16.5 - - - +
449A VAL* 4.5 3.8 - - - +
451A SER* 3.1 25.5 + - - -
452A ASP* 2.7 33.8 + - + +
202C VAL* 3.6 16.1 - - + +
203C ALA 3.3 10.5 + - - -
204C VAL* 4.3 3.5 - - - +
205C LEU* 5.1 0.4 - - - -
211C ILE* 5.0 0.2 - - - +
213C ASP* 1.3 95.5 + - - +
215C ILE* 1.3 72.1 + - - +
216C LYS* 4.5 3.1 - - + +
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Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.3 1.8 - - - -
203C ALA* 2.8 42.1 + - + +
205C LEU* 4.6 17.5 - - + -
214C THR* 1.3 79.6 - - - +
216C LYS* 1.3 68.5 + - - +
218C TRP* 4.6 5.8 - - + -
223C LEU* 3.5 8.7 - - + +
239C THR* 6.2 1.1 - - + -
241C MET* 4.3 17.7 - - + -
255C PHE* 3.7 45.3 - - + -
257C MET* 5.7 0.9 - - - -
262C VAL* 3.7 26.0 - - + -
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Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A SER* 5.0 1.4 - - - +
452A ASP* 2.6 59.6 - - + +
453A THR 5.3 3.1 - - - +
454A VAL* 5.4 4.7 - - + -
200C GLY 5.6 0.4 - - - +
201C ALA 3.5 7.9 - - - +
202C VAL* 4.3 10.8 - - + +
214C THR* 4.2 1.9 - - + +
215C ILE* 1.3 78.0 - - - +
217C SER* 1.3 70.2 + - - +
218C TRP* 3.4 12.6 + - - +
223C LEU* 4.1 2.2 - - - -
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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