Contacts of the strand formed by residues 234 - 241 (chain A) in PDB entry 1HKC
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 THR 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ILE 3.2 15.2 + - - -
230A ILE* 4.6 5.7 - - - +
233A GLY* 1.3 74.4 - - - -
235A ASN* 1.3 65.1 + - - +
261A TRP* 3.0 33.9 + - + +
262A GLY 4.1 4.5 + - - -
293A PHE* 4.9 2.9 - - + -
294A GLU* 3.1 42.7 + - + +
297A VAL* 4.2 27.2 - - + +
298A SER* 4.4 3.6 - - - -
386A VAL* 4.5 3.5 - - - +
918A BGC 3.8 5.7 + - - +
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Residues in contact with ASN 235 (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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208A ASN* 3.4 8.3 + - - -
210A THR* 3.4 8.6 - - + +
228A LEU* 3.8 0.5 - - - -
229A ILE* 2.8 30.4 + - - +
234A THR* 1.3 80.7 + - - +
236A ALA* 1.3 68.8 + - - +
258A ASN* 2.9 22.6 + - - +
260A GLU* 2.9 33.0 + - - -
261A TRP* 3.2 13.4 + - - +
918A BGC 2.8 46.3 + - - +
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Residues in contact with ALA 236 (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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210A THR* 4.0 2.5 - - - -
226A VAL* 5.1 2.9 - - + -
227A GLY 3.2 10.8 - - - +
228A LEU* 4.4 5.6 - - + -
235A ASN* 1.3 84.7 + - - +
237A CYS* 1.3 61.3 + - - +
258A ASN 4.2 0.2 - - - -
259A THR* 2.5 37.0 + - - +
261A TRP* 3.5 36.6 - - + -
390A LEU* 5.4 0.9 - - + -
393A ILE* 3.8 13.9 - - + -
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Residues in contact with CYS 237 (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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210A THR* 3.4 44.6 - - - +
211A VAL* 3.8 5.4 - - + +
214A MET* 4.1 5.8 - - - -
226A VAL* 3.2 7.7 - - - +
227A GLY* 2.8 36.7 + - - -
236A ALA* 1.3 74.5 - - - +
238A TYR* 1.3 61.2 + - - +
256A CYS* 3.4 24.7 - - - -
257A ILE 3.0 18.8 - - - +
258A ASN* 4.2 4.0 - - - -
393A ILE* 5.3 0.4 - - - -
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Residues in contact with TYR 238 (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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47A MET* 4.7 6.6 - - - -
51A LEU* 3.6 4.3 - - - +
63A MET* 3.4 21.2 - - + +
214A MET* 4.9 0.2 - - - -
225A GLU 3.1 14.1 - - - +
226A VAL* 4.1 2.7 - - + -
237A CYS* 1.3 76.8 - - - +
239A MET* 1.3 69.2 + - - +
240A GLU* 2.5 46.5 + - + +
256A CYS* 3.2 7.1 - - - -
257A ILE* 2.7 47.4 + - + +
259A THR* 3.8 28.9 - - + -
393A ILE* 3.9 29.6 - - + -
396A ARG* 4.0 19.7 + - + +
397A LEU* 4.5 10.3 - - + -
400A ASN* 5.0 1.1 - - - -
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Residues in contact with MET 239 (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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68A VAL* 4.2 14.8 - - + +
69A ARG 4.8 4.5 - - - +
70A SER* 4.4 9.9 - - - +
71A ILE* 4.3 14.6 - - + -
214A MET* 3.2 37.7 - - + -
224A CYS 4.8 1.8 - - - +
225A GLU* 2.9 27.8 + - + +
238A TYR* 1.3 76.0 - - - +
240A GLU* 1.3 60.7 + - - +
254A ARG* 3.7 44.3 + - + +
255A MET 3.9 3.1 - - - -
256A CYS* 3.9 22.9 - - + -
397A LEU* 3.5 20.3 - - - +
400A ASN* 4.7 1.9 + - - -
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Residues in contact with GLU 240 (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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51A LEU* 3.5 12.3 - - + +
238A TYR* 2.5 39.7 + - + +
239A MET* 1.3 73.9 - - - +
241A GLU* 1.3 87.2 + - - +
244A HIS* 3.4 8.1 - - + -
245A ILE* 4.0 10.5 - - + +
254A ARG* 3.4 4.5 - - - -
255A MET* 3.1 30.4 + - - +
257A ILE* 3.8 16.4 - - + -
396A ARG* 2.7 43.5 + - - -
400A ASN* 2.8 13.3 + - - +
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Residues in contact with GLU 241 (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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240A GLU* 1.3 77.7 + - - +
242A LEU* 1.3 55.6 + - - +
243A ARG* 3.8 28.6 + - + +
244A HIS* 2.7 56.7 + - + +
245A ILE* 3.5 6.2 + - - +
253A GLY 4.1 8.2 - - - +
254A ARG* 3.0 39.5 + - - +
400A ASN* 3.8 22.0 + - + +
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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