Contacts of the strand formed by residues 223 - 229 (chain A) in PDB entry 3THP
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 GLN 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A HIS* 4.9 9.1 + - - +
179A PHE 3.5 13.1 + - - +
181A TYR* 3.9 24.0 - - + +
200A LEU* 4.0 1.5 - - - +
221A PRO* 4.4 0.2 - - - +
222A ASP* 1.3 90.3 + - - +
224A MSE 1.3 96.1 + - - +
225A THR* 3.1 8.5 + - - -
245A PHE* 3.4 24.7 - - + -
333A PHE* 3.4 7.3 - - - +
334A ARG* 2.5 69.0 + - - +
336A VAL* 5.1 2.2 - - + +
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Residues in contact with MSE 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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177A LYS 4.0 0.3 - - - +
178A HIS* 3.6 0.7 - - - -
179A PHE* 2.9 61.1 + - + -
200A LEU* 3.7 11.4 - - + +
201A PRO* 3.5 36.3 - - + -
204A CYS* 3.8 9.6 - - - -
223A GLN* 1.3 91.7 + - - +
225A THR* 1.3 62.7 + - - +
226A ILE* 3.9 13.7 - - + -
331A PHE* 3.9 12.8 - - + -
332A THR 3.3 12.3 - - - +
333A PHE* 3.4 36.6 - - + -
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Residues in contact with THR 225 (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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176A VAL* 3.9 10.8 - - + -
177A LYS 3.5 2.2 - - - -
178A HIS* 3.4 34.0 + - + +
223A GLN* 3.1 8.8 + - - -
224A MSE 1.3 72.2 - - - +
226A ILE* 1.3 64.4 + - - +
227A ASN* 3.9 14.6 + - - +
330A SER 3.2 4.3 - - - +
331A PHE* 3.8 0.7 - - - -
332A THR* 3.0 33.6 + - - -
334A ARG* 2.7 40.2 + - - +
403A AKG 5.1 0.4 - - - +
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Residues in contact with ILE 226 (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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156A VAL* 5.5 7.0 - - + -
175A ARG* 3.6 24.0 - - - +
176A VAL* 3.2 28.1 - - - +
177A LYS* 2.9 22.2 + - + +
179A PHE* 3.7 26.5 - - + -
224A MSE 3.9 17.9 - - + -
225A THR* 1.3 73.2 - - - +
227A ASN* 1.3 66.9 + - - +
228A GLN 4.2 0.4 - - - +
329A THR* 3.9 20.9 - - + -
330A SER 3.5 1.3 - - - -
331A PHE* 3.6 43.3 - - + -
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Residues in contact with ASN 227 (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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174A ARG* 3.2 15.8 + - - +
175A ARG 3.8 2.5 - - - -
176A VAL* 3.2 24.6 - - - +
225A THR* 3.9 13.6 + - - +
226A ILE* 1.3 76.9 - - - +
228A GLN* 1.3 59.9 + - - +
229A TYR* 3.6 22.9 - - + +
328A ARG 3.3 2.3 - - - +
329A THR* 3.0 4.8 - - - -
330A SER* 2.6 49.3 + - - +
332A THR* 3.9 13.1 + - - -
403A AKG 3.0 25.9 + - - +
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Residues in contact with GLN 228 (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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174A ARG* 3.7 19.4 - - - +
175A ARG* 2.9 69.0 + - + +
226A ILE* 4.2 0.6 - - - +
227A ASN* 1.3 72.1 - - - +
229A TYR* 1.3 63.7 + - - +
230A GLU* 4.6 11.1 + - - +
233A GLN* 4.0 3.6 - - - +
327A LEU* 3.8 34.3 - - + +
328A ARG 3.1 3.8 - - - +
329A THR* 3.7 20.1 + - + +
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Residues in contact with TYR 229 (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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174A ARG* 3.8 20.6 - - - -
227A ASN* 3.6 34.8 + - + +
228A GLN* 1.3 73.7 - - - +
230A GLU* 1.3 64.2 + - - +
233A GLN* 3.9 10.8 - - + +
234A GLY* 3.9 20.2 - - - -
235A ILE* 3.9 23.1 - - - +
258A ILE* 5.9 5.2 - - + -
294A ILE* 3.5 25.3 - - + +
325A ARG* 6.4 1.3 - - - -
326A GLY 3.5 2.2 - - - +
327A LEU* 3.3 9.6 - - - +
328A ARG* 2.5 86.2 + - + +
403A AKG 3.1 14.9 + - - -
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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