Contacts of the helix formed by residues 365 - 378 (chain B) in PDB entry 3OOY
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 ALA 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A SER* 3.6 15.3 - - - +
160A GLU* 4.1 1.3 - - - -
165B GLU* 3.5 32.1 - - + +
362B CYS 3.8 17.5 - - - +
363B TYR 2.9 7.9 + - - +
364B ILE* 1.3 75.9 - - - +
366B GLU* 1.3 62.2 + - - +
367B GLN 3.4 2.5 - - - -
368B ASN* 3.4 5.8 + - + +
369B MET* 3.1 26.6 + - - +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A TPP 2.8 35.3 + - - +
160A GLU* 2.5 29.5 + - - +
340B GLY* 4.6 5.8 - - - +
364B ILE* 3.9 5.9 - - - +
365B ALA* 1.3 74.9 + - - +
367B GLN* 1.3 67.0 + - - +
369B MET* 3.3 15.2 + - + +
370B VAL* 3.2 26.7 + - - +
388B THR* 4.2 18.4 + - + +
392B PHE* 3.7 31.8 - - + +
393B PHE* 5.5 1.3 - - + -
395B ARG* 3.7 14.6 - - + +
396B ALA* 4.0 6.1 - - + -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 5.0 2.4 + - - -
161A GLY 4.7 1.4 - - - +
367A GLN* 3.4 33.2 + - - +
395A ARG* 3.2 31.9 + - - -
161B GLY 4.6 0.6 - - - -
162B SER* 3.7 16.3 - - - +
165B GLU* 3.2 26.5 + - - +
366B GLU* 1.3 78.6 - - - +
368B ASN* 1.3 63.7 + - - +
370B VAL* 3.3 0.9 + - - +
371B SER* 3.2 23.4 + - - -
395B ARG* 3.3 25.4 - - + +
396B ALA* 4.1 3.8 - - - +
399B GLN* 3.3 29.4 + - - +
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Residues in contact with ASN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLY* 3.6 14.9 - - - -
162B SER* 4.5 3.4 - - - +
165B GLU* 2.9 30.3 + - + +
166B ALA* 3.4 29.2 + - - +
169B PHE* 3.5 42.6 - - - +
362B CYS* 5.4 3.8 + - - +
365B ALA* 3.8 9.0 - - + +
366B GLU 3.3 0.2 - - - -
367B GLN* 1.3 75.4 - - - +
369B MET* 1.3 58.2 + - - +
371B SER* 3.0 5.7 + - - -
372B ILE* 2.7 41.0 + - - +
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Residues in contact with MET 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.0 3.9 - - + +
339B ASP* 3.6 16.4 - - - -
340B GLY* 3.6 24.9 - - - +
362B CYS* 3.8 28.6 - - + +
365B ALA 3.1 15.1 + - - +
366B GLU* 3.6 18.2 - - + +
367B GLN 3.2 0.4 - - - -
368B ASN* 1.3 76.3 - - - +
370B VAL* 1.3 64.3 + - - +
372B ILE* 3.3 2.9 + - - +
373B ALA* 3.0 22.2 + - - +
386B CYS* 3.9 22.2 - - + -
387B SER 3.7 13.5 - - - +
388B THR* 4.0 10.5 - - + -
393B PHE* 3.9 27.4 - - + -
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLU 3.2 6.0 + - - +
367B GLN 3.9 5.8 - - - +
368B ASN 3.3 0.2 - - - -
369B MET* 1.3 75.9 - - + +
371B SER* 1.3 59.1 + - - +
373B ALA* 3.2 8.7 + - - +
374B VAL* 3.0 29.4 + - + +
386B CYS* 4.5 3.6 - - - -
393B PHE* 4.2 11.2 - - + -
396B ALA* 3.6 25.1 - - + -
399B GLN* 3.9 26.7 - - + +
400B ILE* 4.0 14.6 - - + -
410B ILE* 4.2 17.7 - - + -
412B LEU* 4.1 20.6 - - + -
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Residues in contact with SER 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLN* 3.9 14.9 + - - +
130B GLY* 3.7 24.7 - - - -
131B ALA* 3.4 14.5 - - - -
367B GLN 3.2 6.5 + - - -
368B ASN* 3.0 9.4 + - - -
370B VAL* 1.3 75.2 - - - +
372B ILE* 1.3 57.8 + - - +
374B VAL* 3.3 7.0 + - - +
375B GLY 2.9 24.9 + - - -
399B GLN* 3.4 24.9 + - - +
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 3.1 21.8 - - - +
133B CYS* 3.2 24.2 - - + -
134B GLY* 3.5 9.6 - - - +
137B TYR* 5.6 0.7 - - + -
169B PHE* 3.9 29.2 - - + -
338B LEU* 3.4 20.6 - - + -
360B ILE* 4.4 5.6 - - + -
362B CYS* 4.8 0.9 - - - -
368B ASN* 2.7 40.8 + - - +
369B MET* 3.6 6.3 - - - +
371B SER* 1.3 70.7 - - - +
373B ALA* 1.3 57.7 + - - +
375B GLY* 3.3 1.9 + - - -
376B CYS* 2.9 45.8 + - - -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B LEU* 3.9 6.0 - - + +
369B MET 3.0 5.2 + - - +
370B VAL* 3.4 8.5 - - - +
372B ILE* 1.3 76.9 - - - +
374B VAL* 1.3 57.1 + - - +
376B CYS* 3.3 2.2 + - - +
377B ALA* 3.0 25.1 + - - +
384B PRO* 3.4 29.7 - - + +
386B CYS* 3.2 35.0 - - - -
410B ILE* 3.9 13.2 - - + -
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 3.7 26.2 - - + -
131B ALA* 4.9 2.9 - - + -
370B VAL* 3.0 21.4 + - + +
371B SER* 3.6 10.5 - - - +
372B ILE 3.3 0.2 - - - -
373B ALA* 1.3 73.7 - - - +
375B GLY* 1.3 65.5 + - - +
377B ALA* 3.4 3.5 + - - +
378B THR* 3.2 21.4 + - + +
399B GLN 5.0 1.6 - - - +
403B ALA* 3.7 29.4 - - + -
406B SER* 4.8 7.2 - - - -
408B SER* 3.8 25.3 + - - +
410B ILE* 3.8 9.6 - - + -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 3.4 29.3 - - - +
135B MET* 3.6 16.2 + - - +
138B THR* 5.5 0.3 - - - -
371B SER 2.9 12.6 + - - -
372B ILE 3.6 3.6 - - - -
374B VAL* 1.3 78.0 - - - +
376B CYS* 1.3 58.1 + - - +
378B THR* 2.7 30.3 + - - +
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Residues in contact with CYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY* 3.6 12.6 - - - -
137B TYR* 5.1 0.9 - - - -
138B THR* 3.4 24.9 + - - +
142B PHE* 4.8 1.8 - - - -
336B ILE* 3.8 22.0 - - + -
360B ILE* 4.3 9.2 - - - -
372B ILE* 2.9 37.5 + - - +
373B ALA* 3.3 6.7 + - - +
375B GLY* 1.3 73.1 - - - +
377B ALA* 1.3 58.5 + - - +
378B THR 3.3 0.6 + - - -
381B ARG* 3.9 8.7 - - - +
382B THR* 2.5 40.1 + - - +
384B PRO* 4.8 0.7 - - + -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B ALA 3.0 16.3 + - - +
374B VAL 3.8 4.9 - - - +
375B GLY 3.2 0.2 - - - -
376B CYS* 1.3 75.7 - - - +
378B THR* 1.3 64.5 + - - +
379B ARG 3.5 0.2 + - - -
380B ASN* 3.0 21.4 + - - -
381B ARG 4.4 0.9 - - - -
382B THR* 3.7 11.3 + - - +
384B PRO* 4.0 10.1 - - + -
408B SER* 4.4 5.6 - - - +
409B ASN* 3.5 29.0 + - + +
410B ILE* 4.1 4.5 - - + -
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Residues in contact with THR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 5.3 4.2 + - - -
119B ASP* 4.0 23.4 - - + +
120B VAL* 3.7 26.0 - - + -
135B MET* 3.6 21.5 - - + +
374B VAL* 3.2 18.6 + - + +
375B GLY 2.7 17.9 + - - +
376B CYS 3.3 1.6 - - - +
377B ALA* 1.3 78.3 - - - +
379B ARG* 1.3 71.8 + - - +
380B ASN 3.0 0.9 + - - -
381B ARG* 3.4 15.9 + - - +
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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