Contacts of the helix formed by residues 365 - 378 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.5 28.0 - - + +
340A GLY* 5.9 0.2 - - - -
362A CYS 3.7 16.8 - - - +
363A TYR 2.8 8.4 + - - -
364A ILE* 1.3 76.2 - - - +
366A GLU* 1.3 64.2 + - - +
367A GLN 3.3 2.7 - - - -
368A ASN* 3.3 6.0 + - + +
369A MET* 3.0 27.5 + - - +
159B SER* 3.6 15.5 - - - +
160B GLU* 4.1 2.0 - - - -
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Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLY* 4.6 7.0 - - - +
363A TYR 5.6 0.2 - - - -
364A ILE* 4.1 3.1 - - - +
365A ALA* 1.3 74.2 + - - +
367A GLN* 1.3 69.9 + - - +
369A MET* 3.3 12.7 + - + +
370A VAL* 3.2 25.6 + - - +
388A THR* 4.1 20.4 + - + +
392A PHE* 3.7 33.1 - - + +
393A PHE* 5.5 1.3 - - + -
395A ARG* 3.9 11.5 - - + +
396A ALA* 4.0 5.6 - - + -
1B TPP 2.8 36.6 + - - +
160B GLU* 2.5 29.6 + - - +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLY 4.6 0.4 - - - -
162A SER* 3.7 16.3 + - - +
165A GLU* 3.1 30.3 + - - +
365A ALA 3.3 0.6 - - - -
366A GLU* 1.3 79.7 - - - +
368A ASN* 1.3 61.7 + - - +
370A VAL* 3.4 1.0 + - - +
371A SER* 3.2 16.3 + - - -
395A ARG* 3.3 25.9 - - + +
396A ALA* 4.0 8.5 - - - +
399A GLN* 3.3 31.7 + - - +
160B GLU* 5.0 2.8 + - - -
161B GLY* 4.6 1.8 - - - +
367B GLN* 3.4 34.3 + - - +
395B ARG* 3.1 31.1 + - - -
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Residues in contact with ASN 368 (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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130A GLY* 3.5 16.1 - - - -
162A SER* 4.6 3.9 - - - +
165A GLU* 3.1 26.4 + - + +
166A ALA* 3.5 28.1 + - - +
169A PHE* 3.5 42.2 - - - +
362A CYS* 5.5 3.0 + - - +
365A ALA* 3.8 8.7 - - + +
366A GLU 3.2 0.4 - - - -
367A GLN* 1.3 75.5 - - - +
369A MET* 1.3 58.5 + - - +
371A SER* 2.9 5.4 + - - +
372A ILE* 2.7 48.2 + - - +
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Residues in contact with MET 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.9 13.8 - - + +
339A ASP* 3.6 32.5 - - - -
340A GLY* 3.6 8.3 - - - +
362A CYS* 3.7 30.3 - - + +
365A ALA 3.0 17.5 + - - +
366A GLU* 3.3 14.8 + - + +
368A ASN* 1.3 74.9 - - - +
370A VAL* 1.3 63.8 + - - +
372A ILE* 3.4 3.2 + - - +
373A ALA* 3.1 22.2 + - - +
386A CYS* 4.0 11.4 - - + -
387A SER 3.7 14.8 - - - +
388A THR* 4.0 11.0 - - + -
393A PHE* 3.9 27.8 - - + -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLU 3.2 4.8 + - - +
367A GLN 3.8 6.7 - - - +
368A ASN 3.2 0.6 - - - -
369A MET* 1.3 78.7 - - + +
371A SER* 1.3 61.9 + - - +
373A ALA* 3.2 8.4 + - - +
374A VAL* 3.0 23.0 + - + +
386A CYS* 4.7 4.0 - - - -
393A PHE* 4.2 11.9 - - + -
396A ALA* 3.6 23.6 - - + -
399A GLN* 3.8 31.4 - - + +
400A ILE* 4.1 9.6 - - + -
410A ILE* 4.2 17.5 - - + -
412A LEU* 4.2 20.4 - - + -
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Residues in contact with SER 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN* 3.9 16.5 + - - +
130A GLY* 3.7 26.5 - - - -
131A ALA* 3.5 12.8 - - - +
367A GLN 3.2 7.1 + - - -
368A ASN* 2.9 9.0 + - - -
370A VAL* 1.3 76.1 - - - +
372A ILE* 1.3 63.2 + - - +
374A VAL* 3.2 8.8 + - - +
375A GLY 3.0 19.2 + - - -
399A GLN* 3.3 25.3 + - - +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 3.4 8.7 - - - +
133A CYS* 3.2 33.9 - - + -
134A GLY* 3.5 8.0 - - - +
137A TYR* 5.6 0.7 - - + -
169A PHE* 3.6 32.5 - - + -
338A LEU* 3.6 20.6 - - + -
360A ILE* 4.3 4.5 - - + -
362A CYS* 4.8 0.2 - - - -
368A ASN* 2.7 43.6 + - - +
369A MET* 3.6 7.2 - - - +
371A SER* 1.3 73.4 - - - +
373A ALA* 1.3 54.6 - - - +
375A GLY* 3.2 3.3 + - - -
376A CYS* 2.8 39.9 + - - -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.0 7.6 - - + +
369A MET 3.1 5.7 + - - -
370A VAL* 3.5 7.4 - - - +
372A ILE* 1.3 75.8 - - - +
374A VAL* 1.3 64.2 + - - +
376A CYS* 3.1 3.9 + - - -
377A ALA* 3.0 19.8 + - - +
384A PRO* 3.6 25.3 - - + +
386A CYS* 3.2 35.2 - - - -
410A ILE* 3.9 12.6 - - + -
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 3.7 26.7 - - + -
131A ALA* 5.1 3.1 - - + -
370A VAL* 3.0 20.6 + - + +
371A SER* 3.2 9.8 + - - +
373A ALA* 1.3 77.8 - - - +
375A GLY* 1.3 62.2 + - - +
377A ALA* 3.3 3.3 + - - +
378A THR* 3.2 21.0 + - + +
399A GLN 5.1 1.8 - - - +
403A ALA* 3.7 28.5 - - + -
406A SER* 4.7 8.1 - - - +
408A SER* 3.8 25.0 + - - +
410A ILE* 3.9 11.0 - - + -
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Residues in contact with GLY 375 (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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131A ALA* 3.3 29.3 - - - +
135A MET* 3.7 15.8 + - - +
138A THR* 4.7 0.7 + - - -
371A SER 3.0 11.1 + - - -
372A ILE 3.5 3.6 - - - -
374A VAL* 1.3 77.4 - - - +
376A CYS* 1.3 58.0 + - - +
378A THR* 2.7 31.3 + - - +
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Residues in contact with CYS 376 (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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134A GLY* 3.8 11.7 - - - -
137A TYR* 5.1 0.9 - - - -
138A THR* 3.4 25.6 + - - +
142A PHE* 4.4 2.5 - - - -
336A ILE* 3.8 24.2 - - + -
338A LEU* 5.2 0.2 - - - -
360A ILE* 4.1 8.7 - - - -
372A ILE* 2.8 38.1 + - - +
373A ALA* 3.1 7.6 + - - +
375A GLY* 1.3 72.2 - - - +
377A ALA* 1.3 59.5 + - - +
378A THR 3.5 0.7 + - - +
381A ARG* 3.9 10.0 - - - +
382A THR* 2.8 34.5 + - - +
384A PRO* 4.5 1.6 - - + -
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Residues in contact with ALA 377 (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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373A ALA 3.0 14.5 + - - +
374A VAL 3.8 4.5 - - - +
375A GLY 3.3 0.2 - - - -
376A CYS* 1.3 75.0 - - - +
378A THR* 1.3 65.5 + - - +
379A ARG 3.5 0.2 + - - -
380A ASN* 3.2 19.9 + - - -
381A ARG 4.5 0.4 - - - -
382A THR* 3.8 12.7 + - - +
384A PRO* 3.9 11.4 - - + +
408A SER* 4.3 6.1 - - - +
409A ASN* 3.6 27.5 + - + +
410A ILE* 4.2 4.5 - - + -
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Residues in contact with THR 378 (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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70A ARG* 5.2 3.3 + - - -
119A ASP* 3.8 28.5 - - + +
120A VAL* 3.6 27.6 - - + -
135A MET* 3.6 17.7 - - + +
374A VAL* 3.2 17.0 + - + +
375A GLY* 2.7 18.0 + - - +
376A CYS 4.0 0.7 - - - +
377A ALA* 1.3 78.1 - - - +
379A ARG* 1.3 70.7 + - - +
380A ASN 3.1 1.0 + - - -
381A ARG* 3.3 15.8 - - - +
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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