Contacts of the helix formed by residues 366 - 377 (chain A) in PDB entry 3D14
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 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A GLU* 2.7 39.9 + - - +
364A PHE 3.8 11.2 - - - +
365A VAL* 1.3 78.6 - - - +
367A GLU* 1.3 59.7 + - - +
368A GLY 4.0 1.3 + - - -
369A ALA* 3.3 6.7 + - - +
370A ARG* 3.0 27.6 + - - +
395A TRP* 3.5 13.2 + - - -
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Residues in contact with GLU 367 (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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365A VAL 4.9 0.5 - - - +
366A THR* 1.3 73.8 - - - +
368A GLY* 1.3 57.6 + - - +
370A ARG* 3.5 35.8 + - - +
371A ASP* 3.0 29.0 + - - +
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Residues in contact with GLY 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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366A THR* 3.3 3.0 + - - -
367A GLU* 1.3 76.0 - - - +
369A ALA* 1.3 63.5 + - - +
371A ASP* 3.4 4.6 + - - +
372A LEU* 3.2 18.2 + - - +
393A HIS* 3.4 13.8 + - - -
395A TRP* 3.7 24.2 - - - +
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Residues in contact with ALA 369 (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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243A GLU* 4.2 1.3 - - - +
332A CYS* 5.6 0.4 - - - -
336A LEU* 3.6 30.5 - - + -
365A VAL* 3.8 8.1 - - + -
366A THR* 3.3 17.9 + - - +
368A GLY* 1.3 71.7 - - - +
370A ARG* 1.3 67.0 + - - +
371A ASP 3.3 0.3 + - - -
372A LEU* 3.3 3.2 + - - +
373A ILE* 3.0 30.6 + - + +
395A TRP* 3.5 27.1 - - + -
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Residues in contact with ARG 370 (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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361A PHE* 3.6 55.8 + - + +
362A PRO 3.0 24.9 + - - -
363A ASP* 3.5 14.5 + - - +
365A VAL* 2.8 26.1 + - + +
366A THR 3.0 12.1 + - - +
367A GLU* 3.6 38.9 + - - +
369A ALA* 1.3 77.5 - - - +
371A ASP* 1.3 56.2 + - - +
374A SER* 2.9 36.6 + - - +
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Residues in contact with ASP 371 (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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367A GLU 3.0 16.6 + - - +
368A GLY* 3.5 8.3 - - - +
369A ALA 3.2 0.2 - - - -
370A ARG* 1.3 74.1 - - - +
372A LEU* 1.3 65.7 + - - +
374A SER* 3.9 3.8 - - - -
375A ARG* 2.8 72.1 + - - +
393A HIS* 2.9 25.4 - - + +
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Residues in contact with LEU 372 (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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250A ILE* 4.7 5.8 - - + -
332A CYS* 4.0 18.4 - - + -
368A GLY 3.2 11.2 + - - +
369A ALA 3.8 6.3 - - - +
371A ASP* 1.3 78.4 - - - +
373A ILE* 1.3 62.8 + - - +
375A ARG* 3.3 5.0 + - - +
376A LEU* 3.2 42.9 + - + +
385A LEU* 3.9 17.9 - - + +
390A VAL* 4.2 13.5 - - + -
393A HIS* 3.6 29.1 - - + +
395A TRP* 3.9 12.6 - - + -
396A ILE* 3.7 32.3 - - + -
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Residues in contact with ILE 373 (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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329A GLY 4.0 8.3 - - - +
332A CYS* 3.9 30.7 - - + -
333A TYR* 3.8 27.8 - - + +
336A LEU* 4.3 9.9 - - + -
337A VAL* 6.4 0.2 - - + -
359A PHE* 4.2 4.3 - - + -
361A PHE* 3.8 32.5 - - + -
365A VAL* 4.8 1.8 - - + -
369A ALA* 3.0 24.5 + - + +
372A LEU* 1.3 76.6 - - - +
374A SER* 1.3 57.7 + - - +
376A LEU* 3.1 7.6 + - - +
377A LEU* 2.9 51.7 + - + +
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Residues in contact with SER 374 (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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359A PHE* 4.6 8.9 - - - -
361A PHE* 3.7 18.0 - - - -
370A ARG* 2.9 22.5 + - - +
371A ASP* 4.0 4.3 - - - -
373A ILE* 1.3 77.2 - - - +
375A ARG* 1.3 61.8 + - - +
376A LEU 3.6 0.3 + - - -
377A LEU* 3.8 8.3 + - - +
378A LYS* 3.6 21.0 + - - +
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Residues in contact with ARG 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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371A ASP* 2.8 54.2 + - - +
372A LEU 3.8 0.9 - - - +
373A ILE 3.2 0.4 - - - -
374A SER* 1.3 77.5 - - - +
376A LEU* 1.3 58.5 + - - +
378A LYS* 3.8 19.4 - - - +
383A GLN 4.3 1.7 - - - +
384A ARG* 3.6 8.0 - - - -
385A LEU* 3.2 56.9 + - + +
393A HIS* 5.0 2.2 - - - -
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Residues in contact with LEU 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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250A ILE* 6.1 0.4 - - + -
325A LEU* 3.4 33.9 - - + +
326A TRP* 3.9 8.0 + - - -
328A LEU* 4.4 9.6 - - + +
329A GLY* 3.8 25.6 - - - +
332A CYS* 5.5 2.2 - - + -
372A LEU* 3.2 39.0 + - + +
373A ILE* 3.1 5.3 + - - +
375A ARG* 1.3 78.4 - - - +
377A LEU* 1.3 58.0 + - - +
378A LYS 3.1 10.4 + - - -
384A ARG* 3.3 23.1 + - - +
385A LEU* 3.6 30.3 - - + +
390A VAL* 3.8 16.6 - - + -
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Residues in contact with LEU 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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326A TRP* 3.4 53.8 - - + +
329A GLY* 4.0 7.0 - - - -
330A VAL* 3.7 15.0 - - + +
341A PRO* 4.1 22.7 - - + -
342A PHE* 4.2 4.7 - - + -
357A VAL* 3.2 19.4 - - + +
359A PHE* 3.8 25.8 - - + -
373A ILE* 2.9 38.4 + - + +
374A SER* 3.8 7.9 + - - +
376A LEU* 1.3 74.1 - - - +
378A LYS* 1.3 61.2 + - - +
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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