Contacts of the helix formed by residues 377 - 389 (chain A) in PDB entry 4P8V
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 TYR 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.4 18.5 - - - -
50A ASN 2.7 29.5 + - - -
51A ILE* 4.0 4.8 - - - -
52A ASP* 4.6 13.2 - - + -
55A LEU* 3.8 27.4 - - + -
362A ILE* 3.5 32.5 - - + +
365A ASP* 3.1 24.0 - - + +
366A ASP 3.0 12.6 + - - -
367A PHE* 3.4 33.7 - - + +
376A PRO* 1.3 80.8 - - + +
378A PRO* 1.3 63.9 - - - +
380A VAL* 4.3 7.0 - - + -
381A GLN* 2.8 35.3 + - + +
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Residues in contact with PRO 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 3.9 21.1 - - + -
339A VAL* 4.1 7.1 - - + +
365A ASP* 3.2 13.9 - - - +
366A ASP* 3.4 16.8 - - + +
372A CYS* 4.5 7.4 - - + -
374A GLN* 4.0 36.8 - - + +
375A GLY 3.3 12.1 - - - +
376A PRO 3.4 2.4 - - - +
377A TYR* 1.3 89.0 - - - +
379A LEU* 1.3 61.2 + - - +
381A GLN* 4.3 3.2 - - + +
382A ALA* 3.2 22.7 + - - +
385A ARG* 5.4 0.7 + - - -
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Residues in contact with LEU 379 (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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267A PRO 4.7 2.2 - - - +
268A THR* 3.9 28.3 - - + -
304A TYR* 3.5 47.8 - - + +
337A ASP 3.8 8.1 - - - +
338A ASP* 3.5 38.1 - - - +
339A VAL* 3.7 7.9 - - + +
342A MET* 3.5 18.6 - - + +
365A ASP* 3.2 14.5 + - - +
378A PRO* 1.3 73.9 - - - +
380A VAL* 1.3 61.8 + - - +
382A ALA* 3.1 5.9 + - - +
383A VAL* 3.0 29.8 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.1 16.4 - - + -
31A CYS* 4.3 3.8 - - - -
55A LEU* 3.7 35.0 - - + -
56A CYS* 4.3 7.2 - - - -
268A THR* 4.6 2.5 - - + -
359A ILE* 4.1 22.2 - - + -
362A ILE* 4.0 20.6 - - + -
365A ASP* 2.9 27.4 + - + +
377A TYR* 4.3 4.0 - - + -
379A LEU* 1.3 76.2 - - - +
381A GLN* 1.3 58.2 + - - +
383A VAL* 3.2 7.2 + - - +
384A LYS* 2.9 26.2 + - - +
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.9 13.5 + - - -
55A LEU* 3.4 25.0 - - + +
376A PRO 3.7 13.4 + - - +
377A TYR* 2.8 24.5 + - + +
378A PRO* 4.3 3.8 - - + +
380A VAL* 1.3 77.6 - - - +
382A ALA* 1.3 55.8 + - - +
384A LYS* 3.3 21.4 + - - +
385A ARG* 2.8 52.8 + - - +
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Residues in contact with ALA 382 (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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339A VAL* 3.8 27.4 - - + +
342A MET* 4.1 13.0 - - + -
343A GLU* 5.5 0.9 - - + +
378A PRO 3.2 18.9 + - - +
379A LEU 3.1 6.1 + - - +
381A GLN* 1.3 75.1 - - - +
383A VAL* 1.3 57.9 + - - +
385A ARG* 3.8 17.7 - - - +
386A SER* 2.7 37.7 + - - +
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Residues in contact with VAL 383 (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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29A LEU* 3.8 24.5 - - + -
266A ILE* 4.2 7.0 - - + -
342A MET* 3.5 29.4 - - + -
346A VAL* 3.9 15.5 - - + -
357A ALA* 3.8 20.2 - - + -
359A ILE* 4.1 15.7 - - + -
379A LEU 3.0 18.7 + - - +
380A VAL* 3.5 8.1 - - - +
382A ALA* 1.3 76.4 - - - +
384A LYS* 1.3 57.1 + - - +
386A SER* 3.3 1.7 + - - -
387A LEU* 2.8 33.2 + - + +
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Residues in contact with LYS 384 (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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29A LEU* 3.8 17.4 - - + +
52A ASP* 5.7 0.8 + - - -
54A PHE* 3.0 31.5 + - - +
55A LEU* 3.5 21.4 - - + +
380A VAL 2.9 15.9 + - - +
381A GLN* 3.3 23.5 + - - +
383A VAL* 1.3 75.3 - - - +
385A ARG* 1.3 58.7 + - - +
387A LEU* 3.2 6.4 + - - +
388A GLY* 2.9 26.9 + - - -
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Residues in contact with ARG 385 (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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339A VAL* 6.0 0.8 - - - +
378A PRO 5.4 0.4 + - - -
381A GLN* 2.8 40.5 + - - +
382A ALA* 3.8 29.8 - - - +
384A LYS* 1.3 74.3 - - - +
386A SER* 1.3 59.7 + - - +
388A GLY* 3.3 1.5 + - - -
389A SER* 3.0 31.6 + - - -
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Residues in contact with SER 386 (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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343A GLU* 3.8 24.7 + - - +
346A VAL* 3.5 26.5 - - - +
350A LYS* 3.0 18.7 + - - -
382A ALA* 2.7 23.0 + - - +
383A VAL 3.8 1.8 - - - -
385A ARG* 1.3 78.4 - - - +
387A LEU* 1.3 61.5 + - - +
388A GLY 3.4 0.3 + - - -
389A SER* 3.5 12.4 + - - -
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Residues in contact with LEU 387 (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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27A TYR* 3.8 43.2 - - + +
28A LYS 3.9 20.0 - - - +
29A LEU* 4.1 16.2 - - + -
346A VAL* 3.8 16.4 - - + -
349A LEU* 4.0 22.0 - - + -
350A LYS* 3.2 20.5 + - - +
356A GLY* 4.9 1.3 - - - -
357A ALA* 4.5 3.4 - - + -
383A VAL* 2.8 38.1 + - + +
384A LYS* 3.6 4.3 - - - +
386A SER* 1.3 75.5 - - - +
388A GLY* 1.3 59.5 + - - +
389A SER 4.1 0.2 - - - +
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Residues in contact with GLY 388 (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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384A LYS 2.9 15.5 + - - -
385A ARG* 3.8 2.2 - - - -
387A LEU* 1.3 76.4 - - - +
389A SER* 1.3 62.4 + - - +
390A LEU* 3.5 11.8 + - - +
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Residues in contact with SER 389 (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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350A LYS* 2.8 28.8 + - - -
385A ARG* 3.0 18.1 + - - -
386A SER* 3.7 10.3 - - - -
387A LEU 3.3 1.2 - - - +
388A GLY* 1.3 75.5 - - - +
390A LEU* 1.3 72.3 + - - +
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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