Contacts of the helix formed by residues 364 - 374 (chain A) in PDB entry 4YC4
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 PHE 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ASP* 3.6 26.2 - - + -
302A TYR* 4.1 26.9 - + - -
305A ARG* 3.3 39.3 - - - -
306A ASN* 3.5 23.1 - - + -
309A ARG* 5.4 2.9 - - + -
363A PRO* 1.3 74.6 - - - +
365A TYR* 1.3 65.5 + - - +
366A TRP* 3.2 40.4 - + + +
367A ALA* 3.1 7.5 + - + +
426A GLN* 4.2 1.6 - - - -
444A VAL* 3.8 18.4 - - + -
1202A ADP 2.7 40.3 + + - +
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Residues in contact with TYR 365 (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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309A ARG 3.3 25.5 + - - +
310A GLY* 4.3 11.2 - - - -
311A ASN* 5.4 4.0 - - - +
363A PRO* 3.7 8.4 + - + -
364A PHE* 1.3 73.3 - - - +
366A TRP* 1.3 60.8 + - - +
367A ALA 2.7 7.3 + - - -
368A TRP* 3.0 33.2 + - + +
369A LEU* 4.3 1.9 + - - +
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 3.7 25.1 - + + -
297A LEU* 4.3 10.1 - - + -
298A VAL* 3.5 54.8 - - + +
301A ASP* 2.8 34.1 + - + +
302A TYR* 4.7 4.0 - + - -
309A ARG* 3.6 18.7 - - + +
311A ASN* 5.1 4.4 + - - +
314A TRP* 5.4 2.2 - - - +
364A PHE* 3.5 30.2 - + + -
365A TYR* 1.3 80.3 - - - +
367A ALA* 1.3 79.7 + - + +
368A TRP 3.2 0.4 - - - -
369A LEU* 3.0 38.0 + - + +
372A ALA* 3.3 9.0 - - - +
440A PRO* 4.1 11.7 - - + -
444A VAL* 3.7 30.5 - - + -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE* 3.1 18.0 + - + +
365A TYR 2.7 5.5 + - - -
366A TRP* 1.3 88.1 - - + +
368A TRP* 1.3 55.7 + - - +
369A LEU 3.3 1.9 - - - +
372A ALA* 3.5 18.1 - - - +
373A LYS* 6.2 0.2 - - - +
441A LEU* 3.8 19.8 - - + +
444A VAL* 3.9 24.2 - - + -
1202A ADP 3.4 20.4 - - + +
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Residues in contact with TRP 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TRP* 4.1 16.2 - + - -
360A ARG* 5.8 2.9 - - + -
363A PRO* 3.8 27.4 - - + -
364A PHE 4.1 1.8 - - - -
365A TYR* 3.0 27.6 + - + +
367A ALA* 1.3 76.6 - - - +
369A LEU* 1.3 63.0 + - - +
370A PRO* 4.0 2.6 - - - +
441A LEU* 6.5 0.7 - - + -
1202A ADP 3.6 41.4 + - - -
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Residues in contact with LEU 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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274A LEU* 4.1 14.8 - - + -
294A PHE* 4.1 9.0 - - + -
311A ASN* 3.8 34.5 - - - +
314A TRP* 4.0 17.5 - - + -
365A TYR 4.3 1.1 + - - +
366A TRP* 3.0 32.0 + - + +
367A ALA 3.9 1.4 - - - +
368A TRP* 1.3 82.9 - - - +
370A PRO* 1.3 80.2 - - + +
371A GLN* 3.6 13.7 - - - +
372A ALA* 3.0 19.2 + - - +
373A LYS* 4.1 4.3 + - - +
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Residues in contact with PRO 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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278A GLU* 5.2 10.3 - - + +
368A TRP 4.3 2.7 - - - +
369A LEU* 1.3 93.7 - - + +
371A GLN* 1.3 73.3 + - - +
373A LYS* 2.8 45.3 + - + +
374A VAL* 4.2 3.8 + - - +
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Residues in contact with GLN 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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274A LEU* 3.8 28.4 - - - +
277A PHE* 6.1 0.2 - - - -
287A ASN* 5.6 2.7 + - - +
290A LEU* 4.5 11.8 - - + +
291A LEU* 3.5 29.4 - - + +
294A PHE* 3.8 32.3 - - + -
314A TRP* 6.6 0.2 - - - -
369A LEU* 3.2 12.6 - - - +
370A PRO* 1.3 95.7 - - - +
372A ALA* 1.3 61.4 + - - +
373A LYS 3.0 1.4 + - - -
374A VAL* 3.2 26.3 + - - +
440A PRO* 4.6 1.7 - - - +
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Residues in contact with ALA 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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294A PHE* 3.8 12.1 - - + -
366A TRP* 3.3 21.5 - - + +
367A ALA* 3.5 19.1 - - - +
369A LEU 3.0 14.2 + - - +
370A PRO 3.0 0.8 - - - -
371A GLN* 1.3 78.6 - - - +
373A LYS* 1.3 56.5 + - + +
374A VAL 3.3 0.4 - - - -
439A SER* 3.2 9.4 - - - -
440A PRO* 3.4 11.4 - - + -
441A LEU* 2.9 36.0 + - + +
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Residues in contact with LYS 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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367A ALA 6.2 0.2 - - - +
369A LEU 4.9 2.2 - - - +
370A PRO* 2.8 29.9 + - + +
372A ALA* 1.3 81.0 - - + +
374A VAL* 1.3 58.1 + - + +
375A PRO* 3.7 4.3 - - - +
439A SER* 3.3 16.6 + - - -
441A LEU* 4.3 22.2 - - + -
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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
----------------------------------------------------------
291A LEU* 4.3 29.2 - - + -
295A GLU* 5.2 6.6 - - - +
370A PRO 4.5 4.3 - - - +
371A GLN* 3.2 19.8 + - - +
373A LYS* 1.3 79.2 - - + +
375A PRO* 1.3 85.7 - - + +
439A SER* 3.9 0.7 - - - -
440A PRO* 3.0 22.3 - - - +
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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