Contacts of the helix formed by residues 347 - 356 (chain A) in PDB entry 1YDY
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLY* 3.6 24.2 - - - -
42A TYR* 3.4 33.9 - + - +
135A ARG* 3.6 11.9 - - + -
315A VAL 4.1 1.6 - - - -
316A ARG* 3.9 4.9 - - - -
317A SER* 3.5 37.7 - - - -
318A ASP* 3.5 34.5 - - + -
331A TYR* 3.4 12.6 + - - +
345A THR* 3.2 8.6 + - - +
346A ASP* 1.3 86.4 - - + +
348A PRO* 1.3 68.0 - - - +
349A ASP* 3.3 5.2 - - - -
350A LYS* 2.9 34.1 + - + -
351A ALA 3.4 0.5 + - - -
161B SER 5.7 0.9 - - - -
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Residues in contact with PRO 348 (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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33A VAL* 4.1 4.7 - - + -
35A ALA* 3.7 28.5 - - + -
38A GLY 4.1 0.9 - - - +
39A ALA* 3.8 17.0 - - + -
42A TYR* 4.7 1.1 - - + -
54A ALA* 4.0 4.9 - - + -
57A GLN* 3.5 27.6 - - + +
59A ALA* 4.4 18.8 - - + +
345A THR* 3.9 10.9 - - + +
346A ASP 3.5 7.9 - - - +
347A PHE* 1.3 85.8 - - - +
349A ASP* 1.3 62.4 + - - +
351A ALA* 3.1 4.2 + - - +
352A VAL* 2.9 29.3 + - - +
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Residues in contact with ASP 349 (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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42A TYR* 2.7 36.3 + - - -
57A GLN* 3.5 43.1 + - + +
347A PHE 3.8 2.3 - - - -
348A PRO* 1.3 75.4 - - - +
350A LYS* 1.3 72.0 + - - +
352A VAL* 3.8 1.1 - - - +
353A LYS* 3.0 55.7 + - - +
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Residues in contact with LYS 350 (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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42A TYR* 3.5 17.6 - - - -
317A SER* 2.9 34.0 + - - +
327A VAL* 4.3 12.3 - - + +
328A ASN* 4.4 3.8 - - - +
331A TYR* 3.7 18.3 - - + +
347A PHE* 2.9 27.2 + - + +
349A ASP* 1.3 91.0 + - - +
351A ALA* 1.3 57.5 + - - +
353A LYS* 3.5 7.3 + - + +
354A PHE* 2.9 27.5 + - - +
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Residues in contact with ALA 351 (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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33A VAL* 3.7 27.4 - - + -
331A TYR* 3.5 33.3 + - + +
335A TYR* 4.3 6.7 - - + +
343A LEU* 4.8 0.7 - - + -
345A THR* 4.0 6.3 - - + -
347A PHE 3.4 1.8 + - - -
348A PRO 3.1 6.5 + - - +
350A LYS* 1.3 74.7 - - - +
352A VAL* 1.3 68.0 + - - +
354A PHE* 3.2 4.3 + - - +
355A LEU* 2.9 27.4 + - - +
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Residues in contact with VAL 352 (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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33A VAL* 4.1 17.0 - - + -
57A GLN 3.3 26.0 - - - +
58A GLY* 3.8 24.7 - - - +
59A ALA 4.3 0.7 - - - +
348A PRO 2.9 22.1 + - - +
349A ASP 3.8 3.1 - - - +
351A ALA* 1.3 77.4 - - - +
353A LYS* 1.3 65.9 + - + +
355A LEU* 3.3 6.2 + - - +
356A ASN* 3.1 35.7 + - - +
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Residues in contact with LYS 353 (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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349A ASP* 3.0 47.2 + - - +
350A LYS* 3.8 7.6 - - + +
352A VAL* 1.3 77.9 - - + +
354A PHE* 1.3 63.4 + - - +
356A ASN* 2.9 25.8 + - - +
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Residues in contact with PHE 354 (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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328A ASN* 3.6 43.3 - - + +
331A TYR* 3.7 22.7 - - + -
332A ASP* 3.5 26.7 - - + -
335A TYR* 3.9 26.5 - + + -
336A ASN* 3.7 18.4 - - - -
350A LYS 2.9 18.9 + - - +
351A ALA 3.5 3.8 - - - +
353A LYS* 1.3 77.1 - - - +
355A LEU* 1.3 69.2 + - + +
356A ASN 3.3 8.1 - - - +
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Residues in contact with LEU 355 (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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30A GLU* 4.9 4.3 - - - +
31A LYS* 3.9 40.4 - - + +
33A VAL* 3.8 28.5 - - + -
60A ASP* 5.6 0.4 - - - +
335A TYR* 3.7 37.9 - - + +
336A ASN* 6.2 0.4 - - - +
351A ALA 2.9 14.2 + - - +
352A VAL* 3.3 4.5 + - - +
354A PHE* 1.3 83.8 - - + +
356A ASN* 1.3 67.7 + - - +
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Residues in contact with ASN 356 (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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352A VAL* 3.1 29.5 + - - +
353A LYS* 2.9 19.4 + - - +
354A PHE 3.3 9.0 - - - +
355A LEU* 1.3 86.5 + - - +
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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