Contacts of the helix formed by residues 345 - 356 (chain G) in PDB entry 5YWB
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 345 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269G ASP 5.4 0.9 - - - -
270G LEU 3.5 15.5 - - - -
271G ALA* 4.1 10.3 - - + -
272G PRO* 3.7 20.9 - - + -
311G TRP* 5.1 0.4 - - - -
344G CYS* 1.3 80.3 - - - +
346G ALA* 1.3 54.4 + - - +
347G ARG* 3.5 5.6 + - - +
348G GLN* 2.9 36.0 + - + +
349G LEU* 2.5 37.3 + - - +
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Residues in contact with ALA 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G LEU* 4.1 10.0 - - + +
261G ILE* 3.8 27.8 - - + -
267G LEU* 5.1 1.3 - - + +
268G TYR* 3.1 37.8 - - + +
270G LEU* 3.8 11.0 + - + +
311G TRP* 5.3 2.3 - - + -
344G CYS 3.9 1.0 + - - -
345G THR* 1.3 74.3 - - - +
347G ARG* 1.3 56.4 + - - +
349G LEU* 3.6 8.1 - - - +
350G ASP* 2.9 22.9 + - - +
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Residues in contact with ARG 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G SER* 4.5 7.5 + - - -
268G TYR* 3.3 50.0 + - + +
269G ASP* 3.6 24.2 + - - +
270G LEU 5.0 0.2 + - - -
345G THR* 3.3 5.7 + - - +
346G ALA* 1.3 77.7 - - - +
348G GLN* 1.3 64.5 + - + +
350G ASP* 3.2 3.1 + - - +
351G GLU* 2.9 57.1 + - - +
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Residues in contact with GLN 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G CYS* 3.6 20.2 - - - -
345G THR* 2.9 28.6 + - + +
347G ARG* 1.3 79.7 - - + +
349G LEU* 1.3 56.2 + - - +
351G GLU* 3.3 32.4 + - - +
352G ASP* 2.9 41.1 + - - +
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Residues in contact with LEU 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G LEU* 5.1 5.4 - - + -
194G GLY 4.8 13.7 - - - +
195G ARG* 5.3 6.5 - - - +
196G LEU* 4.2 32.3 - - + +
342G PRO* 5.6 11.7 - - + -
344G CYS* 4.5 12.3 - - + +
345G THR 2.5 23.1 + - - +
346G ALA* 3.6 10.1 - - - +
347G ARG 3.2 0.2 - - - -
348G GLN* 1.3 74.5 - - - +
350G ASP* 1.3 57.9 + - - +
352G ASP* 3.3 12.8 + - + +
353G ARG* 2.9 30.4 + - + +
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Residues in contact with ASP 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G ARG* 4.6 18.0 + - - +
263G SER* 3.6 20.4 + - - -
268G TYR* 3.2 32.5 + - + +
346G ALA 2.9 12.6 + - - +
347G ARG 3.2 0.2 + - - -
349G LEU* 1.3 75.6 - - - +
351G GLU* 1.3 60.8 + - + +
353G ARG* 3.2 10.5 + - - +
354G SER* 2.9 26.5 + - - -
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Residues in contact with GLU 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G TYR* 5.4 0.2 - - - +
347G ARG* 2.9 42.4 + - - +
348G GLN* 3.3 35.3 + - - +
350G ASP* 1.3 76.8 - - + +
352G ASP* 1.3 59.9 + - - +
354G SER* 3.2 10.7 + - - -
355G LEU* 2.9 25.3 + - - +
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Residues in contact with ASP 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G CYS* 4.3 12.3 - - - +
348G GLN* 2.9 30.9 + - - +
349G LEU* 3.7 15.8 - - + +
351G GLU* 1.3 75.7 - - - +
353G ARG* 1.3 54.3 + - - +
355G LEU* 3.0 9.6 + - - +
356G LEU* 2.4 39.9 + - + +
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Residues in contact with ARG 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G GLY 5.8 3.1 - - - +
195G ARG* 5.7 9.0 - - - +
349G LEU* 2.9 22.5 + - + +
350G ASP* 3.2 13.7 + - - +
352G ASP* 1.3 72.5 - - - +
354G SER* 1.3 65.3 + - - +
356G LEU 3.1 28.2 - - - +
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Residues in contact with SER 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G ASP* 2.9 16.0 + - - -
351G GLU* 3.4 13.0 - - - -
353G ARG* 1.3 75.2 - - - +
355G LEU* 1.3 59.0 + - - +
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Residues in contact with LEU 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351G GLU 2.9 13.7 + - - +
352G ASP* 3.1 12.6 - - - +
354G SER* 1.3 75.5 - - - +
356G LEU* 1.3 61.1 + - + +
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Residues in contact with LEU 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G ASP* 2.4 23.1 + - + +
353G ARG* 3.1 29.0 + - - +
355G LEU* 1.3 75.5 - - + +
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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