Contacts of the helix formed by residues 337 - 354 (chain B) in PDB entry 4Y6O
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 TRP 337 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B MET* 4.8 0.2 - - + -
151B PHE* 4.0 12.3 - + - -
154B LEU* 3.7 31.2 - - + -
155B LEU* 3.8 19.1 - - + -
158B LYS* 3.6 39.8 - - + +
160B LEU* 3.6 29.2 - - + -
332B ALA* 2.8 15.1 + - + +
335B LEU* 3.4 51.9 + - + -
336B GLY* 1.3 80.8 - - - +
338B LYS* 1.3 57.0 + - - +
339B LYS 3.4 2.5 - - - -
340B GLU* 3.3 15.8 + - + +
341B LEU* 2.8 30.7 + - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 3.9 35.9 - - + +
332B ALA* 3.6 9.7 + - + -
333B GLU* 3.3 48.8 + - + +
336B GLY 3.6 2.8 - - - -
337B TRP* 1.3 76.6 - - - +
339B LYS* 1.3 57.5 + - - +
341B LEU* 3.4 3.1 + - - +
342B GLU* 3.0 56.2 + - - +
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLY 5.3 0.8 + - - -
337B TRP 3.4 0.4 - - - -
338B LYS* 1.3 77.8 - - - +
340B GLU* 1.3 58.9 + - + +
342B GLU* 3.4 10.5 + - + +
343B ASP* 2.9 34.2 + - + +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 4.5 3.6 - - - +
154B LEU* 4.4 12.9 - - + +
158B LYS* 2.8 36.6 + - - -
336B GLY 4.6 8.2 + - - +
337B TRP* 3.3 20.2 + - - +
339B LYS* 1.3 79.3 - - + +
341B LEU* 1.3 55.9 + - - +
343B ASP* 3.5 5.1 + - - +
344B LEU* 2.9 30.1 + - - +
347B ARG* 5.0 1.2 + - - -
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.8 29.6 - - + +
150B TYR* 3.7 15.7 - - + +
151B PHE* 3.7 40.2 - - + +
154B LEU* 4.1 14.5 - - + +
328B CYS 4.2 4.5 - - - +
329B LEU* 4.3 10.3 - - + -
332B ALA* 3.7 23.1 - - + -
337B TRP 2.8 21.4 + - - +
338B LYS 3.7 3.6 - - - +
340B GLU* 1.3 71.1 - - - +
342B GLU* 1.3 59.9 + - + +
344B LEU* 3.3 5.9 + - + +
345B VAL* 3.0 36.4 + - + +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 6.1 2.7 - - + -
329B LEU* 3.9 18.7 - - + +
338B LYS* 3.0 53.1 + - - +
339B LYS* 3.9 9.3 - - + +
341B LEU* 1.3 76.3 - - - +
343B ASP* 1.3 56.8 + - - +
345B VAL* 3.5 6.8 + - - +
346B ARG* 3.0 30.6 + - - +
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LYS* 2.9 21.1 + - + +
340B GLU* 3.8 6.7 - - - +
342B GLU* 1.3 75.1 - - - +
344B LEU* 1.3 59.5 + - - +
346B ARG* 2.7 43.5 + - - +
347B ARG* 3.0 58.5 + - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR* 3.6 35.9 - - + +
153B ARG* 3.8 37.0 - - + +
154B LEU* 4.3 20.0 - - + +
157B ASP* 5.0 3.1 - - - +
340B GLU 2.9 17.4 + - - +
341B LEU* 3.3 6.3 + - + +
343B ASP* 1.3 74.2 - - - +
345B VAL* 1.3 61.0 + - - +
347B ARG* 3.4 24.4 + - - +
348B GLU* 2.9 51.8 + - + +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 4.2 29.4 - - + +
150B TYR* 3.7 33.9 - - + -
341B LEU* 3.0 25.4 + - + +
342B GLU* 3.8 7.0 - - - +
344B LEU* 1.3 73.3 - - - +
346B ARG* 1.3 59.4 + - - +
349B HIS* 2.8 67.9 + - + +
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Residues in contact with ARG 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLU 3.0 19.4 + - - +
343B ASP* 2.7 40.0 + - - +
344B LEU 3.3 0.2 - - - -
345B VAL* 1.3 78.6 - - - +
347B ARG* 1.3 69.8 + - - +
349B HIS* 3.9 4.4 - - - +
350B ALA* 3.0 31.2 + - + +
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A CYS 3.8 20.8 + - - -
201A ARG* 4.8 14.1 + - - +
153B ARG* 5.8 1.6 - - - +
340B GLU 5.0 0.8 + - - -
343B ASP* 3.0 36.5 + - - +
344B LEU* 3.6 37.7 - - - +
346B ARG* 1.3 91.9 - - - +
348B GLU* 1.3 66.9 + - - +
350B ALA* 3.3 7.5 + - - +
351B SER* 3.0 31.2 + - - -
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A CYS 5.8 0.2 - - - +
223A ASP* 5.7 0.2 - - - +
150B TYR* 3.3 34.8 + - + +
153B ARG* 2.8 33.1 + - - -
175B ILE 4.9 3.3 - - - +
176B ALA 4.1 4.2 - - - +
344B LEU* 2.9 33.6 + - + +
345B VAL 4.1 0.4 - - - +
347B ARG* 1.3 81.7 + - + +
349B HIS* 1.3 64.5 + - - +
351B SER* 3.4 12.5 + - - -
352B ILE* 3.1 27.8 + - + +
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Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LYS* 3.6 39.7 + - + +
145B PRO 2.8 25.6 + - - -
146B THR* 5.5 2.0 - - - -
147B ILE 5.9 0.2 - - - -
150B TYR* 3.7 19.7 - + - -
345B VAL* 2.8 42.2 + - + +
346B ARG* 3.9 4.5 - - - +
348B GLU* 1.3 71.8 - - - +
350B ALA* 1.3 57.7 + - - +
352B ILE* 3.3 3.7 + - + +
353B ASP* 2.9 37.4 + - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ARG* 3.0 19.2 + - + +
347B ARG* 3.4 9.2 - - - +
349B HIS* 1.3 77.0 - - - +
351B SER* 1.3 56.5 + - - +
353B ASP* 3.4 8.0 + - - +
354B ALA* 3.0 28.9 + - - +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A SER 5.0 7.1 + - - -
347B ARG 3.0 13.8 + - - -
348B GLU* 3.7 17.3 + - - -
349B HIS 3.3 0.2 - - - -
350B ALA* 1.3 72.5 - - - +
352B ILE* 1.3 66.4 + - - +
354B ALA* 3.4 14.5 + - - +
355B GLN* 3.4 18.8 + - - +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLN* 3.7 15.8 + - + +
143B PHE 4.0 9.2 - - - +
144B LYS* 3.7 25.4 - - + -
145B PRO* 3.7 19.7 - - + -
150B TYR* 3.5 20.9 - - - +
175B ILE* 3.8 18.4 - - + +
348B GLU* 3.1 18.0 + - + +
349B HIS* 3.7 6.7 - - + +
351B SER* 1.3 76.9 - - - +
353B ASP* 1.3 61.6 + - - +
355B GLN* 3.0 37.2 + - - +
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Residues in contact with ASP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLN* 2.8 32.7 + - - +
144B LYS* 3.0 27.5 + - - +
349B HIS* 2.9 22.3 + - - +
350B ALA* 3.4 8.1 + - - +
352B ILE* 1.3 76.1 - - - +
354B ALA* 1.3 59.7 + - - +
355B GLN 3.4 4.7 + - - -
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ALA 3.0 18.0 + - - +
351B SER* 3.6 10.3 - - - +
352B ILE 3.1 0.4 - - - -
353B ASP* 1.3 76.1 - - - +
355B GLN* 1.3 58.9 + - - +
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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
------------------------------------------------------------
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