Contacts of the helix formed by residues 337 - 354 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A MET* 4.4 3.8 - - + -
72A GLN* 6.3 0.2 - - - +
151A PHE* 3.9 25.1 - + - -
154A LEU* 4.0 26.2 - - + -
155A LEU* 4.0 13.5 - - + -
158A LYS* 3.5 43.3 - - + +
160A LEU* 3.9 22.4 - - + -
332A ALA* 2.7 21.2 + - + +
335A LEU* 3.4 56.3 + - + +
336A GLY* 1.3 76.7 - - - +
338A LYS* 1.3 52.5 + - - +
339A LYS 3.4 2.5 - - - -
340A GLU* 3.1 13.7 + - - +
341A LEU* 2.8 33.8 + - - +
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Residues in contact with LYS 338 (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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329A LEU* 5.1 8.7 - - + +
332A ALA* 3.5 13.2 + - + -
333A GLU* 3.8 46.7 - - + +
336A GLY 3.6 2.8 - - - -
337A TRP* 1.3 75.7 - - - +
339A LYS* 1.3 59.7 + - - +
341A LEU* 3.4 2.3 + - - +
342A GLU* 3.0 66.1 + - + +
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Residues in contact with LYS 339 (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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336A GLY 5.3 1.5 + - - +
337A TRP 3.4 0.2 - - - -
338A LYS* 1.3 76.8 - - - +
340A GLU* 1.3 66.6 + - - +
342A GLU* 3.3 6.6 + - - +
343A ASP* 3.0 59.2 + - - +
346A ARG* 5.2 3.8 - - - +
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Residues in contact with GLU 340 (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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154A LEU* 3.6 21.5 - - + +
157A ASP* 6.0 1.2 - - - +
158A LYS* 2.8 39.0 + - - +
336A GLY 5.5 0.8 + - - +
337A TRP* 3.1 18.3 + - - +
339A LYS* 1.3 79.0 - - - +
341A LEU* 1.3 61.7 + - - +
343A ASP* 3.8 5.7 - - - +
344A LEU* 3.1 24.9 + - - +
347A ARG* 4.9 6.0 + - - +
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Residues in contact with LEU 341 (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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147A ILE* 3.8 28.5 - - + +
150A TYR* 3.7 15.9 - - + +
151A PHE* 3.6 38.1 - - + +
154A LEU* 3.8 15.7 - - + +
328A CYS 4.2 7.0 - - - +
329A LEU* 4.2 12.6 - - + -
332A ALA* 3.7 22.7 - - + -
337A TRP 2.8 20.0 + - - +
338A LYS 3.8 3.8 - - - +
340A GLU* 1.3 74.4 - - - +
342A GLU* 1.3 56.6 + - + +
344A LEU* 3.3 5.0 + - + +
345A VAL* 2.9 37.4 + - + +
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Residues in contact with GLU 342 (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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147A ILE* 6.3 0.9 - - + -
329A LEU* 3.8 30.1 - - + +
338A LYS* 3.0 55.2 + - - +
339A LYS* 4.0 4.4 - - - +
341A LEU* 1.3 71.9 - - - +
343A ASP* 1.3 60.2 + - - +
345A VAL* 3.5 6.5 + - - +
346A ARG* 3.0 52.8 + - - +
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Residues in contact with ASP 343 (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 LYS* 3.0 51.4 + - - +
340A GLU* 3.8 6.0 - - - +
342A GLU* 1.3 72.5 - - - +
344A LEU* 1.3 59.3 + - - +
346A ARG* 2.8 28.8 + - - +
347A ARG* 2.9 50.8 + - - +
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Residues in contact with LEU 344 (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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150A TYR* 3.5 41.3 - - + +
153A ARG* 3.9 31.0 - - + +
154A LEU* 3.7 23.3 - - + -
157A ASP* 5.4 2.0 - - - +
340A GLU 3.1 17.3 + - - +
341A LEU* 3.5 4.5 - - + +
343A ASP* 1.3 73.4 - - - +
345A VAL* 1.3 66.1 + - - +
347A ARG* 3.5 28.1 - - - +
348A GLU* 3.0 47.3 + - + +
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Residues in contact with VAL 345 (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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147A ILE* 4.0 32.3 - - + +
150A TYR* 3.7 33.2 - - + -
341A LEU* 2.9 26.5 + - + +
342A GLU* 3.9 6.7 - - + +
344A LEU* 1.3 73.4 - - - +
346A ARG* 1.3 62.3 + - + +
348A GLU* 3.9 0.2 - - - -
349A HIS* 2.8 64.6 + - + +
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Residues in contact with ARG 346 (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 LYS* 5.2 5.5 - - - +
342A GLU* 3.0 32.7 + - - +
343A ASP* 2.8 35.4 + - - +
345A VAL* 1.3 79.6 - - + +
347A ARG* 1.3 57.5 + - - +
349A HIS* 3.9 4.6 - - - +
350A ALA* 3.0 29.5 + - - +
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Residues in contact with ARG 347 (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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154A LEU* 6.3 0.4 - - - +
340A GLU* 4.9 6.1 + - - +
343A ASP* 2.9 47.8 + - - +
344A LEU* 3.5 35.2 - - - +
346A ARG* 1.3 72.3 - - - +
348A GLU* 1.3 70.6 + - - +
350A ALA* 3.4 7.6 + - - +
351A SER* 3.0 31.5 + - - -
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Residues in contact with GLU 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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150A TYR* 3.4 35.9 + - + +
153A ARG* 4.6 16.3 + - - +
175A ILE 4.8 7.6 - - - +
344A LEU* 3.0 33.7 + - + +
345A VAL 4.0 0.2 - - - +
347A ARG* 1.3 86.9 + - + +
349A HIS* 1.3 60.6 + - - +
351A SER* 3.3 13.0 + - - -
352A ILE* 3.0 37.2 + - - +
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Residues in contact with HIS 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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144A LYS* 3.4 39.4 + - + +
145A PRO 2.8 26.8 + - - -
146A THR* 5.4 2.7 - - - -
147A ILE* 5.7 0.7 - - + -
150A TYR* 3.8 16.8 - + - -
345A VAL* 2.8 41.6 + - + +
346A ARG* 4.0 4.9 - - - +
348A GLU* 1.3 69.5 - - - +
350A ALA* 1.3 58.6 + - - +
352A ILE* 3.2 5.8 + - + +
353A ASP* 2.9 37.9 + - - +
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Residues in contact with ALA 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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346A ARG 3.0 20.2 + - - +
347A ARG* 3.6 8.3 - - - +
349A HIS* 1.3 75.5 - - - +
351A SER* 1.3 56.3 + - - +
353A ASP* 3.3 7.4 + - - +
354A ALA* 2.9 32.0 + - - +
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Residues in contact with SER 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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347A ARG* 3.0 17.4 + - - +
348A GLU* 3.5 19.9 + - - -
350A ALA* 1.3 75.7 - - - +
352A ILE* 1.3 62.1 + - - +
354A ALA* 3.3 14.3 + - - +
355A GLN* 3.3 20.5 + - - +
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Residues in contact with ILE 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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142A GLN* 3.8 25.6 - - + +
143A PHE 3.9 14.1 - - - +
144A LYS* 4.5 11.4 - - + -
145A PRO* 3.7 19.3 - - + -
150A TYR* 3.6 20.2 - - - +
175A ILE* 3.9 16.4 - - + +
348A GLU* 3.0 24.8 + - + +
349A HIS* 3.2 4.7 + - - +
351A SER* 1.3 76.0 - - - +
353A ASP* 1.3 61.5 + - - +
355A GLN* 3.3 41.1 + - - +
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Residues in contact with ASP 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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142A GLN* 2.8 24.0 + - - +
144A LYS* 2.9 27.9 + - - -
349A HIS* 2.9 22.8 + - - +
350A ALA* 3.3 6.9 + - - +
352A ILE* 1.3 75.0 - - - +
354A ALA* 1.3 59.2 + - - +
355A GLN 3.3 6.4 + - - +
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Residues in contact with ALA 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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350A ALA 2.9 17.8 + - - +
351A SER* 3.8 8.1 - - - +
352A ILE 3.3 0.6 - - - -
353A ASP* 1.3 73.9 - - - +
355A GLN* 1.3 62.5 + - - +
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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