Contacts of the helix formed by residues 337 - 349 (chain A) in PDB entry 5CQD
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ILE 3.9 7.9 - - - +
336A MET* 1.3 74.8 - - - +
338A TYR* 1.3 67.5 + - - +
339A ASP* 3.4 13.6 + - - +
340A GLU* 2.6 38.4 + - - +
341A PHE* 3.0 19.1 + - - -
366A SER* 3.5 19.5 - - - +
370A SER* 6.3 2.5 - - - -
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Residues in contact with TYR 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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337A THR* 1.3 73.9 - - - +
339A ASP* 1.3 63.1 + - - +
341A PHE* 3.4 3.3 + - - +
342A GLU* 2.9 47.5 + - + +
356A PHE* 3.7 16.4 + + - -
358A PRO* 3.2 45.7 - - + +
362A LEU* 3.5 33.5 - - + +
363A GLU* 5.5 14.3 - - + +
366A SER* 5.3 0.2 - - - -
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Residues in contact with ASP 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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337A THR* 3.0 12.2 + - - +
338A TYR* 1.3 81.4 - - - +
340A GLU* 1.3 68.2 + - - +
342A GLU* 4.0 4.1 - - - +
343A TYR* 3.1 28.1 + - - +
505A GOL 5.5 2.4 + - - -
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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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278A PHE* 4.0 10.1 - - + -
308A LYS* 3.5 42.6 + - + +
335A ILE 4.2 2.5 - - - +
336A MET* 3.7 25.6 - - + -
337A THR* 2.6 49.1 + - - +
339A ASP* 1.3 88.7 - - - +
341A PHE* 1.3 65.8 + - - +
343A TYR* 3.2 7.5 + - - +
344A CYS* 3.0 27.5 + - - -
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Residues in contact with PHE 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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198A PHE* 3.6 11.8 - + + -
202A PHE* 3.1 34.5 - + + -
204A ASN* 3.8 22.0 - - - -
310A ALA* 3.8 14.6 - - + -
336A MET* 3.5 51.1 - - + -
337A THR 3.0 25.5 + - - -
338A TYR 3.8 3.6 - - - +
340A GLU* 1.3 74.8 - - - +
342A GLU* 1.3 58.0 + - - +
344A CYS 3.3 0.9 + - - -
345A TRP* 3.0 27.5 + - - +
356A PHE* 3.7 20.6 - - + -
359A TRP* 3.4 19.7 - + + -
362A LEU* 3.7 18.6 - - + -
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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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338A TYR* 2.9 38.0 + - - +
339A ASP* 4.0 4.4 - - - +
341A PHE* 1.3 74.2 - - - +
343A TYR* 1.3 62.0 + - - +
345A TRP* 3.6 1.1 - - - +
346A ASP* 3.0 38.8 + - - +
355A PRO* 5.4 3.3 - - - +
356A PHE* 3.9 38.1 + - + +
505A GOL 2.9 41.3 + - - +
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Residues in contact with TYR 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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219A GLU* 2.6 33.8 + - - -
230A LYS* 3.7 16.6 + - - +
235A MET* 4.1 8.0 - - - +
278A PHE* 3.7 33.0 - + - -
339A ASP* 3.1 20.8 + - - +
340A GLU* 3.2 5.8 + - - +
342A GLU* 1.3 78.3 - - - +
344A CYS* 1.3 57.6 + - - +
346A ASP* 3.3 5.8 + - + -
347A THR* 2.6 59.4 + - + +
348A PHE* 4.5 1.6 - + - -
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Residues in contact with CYS 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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198A PHE* 3.6 21.1 - - + -
202A PHE* 5.1 0.9 - - - -
217A CYS* 4.8 4.5 - - - -
278A PHE* 3.2 51.4 - - - -
336A MET* 4.1 6.5 - - - -
340A GLU 3.0 19.4 + - - +
341A PHE* 3.8 1.8 - - - +
343A TYR* 1.3 74.5 - - - +
345A TRP* 1.3 61.5 + - - +
348A PHE* 2.8 48.9 + - + +
349A VAL* 3.7 4.7 - - - +
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Residues in contact with TRP 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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195A PRO* 3.6 42.8 - - + -
198A PHE* 3.5 26.5 - + + -
199A THR* 4.2 8.3 - - - -
341A PHE 3.0 16.7 + - - +
342A GLU 3.6 4.0 - - - +
344A CYS* 1.3 78.2 - - - +
346A ASP* 1.3 68.2 + - - +
347A THR 3.4 0.3 + - - -
349A VAL* 3.4 35.3 + - + +
351A ARG* 3.4 38.9 - - + +
354A CYS* 2.7 34.4 + - + -
355A PRO 4.2 6.5 - - - -
356A PHE* 3.3 43.5 - + + +
357A GLN* 5.2 4.9 - - + -
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Residues in contact with ASP 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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342A GLU* 3.0 29.7 + - - +
343A TYR* 3.8 7.8 - - + +
345A TRP* 1.3 87.9 - - - +
347A THR* 1.3 60.3 + - - +
349A VAL 5.1 1.6 - - - +
351A ARG* 3.4 40.4 + - - +
355A PRO* 5.1 0.7 - - - +
356A PHE 4.7 2.8 + - - -
505A GOL 2.9 28.5 + - - -
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Residues in contact with THR 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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188A ILE* 4.3 9.1 - - + +
192A LEU* 3.8 12.9 - - - +
235A MET* 3.3 33.7 - - + -
343A TYR* 2.6 45.8 + - + +
346A ASP* 1.3 82.0 - - - +
348A PHE* 1.3 77.7 + - + +
349A VAL 3.7 1.3 - - - -
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.7 20.4 - - + -
192A LEU* 3.8 7.9 - - - +
193A MET* 2.9 30.6 + - + +
217A CYS* 3.7 36.6 - - + -
218A TYR 3.5 21.8 - - - -
219A GLU* 4.5 2.7 - - - -
235A MET* 4.3 12.1 - - + -
236A GLY 3.5 28.3 - - - -
237A PHE* 4.3 5.3 - + + -
278A PHE* 3.9 22.7 - + - -
343A TYR* 4.5 2.2 - + - -
344A CYS* 2.8 30.9 + - + +
347A THR* 1.3 94.2 - - + +
349A VAL* 1.3 61.4 + - + +
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Residues in contact with VAL 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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192A LEU* 3.8 13.2 - - - +
193A MET* 3.3 16.6 - - + +
194A ASP 4.1 0.2 - - - -
195A PRO* 3.6 28.7 - - + -
198A PHE* 3.7 33.0 - - + -
344A CYS 3.7 13.0 - - - +
345A TRP* 3.4 33.8 + - + +
346A ASP 5.3 1.2 - - - +
347A THR 3.7 1.4 - - - -
348A PHE* 1.3 83.5 - - + +
350A TYR* 1.3 68.6 + - - +
351A ARG* 2.9 14.2 + - + +
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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