Contacts of the helix formed by residues 330 - 348 (chain A) in PDB entry 5IXC
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 GLY 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLY* 1.3 73.2 - - - -
331A GLY* 1.3 69.6 + - - +
332A ALA 3.4 0.2 + - - -
333A ARG* 3.2 38.2 + - - +
334A ALA* 3.2 8.6 + - - -
674A TYR* 5.1 0.2 - - - -
768A LEU* 3.6 20.4 - - - +
901A 7FA 2.9 9.0 + - - -
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Residues in contact with GLY 331 (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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330A GLY* 1.3 75.5 - - - +
332A ALA* 1.3 62.1 + - - -
335A MET* 3.2 18.2 + - - +
362A GLY* 3.4 16.9 - - - -
365A TRP* 3.7 11.7 - - - -
768A LEU* 3.5 6.1 - - - +
901A 7FA 2.9 34.4 + - - -
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLY 3.4 0.4 + - - -
331A GLY* 1.3 69.8 - - - -
333A ARG* 1.3 63.7 + - - +
335A MET* 3.2 7.9 + - + +
336A THR* 2.9 32.4 + - - +
365A TRP* 3.7 8.0 - - - -
392A LEU* 4.2 12.8 - - + -
767A THR 6.0 0.2 - - - +
768A LEU* 5.2 2.6 + - - +
770A ASN 3.7 22.9 + - - +
771A MET* 4.0 18.9 - - + +
773A TYR* 3.5 17.7 - - + +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLY* 3.2 22.6 + - - +
332A ALA* 1.3 73.2 - - - +
334A ALA* 1.3 66.3 + - - +
337A SER* 3.0 28.8 + - - -
674A TYR* 2.4 40.8 + - + +
675A SER* 3.9 5.5 - - - +
676A LEU* 3.4 29.0 - - - +
732A LEU* 3.4 24.9 - - + -
766A TYR* 2.9 28.4 + - + +
767A THR 5.6 1.2 + - - +
768A LEU* 3.7 30.9 - - - +
773A TYR* 3.1 19.6 + - - +
781A LEU* 3.9 15.2 - - + +
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Residues in contact with ALA 334 (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 THR 4.1 0.4 - - - +
329A GLY 3.6 24.9 - - - +
330A GLY 3.2 3.5 + - - +
331A GLY 3.7 8.1 - - - +
333A ARG* 1.3 81.3 - - - +
335A MET* 1.3 64.4 + - - +
337A SER* 4.1 0.2 - - - -
338A LEU* 2.9 28.6 + - - +
362A GLY 4.8 0.9 - - - -
363A SER* 4.0 14.4 - - - +
674A TYR* 3.6 33.2 - - + -
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Residues in contact with MET 335 (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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331A GLY 3.2 11.0 + - - +
332A ALA* 3.2 11.6 + - - +
334A ALA* 1.3 81.2 - - - +
336A THR* 1.3 64.4 + - + +
339A TYR* 3.2 31.2 + - + -
362A GLY 3.8 10.5 + - - +
365A TRP* 3.9 25.8 - - + -
366A THR* 2.7 37.9 + - - +
388A ALA* 4.8 14.4 - - + +
392A LEU* 3.7 38.4 - - + -
436A LEU* 4.1 17.0 - - + -
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Residues in contact with THR 336 (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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332A ALA 2.9 17.9 + - - +
333A ARG 4.6 0.2 - - - +
335A MET* 1.3 75.8 - - + +
337A SER* 1.3 68.2 + - - +
339A TYR* 3.1 23.0 + - - +
340A GLY 3.1 9.2 + - - -
392A LEU* 3.6 28.0 - - + -
773A TYR* 3.8 11.5 - - + -
778A PHE* 3.6 28.7 + - + -
781A LEU* 3.3 25.5 - - - +
782A LEU* 3.5 9.0 + - - +
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Residues in contact with SER 337 (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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333A ARG* 3.0 18.7 + - - -
336A THR* 1.3 82.3 + - - +
338A LEU* 1.3 57.7 - - - +
340A GLY 3.2 1.7 + - - -
341A HIS* 3.0 27.7 + - - -
674A TYR* 3.1 27.1 - - - -
732A LEU* 4.0 8.6 - - - +
781A LEU* 4.2 13.5 - - - -
785A SER* 2.6 34.1 + - - -
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Residues in contact with LEU 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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327A ALA* 4.7 3.8 - - + -
334A ALA 2.9 17.9 + - - +
335A MET 3.8 3.6 - - - +
337A SER* 1.3 75.1 - - - +
339A TYR* 1.3 61.3 + - - +
341A HIS* 3.1 3.4 + - + +
342A LEU* 2.9 38.0 + - + +
357A PHE* 3.9 32.3 - - + -
363A SER* 3.6 40.6 - - - +
366A THR* 3.7 16.6 - - + -
672A PHE* 4.2 15.9 - - + -
674A TYR* 3.3 21.7 + - + +
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Residues in contact with TYR 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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335A MET* 3.2 30.0 + - + -
336A THR* 3.1 11.8 + - - +
338A LEU* 1.3 78.4 - - - +
340A GLY* 1.3 56.6 + - - +
342A LEU* 3.3 4.5 + - + +
343A LEU* 3.0 30.1 + - - +
365A TRP 4.7 0.3 + - - -
366A THR* 3.8 31.6 + - + +
369A HIS* 3.4 33.6 + - - +
370A LEU* 3.9 25.1 - - + +
381A LEU* 5.2 3.6 - - + +
384A PRO* 4.1 14.2 + - + -
385A ILE* 3.4 30.0 - - + +
388A ALA* 3.6 29.5 - - + +
778A PHE* 5.2 2.0 - + - -
782A LEU* 3.7 7.0 - - + -
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Residues in contact with GLY 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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336A THR 3.1 7.7 + - - -
337A SER 3.5 4.5 - - - -
338A LEU 3.2 0.4 - - - -
339A TYR* 1.3 79.4 - - - +
341A HIS* 1.3 60.7 + - - +
343A LEU* 3.6 5.0 - - - +
344A ALA 3.3 11.4 + - - -
782A LEU* 3.2 32.2 - - - +
785A SER* 4.1 0.4 - - - -
786A ASP* 3.2 27.6 - - - +
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Residues in contact with HIS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 3.0 13.2 + - - -
338A LEU* 3.1 8.9 + - + +
340A GLY* 1.3 75.4 - - - +
342A LEU* 1.3 65.6 + - - +
344A ALA* 3.4 4.5 + - - +
345A LEU* 3.1 26.7 + - - +
672A PHE* 3.5 37.3 - + + -
673A ASP 5.4 0.4 - - - -
674A TYR* 2.8 42.6 + + - -
730A PHE* 4.9 11.8 - - - +
731A PRO 5.8 1.9 + - - -
732A LEU* 6.0 3.1 - - + +
785A SER* 3.3 33.9 + - - -
788A ASN* 5.0 5.9 + - - +
789A VAL* 3.3 21.3 - - + +
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Residues in contact with LEU 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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325A ILE* 4.1 19.1 - - + -
338A LEU* 2.9 25.7 + - + +
339A TYR* 3.8 5.4 - - + +
341A HIS* 1.3 72.1 - - - +
343A LEU* 1.3 62.3 - - - +
345A LEU* 3.0 10.2 + - + +
346A GLN* 2.8 29.6 + - - +
351A LEU* 4.3 17.4 - - + +
357A PHE* 3.9 34.5 - - + -
366A THR* 4.0 8.7 - - + -
370A LEU* 3.4 33.0 - - + -
376A TRP* 4.4 6.5 - - + -
381A LEU* 3.7 15.3 - - + +
672A PHE* 5.6 0.7 - - + -
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Residues in contact with LEU 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 TYR 3.0 16.4 + - - +
340A GLY* 3.6 5.8 - - - +
342A LEU* 1.3 76.5 - - - +
344A ALA* 1.3 57.1 + - - +
346A GLN* 3.1 10.1 + - - +
347A LYS* 2.9 68.1 + - + +
380A ASP* 5.1 2.7 - - - +
381A LEU* 3.7 30.4 - - + +
382A GLU* 4.0 28.3 - - - +
385A ILE* 5.3 4.7 - - + -
782A LEU* 4.7 14.6 - - + -
786A ASP* 4.1 18.8 - - + +
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Residues in contact with ALA 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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340A GLY 3.3 6.8 + - - +
341A HIS 3.5 4.5 - - - +
342A LEU 3.2 0.6 - - - -
343A LEU* 1.3 77.8 - - - +
345A LEU* 1.3 60.7 + - - +
347A LYS* 4.0 0.9 - - - +
348A LEU* 3.1 34.2 + - - +
786A ASP* 3.3 36.5 + - - +
789A VAL* 3.4 25.1 - - + -
790A GLN* 3.7 10.8 - - + +
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Residues in contact with LEU 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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325A ILE* 4.0 26.7 - - + -
341A HIS 3.1 13.9 + - - +
342A LEU* 3.0 14.4 + - + +
344A ALA* 1.3 76.5 - - - +
346A GLN* 1.3 62.5 + - - +
348A LEU* 3.8 1.3 + - + -
349A GLY 3.4 1.4 + - - -
350A LEU* 2.8 49.2 + - + -
351A LEU* 2.9 22.8 + - + +
354A VAL* 4.8 4.3 - - + -
670A LEU* 4.1 21.3 - - + -
672A PHE* 4.1 16.8 - - + -
789A VAL* 3.9 19.3 - - + -
796A ILE* 4.5 9.6 - - + -
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Residues in contact with GLN 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 LEU 2.8 12.3 + - - +
343A LEU* 3.5 12.5 - - - +
345A LEU* 1.3 75.2 - - - +
347A LYS* 1.3 63.8 + - + +
349A GLY* 2.9 21.5 + - - -
351A LEU* 4.0 12.7 - - + +
377A SER* 2.9 25.2 + - - +
378A GLN 4.3 3.2 + - - -
379A ARG 2.7 28.2 + - - -
380A ASP* 4.0 8.3 - - - +
381A LEU* 3.4 39.0 + - + +
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Residues in contact with LYS 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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343A LEU* 2.9 54.5 + - + +
344A ALA 4.0 0.7 - - - +
346A GLN* 1.3 78.9 - - + +
348A LEU* 1.3 59.8 + - - +
349A GLY 3.3 0.7 + - - -
382A GLU* 4.5 7.2 + - - -
786A ASP* 4.1 9.4 + - - +
790A GLN* 3.4 29.4 - - - +
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Residues in contact with LEU 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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308A ALA* 5.3 3.3 - - - +
344A ALA 3.1 21.9 + - - +
345A LEU* 4.2 2.0 - - - +
347A LYS* 1.3 78.1 - - - +
349A GLY* 1.3 62.5 + - - +
350A LEU* 3.3 37.7 + - + +
789A VAL* 4.3 13.2 - - + +
790A GLN* 4.1 35.9 - - + +
793A GLN* 3.6 46.4 + - + +
796A ILE* 4.8 0.9 - - + -
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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