Contacts of the helix formed by residues 330 - 348 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLY* 1.3 74.0 - - - -
331B GLY* 1.3 70.0 + - - +
332B ALA 3.4 0.2 + - - -
333B ARG* 3.2 38.3 + - - +
334B ALA* 3.2 8.5 + - - -
362B GLY 4.4 0.2 - - - +
768B LEU* 3.6 20.3 - - - +
901B 7FA 2.9 8.0 + - - -
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY* 1.3 75.7 - - - +
332B ALA* 1.3 62.7 + - - -
335B MET* 3.2 18.2 + - - +
362B GLY* 3.4 16.7 - - - -
365B TRP* 3.6 12.1 - - - -
768B LEU* 3.5 6.1 - - - +
901B 7FA 3.0 34.2 + - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY 3.4 0.4 + - - -
331B GLY* 1.3 69.2 - - - -
333B ARG* 1.3 63.9 + - - +
335B MET* 3.2 8.1 + - + +
336B THR* 2.9 32.2 + - - +
365B TRP* 3.7 7.8 - - - -
392B LEU* 4.2 12.6 - - + -
767B THR 6.0 0.2 - - - +
768B LEU* 5.2 2.8 + - - +
770B ASN 3.7 22.9 + - - +
771B MET* 4.0 18.7 - - + +
773B TYR* 3.5 17.5 - - + +
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY* 3.2 22.1 + - - +
332B ALA* 1.3 75.7 - - - +
334B ALA* 1.3 63.3 + - - +
337B SER* 3.0 28.6 + - - -
674B TYR* 2.4 40.0 + - + +
675B SER* 3.9 8.1 - - - +
676B LEU* 3.4 27.6 - - - +
732B LEU* 3.4 24.9 - - + -
766B TYR* 2.9 28.8 + - + +
767B THR 5.6 1.2 + - - +
768B LEU* 3.7 30.5 - - - +
773B TYR* 3.0 19.4 + - - +
781B LEU* 3.9 15.0 - - + +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR 4.1 0.2 - - - +
329B GLY 3.7 25.4 - - - +
330B GLY* 3.2 4.9 + - - +
331B GLY 3.7 8.1 - - - +
332B ALA 3.3 0.4 - - - -
333B ARG* 1.3 78.1 - - - +
335B MET* 1.3 66.8 + - - +
337B SER* 4.1 0.2 - - - -
338B LEU* 2.9 29.0 + - - +
362B GLY 4.8 0.9 - - - -
363B SER* 4.0 14.1 - - - +
674B TYR* 3.6 32.5 - - + -
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Residues in contact with MET 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLY 3.2 10.6 + - - +
332B ALA* 3.2 11.4 + - - +
334B ALA* 1.3 80.9 - - - +
336B THR* 1.3 64.0 + - + +
339B TYR* 3.2 31.9 + - + -
362B GLY 3.8 10.5 + - - +
365B TRP* 3.9 25.4 - - + -
366B THR* 2.7 37.9 + - - +
388B ALA* 4.8 14.8 - - + +
392B LEU* 3.7 38.1 - - + -
436B LEU* 4.1 17.3 - - + -
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Residues in contact with THR 336 (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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332B ALA 2.9 18.1 + - - +
335B MET* 1.3 75.5 - - + +
337B SER* 1.3 68.7 + - - +
339B TYR* 3.1 23.0 + - - +
340B GLY 3.1 9.2 + - - -
392B LEU* 3.6 27.4 - - + -
773B TYR* 3.8 11.3 - - + -
778B PHE* 3.6 28.8 + - + -
781B LEU* 3.3 25.6 - - - +
782B LEU* 3.5 8.4 + - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ARG* 3.0 18.5 + - - -
336B THR* 1.3 81.9 + - - +
338B LEU* 1.3 56.5 - - - +
340B GLY 3.3 0.5 + - - -
341B HIS* 3.0 27.7 + - - -
674B TYR* 3.2 27.6 - - - -
732B LEU* 4.0 8.8 - - - +
781B LEU* 4.1 13.7 - - - -
785B SER* 2.6 35.2 + - - -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 4.7 3.8 - - + -
334B ALA 2.9 17.9 + - - +
335B MET 3.8 3.8 - - - +
337B SER* 1.3 73.7 - - - +
339B TYR* 1.3 61.8 + - - +
341B HIS* 3.1 3.2 + - + -
342B LEU* 2.9 37.9 + - + +
357B PHE* 3.9 32.3 - - + -
363B SER* 3.6 40.2 - - - +
366B THR* 3.7 16.6 - - + +
672B PHE* 4.2 16.2 - - + -
674B TYR* 3.3 21.7 + - + +
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Residues in contact with TYR 339 (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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335B MET* 3.2 32.4 + - + -
336B THR* 3.1 12.7 + - - +
338B LEU* 1.3 77.5 - - - +
340B GLY* 1.3 58.0 + - - +
342B LEU* 3.3 4.7 + - + +
343B LEU* 3.0 29.6 + - - +
365B TRP 4.7 0.2 + - - -
366B THR* 3.8 32.2 + - + +
369B HIS* 3.4 33.8 + - - +
370B LEU* 4.0 20.6 - - + -
381B LEU* 5.2 3.6 - - + +
384B PRO* 4.1 18.2 + - + -
385B ILE* 3.4 31.0 - - + +
388B ALA* 3.6 29.7 - - + +
778B PHE* 5.2 2.0 - + - -
782B LEU* 3.7 6.7 - - + -
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Residues in contact with GLY 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B THR 3.1 7.7 + - - -
337B SER 3.6 4.7 - - - -
338B LEU 3.2 0.4 - - - -
339B TYR* 1.3 79.7 - - - +
341B HIS* 1.3 60.3 + - - +
343B LEU* 3.6 4.8 - - - +
344B ALA 3.3 11.4 + - - -
782B LEU* 3.2 32.4 - - - +
785B SER* 4.1 0.4 - - - -
786B ASP* 3.2 27.9 - - - +
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Residues in contact with HIS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 3.0 12.8 + - - -
338B LEU* 3.1 9.2 + - + +
340B GLY* 1.3 75.6 - - - +
342B LEU* 1.3 65.8 + - - +
344B ALA* 3.4 4.6 + - - +
345B LEU* 3.2 26.9 + - - +
672B PHE* 3.5 37.9 - + + -
673B ASP 5.4 0.4 - - - -
674B TYR* 2.8 43.0 + + - -
730B PHE* 4.9 11.7 + - - +
731B PRO 5.8 1.6 + - - -
732B LEU* 6.0 3.1 - - + +
785B SER* 3.3 33.5 + - - -
788B ASN* 5.0 5.9 + - - +
789B VAL* 3.3 21.1 - - + +
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Residues in contact with LEU 342 (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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325B ILE* 4.1 19.7 - - + -
338B LEU* 2.9 24.9 + - + +
339B TYR* 3.3 5.8 + - + +
341B HIS* 1.3 73.1 - - - +
343B LEU* 1.3 61.9 + - - +
345B LEU* 3.0 10.3 + - + +
346B GLN* 2.8 29.6 + - - +
351B LEU* 4.3 17.4 - - + +
357B PHE* 3.9 33.7 - - + -
366B THR* 4.0 9.2 - - + -
370B LEU* 3.4 33.7 - - + -
376B TRP* 4.4 5.8 - - + -
381B LEU* 3.7 15.6 - - + +
672B PHE* 5.6 0.9 - - + -
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Residues in contact with LEU 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 TYR 3.0 17.0 + - - +
340B GLY* 3.6 5.8 - - - +
342B LEU* 1.3 75.8 - - - +
344B ALA* 1.3 62.9 + - - +
346B GLN* 3.1 9.5 + - - +
347B LYS* 2.9 62.4 + - + +
380B ASP* 5.0 3.4 - - - +
381B LEU* 3.7 29.7 - - + +
382B GLU* 4.0 27.6 - - - +
385B ILE* 5.3 4.5 - - + -
782B LEU* 4.7 14.6 - - + -
786B ASP* 4.1 18.2 - - + +
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Residues in contact with ALA 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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340B GLY 3.3 7.0 + - - +
341B HIS 3.5 4.3 - - - +
342B LEU 3.3 0.2 - - - -
343B LEU* 1.3 79.3 - - - +
345B LEU* 1.3 60.1 + - - +
347B LYS* 3.5 1.0 + - - +
348B LEU* 3.1 33.8 + - - +
786B ASP* 3.3 36.2 + - - +
789B VAL* 3.4 25.4 - - + -
790B GLN* 3.7 11.2 - - + +
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Residues in contact with LEU 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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325B ILE* 4.0 26.5 - - + -
341B HIS 3.2 14.8 + - - +
342B LEU* 3.0 13.2 + - + +
344B ALA* 1.3 75.2 - - - +
346B GLN* 1.3 62.6 + - - +
348B LEU* 3.8 1.3 + - + -
349B GLY 3.4 1.6 + - - -
350B LEU* 2.8 50.1 + - + +
351B LEU* 2.9 23.5 + - + +
354B VAL* 4.8 4.3 - - + -
670B LEU* 4.1 21.8 - - + -
672B PHE* 4.1 16.6 - - + -
789B VAL* 3.9 19.3 - - + -
796B ILE* 4.5 9.6 - - + -
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Residues in contact with GLN 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 LEU 2.8 12.3 + - - +
343B LEU* 3.5 12.3 - - - +
345B LEU* 1.3 75.4 - - - +
347B LYS* 1.3 64.0 + - + +
349B GLY* 2.9 21.5 + - - -
351B LEU* 3.9 12.0 - - + +
377B SER* 2.9 25.6 + - - +
378B GLN 4.3 3.0 + - - -
379B ARG 2.7 28.2 + - - -
380B ASP* 4.0 8.4 - - - +
381B LEU* 3.4 38.9 + - + +
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Residues in contact with LYS 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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343B LEU* 2.9 53.8 + - + +
344B ALA 4.0 0.9 - - - +
346B GLN* 1.3 79.3 - - + +
348B LEU* 1.3 60.5 + - - +
349B GLY 3.3 0.8 + - - -
382B GLU* 4.5 7.6 + - - -
786B ASP* 4.2 9.0 + - - +
790B GLN* 3.4 30.0 + - - +
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Residues in contact with LEU 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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308B ALA* 5.3 3.1 - - - +
344B ALA 3.1 24.1 + - - +
345B LEU* 4.2 2.0 - - - +
346B GLN 3.2 0.6 - - - -
347B LYS* 1.3 77.9 - - - +
349B GLY* 1.3 61.8 + - - +
350B LEU* 3.3 37.0 + - + +
789B VAL* 4.3 13.7 - - + +
790B GLN* 4.1 35.7 - - + +
793B GLN* 3.6 45.1 + - + +
796B 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
------------------------------------------------------------
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