Contacts of the helix formed by residues 381 - 394 (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 LEU 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B TYR* 5.2 4.9 - - + +
342B LEU* 3.7 16.8 - - + +
343B LEU* 3.7 37.2 - - + +
346B GLN* 3.4 34.9 + - + +
351B LEU* 4.6 6.5 - - + -
370B LEU* 3.4 35.7 - - + -
376B TRP* 3.9 18.2 - - + +
379B ARG 4.5 0.4 - - - +
380B ASP* 1.3 73.2 + - - +
382B GLU* 1.3 60.3 + - - +
383B GLY 3.1 6.5 + - - -
384B PRO* 3.2 8.5 - - + +
385B ILE* 3.0 32.0 + - + +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 4.0 27.6 - - - +
347B LYS* 4.5 8.5 + - - -
380B ASP* 3.3 19.1 + - - +
381B LEU* 1.3 77.3 - - - +
383B GLY* 1.3 63.7 + - - +
385B ILE* 3.6 14.8 - - + +
386B ARG* 3.2 20.8 + - - +
389B ARG* 4.8 9.8 + - - +
779B GLU* 5.3 1.7 - - - +
782B LEU* 4.6 11.8 - - - +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ASP* 3.6 7.1 + - - +
381B LEU 3.1 1.6 - - - -
382B GLU* 1.3 77.1 - - - +
384B PRO* 1.4 68.3 - - - +
386B ARG* 3.1 19.2 + - - +
387B TYR* 3.2 11.4 + - - +
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Residues in contact with PRO 384 (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* 4.1 13.4 + - + -
369B HIS* 4.2 16.4 - - + +
370B LEU* 3.9 30.3 - - + -
373B ASP* 6.0 2.9 - - + +
376B TRP* 5.7 4.7 - - + +
380B ASP 3.5 13.2 - - - +
381B LEU* 3.2 15.3 - - + +
383B GLY* 1.4 85.3 - - - +
385B ILE* 1.3 61.0 + - - +
387B TYR* 3.4 10.0 - - + +
388B ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TYR* 3.4 46.0 - - + +
343B LEU* 5.3 6.1 - - + -
381B LEU* 3.0 29.2 + - + +
382B GLU* 3.6 23.1 - - + +
383B GLY 3.2 0.2 - - - -
384B PRO* 1.3 72.7 - - - +
386B ARG* 1.3 62.0 + - - +
388B ALA* 3.3 6.5 + - - +
389B ARG* 2.9 36.8 + - - +
778B PHE* 3.6 25.9 - - + -
782B LEU* 3.7 23.1 - - + -
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU 3.2 10.1 + - - +
383B GLY* 3.1 13.1 + - - +
385B ILE* 1.3 78.7 - - - +
387B TYR* 1.3 58.1 + - - +
389B ARG* 3.3 25.0 + - - +
390B GLU* 2.9 71.3 + - - +
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Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS* 3.4 36.6 - + + -
383B GLY 3.2 8.2 + - - +
384B PRO* 3.4 10.5 - - + +
386B ARG* 1.3 79.9 - - - +
388B ALA* 1.3 66.7 + - - +
390B GLU* 4.0 5.0 - - - +
391B HIS* 2.7 61.3 + + - -
436B LEU 3.7 6.1 - - - -
437B HIS* 2.7 40.9 + + - +
438B GLY 4.9 0.2 + - - -
439B GLN* 5.7 1.2 - - - +
441B MET* 4.2 11.3 - - + -
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 4.8 13.6 - - + +
339B TYR* 3.6 37.2 - - + +
384B PRO 3.1 8.8 + - - +
385B ILE 3.3 4.2 + - - +
387B TYR* 1.3 85.2 - - + +
389B ARG* 1.3 57.8 + - - +
391B HIS* 3.8 2.8 - - - +
392B LEU* 2.8 32.2 + - - +
436B LEU 6.0 0.2 - - - -
778B PHE* 4.2 9.9 - - + -
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Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 4.8 10.5 + - - +
385B ILE* 2.9 30.2 + - - +
386B ARG* 3.6 36.0 - - - +
388B ALA* 1.3 76.0 - - - +
390B GLU* 1.3 61.2 + - - +
392B LEU* 3.3 2.1 + - - +
393B ALA* 2.9 29.1 + - - +
773B TYR 4.7 0.9 - - - +
775B GLU* 3.1 40.4 + - + +
778B PHE* 3.6 38.2 - - + -
779B GLU* 2.8 34.0 + - - +
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Residues in contact with GLU 390 (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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386B ARG* 2.9 62.3 + - + +
387B TYR* 4.0 5.5 - - - +
389B ARG* 1.3 80.2 + - - +
391B HIS* 1.3 67.8 + - + +
393B ALA* 3.3 2.6 + - - +
394B LYS* 3.0 23.0 + - - +
775B GLU* 4.3 20.4 - - - +
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B TYR* 2.7 65.0 + + - +
388B ALA* 3.9 3.6 - - - +
390B GLU* 1.3 81.5 - - + +
392B LEU* 1.3 52.6 + - - +
394B LYS* 3.5 23.2 - - + +
396B LYS* 2.5 30.5 + - - -
435B MET 4.0 5.1 - - - +
436B LEU* 3.6 19.1 - - - +
437B HIS* 3.7 24.5 - - - -
438B GLY* 3.7 14.3 + - - -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 4.2 6.5 - - + -
335B MET* 3.7 16.4 - - + -
336B THR* 3.6 31.4 - - + -
388B ALA 2.8 18.3 + - - +
389B ARG* 3.7 5.4 - - - +
390B GLU 3.2 0.2 - - - -
391B HIS* 1.3 77.9 - - - +
393B ALA* 1.3 59.1 + - - +
394B LYS 3.8 0.2 - - - +
396B LYS* 3.6 5.9 + - - +
435B MET 5.8 1.3 - - - +
436B LEU* 6.1 0.9 - - + -
771B MET* 3.3 46.4 - - + +
772B THR* 3.3 11.4 - - - -
773B TYR* 3.0 49.4 + - + -
778B PHE* 4.0 7.6 - - + -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ARG 2.9 16.6 + - - +
390B GLU 3.3 3.6 + - - +
392B LEU* 1.3 75.0 - - - +
394B LYS* 1.3 65.7 + - - +
395B SER* 3.3 4.0 + - - -
772B THR* 5.1 3.8 - - - -
773B TYR 3.1 21.2 + - - +
774B LYS* 4.8 1.6 - - - -
775B GLU* 3.7 30.5 - - + +
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Residues in contact with LYS 394 (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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390B GLU 3.0 12.8 + - - +
391B HIS* 3.5 26.9 - - + +
392B LEU 3.8 0.7 - - - +
393B ALA* 1.3 76.2 - - - +
395B SER* 1.3 71.3 + - - +
396B LYS* 2.8 32.8 + - - +
398B GLU* 5.6 3.2 + - - +
404B ARG* 4.0 30.1 - - - +
434B SER 4.9 11.4 - - - -
435B MET 6.0 1.1 - - - +
437B HIS 5.1 0.7 - - - -
438B GLY* 5.0 12.4 - - - -
772B THR* 4.2 1.2 - - - +
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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