Contacts of the helix formed by residues 396 - 413 (chain B) in PDB entry 2O5C
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 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ASN 5.9 0.2 - - - +
395B LEU* 1.3 77.8 - - - +
397B GLU* 1.3 59.5 + - - +
398B ASN* 3.8 5.6 + - - +
399B GLU* 3.0 40.9 + - - +
400B ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B THR* 1.3 73.7 - - - +
398B ASN* 1.3 62.7 + - - +
400B ALA* 3.3 6.4 + - - +
401B LYS* 3.0 59.8 + - + +
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Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.7 28.8 - - + +
311B ASN* 4.4 8.1 + - - +
315B ILE* 3.9 20.3 - - + +
396B THR* 3.3 6.2 + - - +
397B GLU* 1.3 79.2 - - - +
399B GLU* 1.3 64.5 - - - +
401B LYS* 3.5 20.1 + - - +
402B VAL* 3.0 29.8 + - - +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 3.7 26.7 - - + +
318B LYS* 3.6 19.2 - - + +
319B LEU* 4.0 14.1 - - + +
323B HIS* 3.1 32.3 + - - -
394B ASN 4.4 0.9 - - - +
395B LEU* 3.7 16.5 - - + -
396B THR* 3.0 46.3 + - - +
398B ASN* 1.3 75.4 - - - +
400B ALA* 1.3 56.6 + - - +
402B VAL* 3.5 0.5 + - - -
403B TYR* 3.0 30.5 + - - +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B HIS 6.0 1.1 - - - +
395B LEU* 4.1 20.6 - - + +
396B THR 2.9 18.8 + - - +
397B GLU* 3.5 6.5 - - - +
399B GLU* 1.3 74.3 - - - +
401B LYS* 1.3 66.0 + - + +
403B TYR* 3.6 0.6 + - - -
404B ASN* 2.8 37.9 + - - +
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Residues in contact with LYS 401 (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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305B PHE* 3.7 61.6 + - + +
307B LEU* 4.9 2.2 - - + -
397B GLU* 3.0 45.2 + - + +
398B ASN* 3.6 20.9 + - - +
400B ALA* 1.3 77.1 - - - +
402B VAL* 1.3 57.8 + - + +
404B ASN* 3.6 5.7 + - - +
405B LEU* 3.2 30.7 + - - +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 4.1 9.6 - - + -
301B ALA* 5.1 5.2 - - + -
305B PHE* 6.0 0.4 - - + -
307B LEU* 4.3 13.9 - - + -
312B VAL* 4.8 12.1 - - + +
315B ILE* 3.9 28.7 - - + -
316B CYS* 3.9 23.6 - - - -
319B LEU* 3.9 15.5 - - + -
398B ASN 3.0 21.0 + - - +
399B GLU 4.0 0.4 - - - +
400B ALA 3.2 0.2 - - - -
401B LYS* 1.3 74.0 - - - +
403B TYR* 1.3 66.5 + - - +
405B LEU* 3.3 9.3 + - + +
406B ILE* 3.1 27.1 + - + +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.0 12.9 - - + +
325B LEU* 3.4 40.8 - - + +
326B ILE* 3.8 16.6 - - + -
350B ALA* 3.9 2.8 - - - +
351B ILE* 3.6 22.9 + - - -
354B HIS* 3.6 36.0 - - + -
355B ALA* 4.0 10.8 - - + -
386B PRO* 3.6 23.3 - - + +
387B THR 4.8 0.3 + - - -
395B LEU* 4.5 8.5 - - + -
399B GLU 3.0 18.5 + - - +
400B ALA 3.9 3.4 - - - +
402B VAL* 1.3 76.4 - - - +
404B ASN* 1.3 64.6 + - - +
406B ILE* 3.2 6.0 + - + +
407B ALA* 2.7 49.1 + - + +
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Residues in contact with ASN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B HIS 4.4 3.6 + - - -
355B ALA* 3.6 31.7 - - - +
357B ASP* 5.4 5.2 - - - +
358B LEU* 3.6 19.8 + - + +
400B ALA* 2.8 34.9 + - - +
401B LYS* 3.8 6.7 - - - +
403B TYR* 1.3 78.7 - - - +
405B LEU* 1.3 57.9 + - - +
407B ALA* 4.3 0.7 - - - -
408B ARG* 2.7 37.7 + - - +
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Residues in contact with LEU 405 (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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292B PHE* 3.4 8.8 - - + -
297B LEU* 4.0 15.7 - - + -
300B GLU* 4.1 16.6 - - + +
301B ALA* 3.8 33.9 - - + +
304B ARG* 4.4 14.1 - - + +
305B PHE* 3.7 25.4 - - + -
401B LYS 3.2 14.4 + - - +
402B VAL* 3.3 10.7 + - - +
404B ASN* 1.3 75.6 - - - +
406B ILE* 1.3 56.3 + - - +
408B ARG* 3.6 34.5 + - - +
409B GLN* 3.0 31.7 + - - +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 4.2 9.4 - - + -
297B LEU* 3.8 32.3 - - + -
316B CYS* 4.4 0.2 - - - -
319B LEU* 4.7 0.2 - - + -
326B ILE* 3.9 32.8 - - + -
384B ILE* 3.5 38.6 - - + +
385B ILE* 3.8 21.1 - - - -
386B PRO* 3.9 3.6 - - + -
402B VAL* 3.1 23.8 + - + +
403B TYR* 3.5 7.6 - - + +
405B LEU* 1.3 75.6 - - - +
407B ALA* 1.3 62.9 + - - +
409B GLN* 3.5 2.8 + - - +
410B TYR* 3.2 21.5 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 4.0 17.6 - - + +
358B LEU* 3.8 17.9 - - + -
386B PRO* 3.7 22.7 - - + -
403B TYR* 2.7 31.3 + - + +
406B ILE* 1.3 71.9 - - - +
408B ARG* 1.3 64.3 + - - +
410B TYR* 3.3 4.3 + - - +
411B LEU* 3.1 25.5 + - - +
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLU* 3.7 17.4 + - - +
304B ARG* 3.9 20.5 - - - +
358B LEU* 3.7 24.6 - - + +
404B ASN 2.7 22.8 + - - +
405B LEU* 3.6 29.7 + - - +
407B ALA* 1.3 72.5 - - - +
409B GLN* 1.3 69.1 + - - +
411B LEU* 3.1 7.8 + - - +
412B MET* 3.0 41.4 + - + +
449B LEU* 3.4 39.8 + - + +
450B LEU* 3.8 26.3 - - - +
451B GLY 4.7 3.4 - - - +
454B GLU* 4.0 6.5 + - - -
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Residues in contact with GLN 409 (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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289B PRO* 3.6 25.1 - - - +
290B LEU 2.8 29.9 + - - +
291B PRO* 3.7 12.1 - - + +
292B PHE* 3.3 38.5 - - + +
300B GLU* 6.1 0.2 - - - -
334B ARG* 3.8 8.3 - - - +
405B LEU 3.0 16.7 + - - +
406B ILE 3.8 3.4 - - - +
408B ARG* 1.3 81.3 + - - +
410B TYR* 1.3 59.8 + - - +
412B MET* 3.5 27.1 - - - +
413B GLN* 3.0 29.0 + - - +
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Residues in contact with TYR 410 (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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291B PRO* 5.2 2.9 - - + +
336B LEU* 4.3 4.5 - - + -
340B HIS 5.0 1.0 + - - -
344B ARG* 3.4 31.0 - - - +
347B VAL* 3.4 26.5 - - + +
348B MET* 4.5 11.0 - - + -
351B ILE* 3.7 20.6 - - + -
373B TRP* 4.1 20.7 - + - -
385B ILE* 3.7 43.7 - - + -
386B PRO* 3.9 11.0 - - + -
406B ILE 3.2 13.7 + - - +
407B ALA 3.4 7.4 - - - +
409B GLN* 1.3 78.1 - - - +
411B LEU* 1.3 63.8 + - + +
413B GLN* 3.3 25.3 + - + +
414B PHE* 3.4 25.8 - + - -
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Residues in contact with LEU 411 (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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348B MET* 4.0 30.3 - - + -
351B ILE* 4.0 16.6 - - + -
358B LEU* 4.0 28.7 - - + +
359B LEU* 3.9 25.6 - - + -
364B VAL* 4.0 24.3 - - + +
407B ALA 3.1 18.4 + - - +
408B ARG* 3.1 8.9 + - - +
410B TYR* 1.3 73.2 - - + +
412B MET* 1.3 65.8 + - - +
413B GLN 3.0 2.7 - - - -
414B PHE* 2.9 19.6 + - - +
415B CYS* 3.4 11.4 - - - -
449B LEU* 3.8 15.5 - - + -
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Residues in contact with MET 412 (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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288B ALA* 3.3 23.6 - - + +
289B PRO* 3.8 21.3 - - + -
408B ARG* 3.0 50.6 + - + +
409B GLN* 3.5 34.1 - - - +
410B TYR 3.3 0.6 - - - -
411B LEU* 1.3 75.7 - - - +
413B GLN* 1.3 62.7 + - - +
414B PHE 3.1 0.2 - - - -
415B CYS* 3.1 30.3 + - - +
446B TRP* 3.9 16.4 - - + +
449B LEU* 3.8 13.0 - - + +
450B LEU* 3.6 24.7 - - + -
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA* 4.3 1.7 - - - +
289B PRO 2.6 29.6 + - - +
290B LEU* 3.8 3.5 + - - +
291B PRO* 3.5 36.5 - - + +
368B ILE* 3.8 10.7 - - - +
370B ASN* 2.9 56.9 + - - +
372B CYS* 3.7 12.9 - - - +
373B TRP* 4.9 3.2 + - + +
409B GLN 3.0 20.5 + - - +
410B TYR* 3.3 21.1 - - + +
411B LEU 3.0 0.6 - - - -
412B MET* 1.3 78.8 - - - +
414B PHE* 1.3 65.2 + - + +
415B CYS 3.4 2.5 - - - +
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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
------------------------------------------------------------
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