Contacts of the helix formed by residues 343 - 355 (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 GLY 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU 4.5 1.6 + - - -
340B HIS* 3.2 12.3 + - - +
341B PHE 3.1 1.2 - - - -
342B ALA* 1.3 76.5 - - - +
344B ARG* 1.3 62.8 + - - +
345B HIS 3.4 2.7 - - - -
346B ALA* 3.4 12.5 + - - +
347B VAL* 3.1 26.5 + - - +
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Residues in contact with ARG 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 HIS 3.8 2.1 + - - +
341B PHE* 2.9 56.1 + - - +
342B ALA* 3.4 12.1 + - - +
343B GLY* 1.3 75.5 - - - +
345B HIS* 1.3 86.9 + - + +
347B VAL* 3.1 2.1 + - - +
348B MET* 2.7 44.2 + - - +
366B PRO* 2.6 32.1 + - - -
367B ASP* 4.7 8.7 + - - +
373B TRP* 5.3 0.2 - - + -
410B TYR* 3.4 21.8 - - - +
414B PHE* 3.7 24.2 - - + -
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA 4.9 6.5 + - - +
343B GLY 3.4 0.6 - - - -
344B ARG* 1.3 104.8 + - + +
346B ALA* 1.3 53.4 + - - +
348B MET* 3.2 9.1 + - - +
349B ASN* 2.7 36.9 + - - +
366B PRO* 3.8 31.8 - - + +
367B ASP* 5.9 0.9 - - - -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY* 3.4 12.6 + - - +
344B ARG 3.3 0.2 - - - -
345B HIS* 1.3 78.7 - - - +
347B VAL* 1.3 59.8 + - - +
349B ASN* 3.7 8.2 + - - +
350B ALA* 3.4 14.6 + - - +
388B ALA* 3.6 31.9 - - + +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B HIS 5.7 1.3 - - - +
343B GLY 3.1 16.5 + - - +
344B ARG 3.6 1.1 - - - +
346B ALA* 1.3 74.0 - - - +
348B MET* 1.3 63.9 + - - +
350B ALA* 3.2 5.9 + - - +
351B ILE* 3.1 21.4 + - + +
385B ILE* 5.1 5.6 - - + -
386B PRO* 3.9 36.6 - - + +
387B THR* 4.2 10.9 - - - +
388B ALA* 4.5 4.3 - - + +
410B TYR* 3.4 48.0 - - + +
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Residues in contact with MET 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 2.7 26.2 + - + +
345B HIS* 3.6 8.7 - - - +
347B VAL* 1.3 72.5 - - - +
349B ASN* 1.3 62.0 + - - +
351B ILE* 3.3 5.1 + - - -
352B SER* 3.1 19.8 + - - -
359B LEU* 3.3 22.2 - - + +
364B VAL* 3.7 20.4 - - + -
366B PRO* 4.2 26.2 - - + -
410B TYR* 4.5 4.3 - - + -
411B LEU* 4.0 19.1 - - + -
414B PHE* 3.5 50.9 - - + -
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Residues in contact with ASN 349 (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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345B HIS 2.7 20.9 + - - +
346B ALA* 4.0 9.3 + - - +
347B VAL 3.3 0.2 - - - -
348B MET* 1.3 72.2 - - - +
350B ALA* 1.3 60.2 + - - +
352B SER* 2.6 27.4 + - - -
353B VAL* 3.4 13.1 - - - +
388B ALA 5.6 0.4 + - - -
390B SER* 3.7 24.0 + - - -
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Residues in contact with ALA 350 (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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346B ALA 3.4 8.9 + - - +
347B VAL 3.2 6.1 + - - +
349B ASN* 1.3 76.0 - - - +
351B ILE* 1.3 64.4 + - - +
353B VAL* 3.2 2.9 + - - +
354B HIS* 3.0 31.9 + - + -
387B THR 3.3 27.1 - - - +
388B ALA 3.8 7.0 - - - +
389B ARG 3.5 19.1 - - - +
390B SER* 4.1 10.8 - - - -
403B TYR* 3.9 2.7 - - - +
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Residues in contact with ILE 351 (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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347B VAL* 3.1 15.9 + - + +
348B MET* 3.3 8.9 + - - +
350B ALA* 1.3 75.4 - - - +
352B SER* 1.3 56.1 + - - +
355B ALA* 2.7 40.1 + - + +
358B LEU* 4.3 6.5 - - + -
359B LEU* 4.2 6.5 - - + -
386B PRO* 3.9 19.7 - - + -
403B TYR* 3.6 17.7 - - - +
407B ALA* 4.0 25.6 - - + +
410B TYR* 3.7 32.1 - - + -
411B LEU* 4.0 25.8 - - + -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B MET 3.1 11.1 + - - -
349B ASN* 2.6 29.7 + - - -
351B ILE* 1.3 76.9 - - - +
353B VAL* 1.3 61.6 + - - +
355B ALA 4.5 0.2 - - - -
356B PRO* 3.4 21.6 - - - +
359B LEU* 3.9 32.9 - - - +
360B PRO* 5.7 1.1 - - - -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ASN* 3.4 19.5 - - - +
350B ALA 3.2 6.6 + - - +
352B SER* 1.3 79.3 + - - +
354B HIS* 1.3 77.0 + - + +
356B PRO* 3.4 13.2 - - - +
390B SER* 3.4 34.8 - - - +
391B SER 4.9 2.0 - - - +
392B ALA* 5.1 6.3 - - + -
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Residues in contact with HIS 354 (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 LEU* 3.4 33.4 - - + +
350B ALA* 3.0 24.3 + - + +
353B VAL* 1.3 87.3 - - + +
355B ALA* 1.3 59.3 + - - +
356B PRO* 3.5 4.7 - - - +
389B ARG 2.6 28.7 + - - -
390B SER* 3.8 3.4 - - - -
391B SER 3.0 27.1 + - - -
393B ILE* 3.8 17.1 + - + +
395B LEU* 4.8 11.2 - - + +
400B ALA* 6.0 1.4 - - - +
403B TYR* 3.6 30.6 - - + -
404B ASN* 4.4 6.1 + - - -
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ILE* 2.7 24.0 + - + +
354B HIS* 1.3 74.9 - - - +
356B PRO* 1.4 59.5 - - - +
357B ASP 3.1 3.4 - - - -
358B LEU* 2.9 38.4 + - + +
359B LEU 3.6 2.4 + - - -
403B TYR* 4.0 11.4 - - + -
404B ASN* 3.6 33.0 - - - +
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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