Contacts of the helix formed by residues 346 - 357 (chain B) in PDB entry 5WWZ
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 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B VAL* 3.3 29.7 - - - +
343B GLY 3.2 5.5 + - - -
344B PRO 3.1 2.2 - - - -
345B LYS* 1.3 78.1 - - - +
347B ALA* 1.3 62.2 + - - +
349B ILE* 3.4 7.4 - - - +
350B LYS* 3.1 26.4 + - - +
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Residues in contact with ALA 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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342B VAL 3.5 1.2 + - - -
344B PRO* 3.2 23.8 + - + +
345B LYS* 3.3 2.5 - - + +
346B GLY* 1.3 76.9 - - - +
348B THR* 1.3 57.3 + - - +
350B LYS* 3.8 5.4 - - - +
351B ARG* 3.0 28.4 + - - +
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Residues in contact with THR 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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323A LEU* 5.5 3.1 - - + -
324A PRO* 6.1 6.5 - - + +
340B LEU 3.8 6.2 + - - +
341B VAL 3.2 17.9 - - - +
342B VAL 3.1 8.5 + - - -
343B GLY* 3.6 13.0 - - - -
344B PRO* 4.3 5.7 - - - +
347B ALA* 1.3 75.5 - - - +
349B ILE* 1.3 63.8 + - - +
351B ARG* 3.2 8.1 + - + +
352B ILE* 3.1 26.2 + - + +
390B HIS* 3.4 32.8 - - + +
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Residues in contact with ILE 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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341B VAL* 3.2 31.6 + - + +
342B VAL* 3.2 20.1 + - + +
346B GLY* 3.4 16.8 - - - +
348B THR* 1.3 78.4 - - - +
350B LYS* 1.3 65.2 + - + +
352B ILE* 3.5 9.0 + - + -
353B GLN* 3.2 35.2 + - - +
360B ILE* 3.7 35.2 - - + +
362B THR* 4.0 20.0 - - - +
371B PHE* 4.2 5.6 - - + -
387B ILE* 4.8 2.0 - - + -
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Residues in contact with LYS 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 GLY 3.1 21.0 + - - +
347B ALA* 3.8 6.7 - - - +
349B ILE* 1.3 78.3 - - + +
351B ARG* 1.3 61.0 + - - +
353B GLN* 3.5 12.2 + - - +
354B GLN* 3.2 42.0 + - - +
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Residues in contact with ARG 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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321A PRO* 3.9 18.8 - - - +
322A ASN 3.8 17.5 + - - -
323A LEU* 3.6 20.4 - - + -
324A PRO* 4.2 22.0 - - + +
347B ALA 3.0 18.6 + - - +
348B THR* 3.2 8.0 + - - +
350B LYS* 1.3 75.5 - - - +
352B ILE* 1.3 59.1 + - - +
354B GLN* 3.9 13.4 - - - -
355B GLN* 3.0 54.8 + - - +
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Residues in contact with ILE 352 (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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323A LEU* 4.0 13.9 - - + -
341B VAL* 4.5 11.7 - - + -
348B THR* 3.1 16.2 + - + +
349B ILE* 3.8 10.8 - - + +
350B LYS 3.3 0.4 - - - -
351B ARG* 1.3 77.7 - - - +
353B GLN* 1.3 54.9 + - - +
356B THR* 2.4 41.5 + - - +
360B ILE* 3.8 20.4 - - + -
383B ALA* 4.2 10.3 - - + +
386B GLU* 3.3 49.1 - - + +
387B ILE* 4.1 17.7 - - + -
390B HIS* 4.3 7.4 - - + -
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Residues in contact with GLN 353 (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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349B ILE* 3.2 32.3 + - - +
350B LYS* 3.8 10.1 - - - +
351B ARG 3.3 0.4 - - - -
352B ILE* 1.3 77.3 - - - +
354B GLN* 1.3 59.0 + - + +
357B HIS* 2.9 24.9 + - - -
358B THR* 3.1 28.7 + - - +
359B TYR* 3.7 12.3 - - - -
360B ILE* 2.9 51.9 + - + +
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Residues in contact with GLN 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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350B LYS* 3.2 30.2 + - - +
351B ARG* 3.4 15.4 + - - +
353B GLN* 1.3 78.5 - - + +
355B GLN* 1.3 61.3 + - - +
357B HIS* 3.7 20.3 + - - +
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Residues in contact with GLN 355 (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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320A SER* 4.0 7.9 - - - -
321A PRO* 3.0 28.6 + - + +
323A LEU* 3.8 9.8 - - - +
351B ARG* 3.0 51.3 + - - +
352B ILE 4.3 1.6 - - - +
354B GLN* 1.3 79.4 - - - +
356B THR* 1.3 59.5 + - - +
357B HIS* 4.0 12.1 + - - -
386B GLU* 3.8 21.8 + - - +
318C HIS* 4.6 2.8 - - - -
359C TYR* 6.6 0.7 - - + -
401C SO4 3.6 31.1 + - - +
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Residues in contact with THR 356 (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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352B ILE 2.4 23.4 + - - +
355B GLN* 1.3 77.9 - - - +
357B HIS* 1.3 72.0 + - - +
358B THR* 2.8 21.5 + - - +
379B ASN* 3.2 35.9 - - - +
382B ARG* 4.0 10.8 - - + -
383B ALA* 3.6 21.0 - - - +
386B GLU* 3.4 32.1 - - - +
401C SO4 4.4 4.9 - - - +
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Residues in contact with HIS 357 (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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326B GLN* 5.6 2.6 + - - -
353B GLN 2.9 10.6 + - - -
354B GLN 3.7 11.3 + - - -
355B GLN 3.5 13.2 + - - -
356B THR* 1.3 81.9 + - - +
358B THR* 1.3 59.5 + - - +
374B THR 4.6 1.0 - - - +
375B GLY* 4.6 5.9 - - - -
376B MET 5.2 0.2 + - - -
379B ASN* 4.2 21.9 + - - +
323C LEU* 6.0 2.2 - - - +
357C HIS* 6.4 0.4 - - - -
359C TYR* 6.0 7.6 - + + -
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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