Contacts of the helix formed by residues 332 - 347 (chain B) in PDB entry 4R1Z
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 ASN 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B TYR* 3.0 24.0 + - - +
329B LEU 2.8 14.5 + - - +
331B HIS* 1.3 94.0 + - - +
333B PRO* 1.3 66.4 - - - +
334B GLN* 2.9 29.3 + - - +
335B VAL* 3.4 19.5 + - + +
336B GLN 3.5 7.1 + - - -
423B PHE* 4.1 32.0 - - + +
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Residues in contact with PRO 333 (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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329B LEU 3.7 4.7 - - - +
330B VAL 4.1 9.2 - - - +
331B HIS 3.4 10.3 - - - +
332B ASN* 1.3 83.6 - - - +
334B GLN* 1.3 69.8 + - - +
335B VAL 3.5 0.2 - - - -
336B GLN* 3.5 11.5 - - + +
337B ARG* 3.3 28.9 + - - +
476B LEU 6.2 0.2 - - - +
484B LEU* 6.1 1.6 - - + -
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS 4.7 0.2 - - - +
332B ASN* 2.9 34.1 + - - +
333B PRO* 1.3 88.2 - - - +
335B VAL* 1.3 76.1 + - + +
337B ARG* 3.5 27.5 + - - +
338B LYS* 3.3 27.6 + - - +
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 4.0 12.6 - - + -
332B ASN* 3.4 25.4 + - + +
334B GLN* 1.3 86.2 - - + +
336B GLN* 1.3 57.8 + - - +
338B LYS* 2.7 28.2 + - - +
339B ILE* 2.9 25.4 + - + -
363B TYR* 3.6 25.6 - - + +
367B THR* 3.9 24.5 - - + +
423B PHE* 4.3 7.9 - - + +
425B PRO* 4.1 17.3 - - + -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 2.8 51.2 + - + +
330B VAL* 3.8 0.6 - - - +
332B ASN 3.5 3.9 + - - +
333B PRO* 3.5 15.1 - - + +
335B VAL* 1.3 84.5 - - - +
337B ARG* 1.3 57.8 + - + +
339B ILE* 3.5 7.7 + - - +
340B GLN* 3.2 33.5 + - - +
471B LEU* 3.7 25.0 - - + +
475B THR* 3.6 11.8 + - - +
476B LEU* 2.7 48.9 + - - +
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Residues in contact with ARG 337 (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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333B PRO* 3.3 14.1 + - - +
334B GLN* 3.8 25.6 + - - +
335B VAL 3.2 0.4 - - - -
336B GLN* 1.3 79.6 - - + +
338B LYS* 1.3 60.5 + - - +
340B GLN* 3.6 22.4 - - - +
341B GLU* 3.4 40.4 + - - +
475B THR* 6.0 1.3 - - - +
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Residues in contact with LYS 338 (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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334B GLN* 3.3 17.5 + - - +
335B VAL* 2.7 15.1 + - - +
337B ARG* 1.3 82.3 - - + +
339B ILE* 1.3 63.0 + - - +
340B GLN 3.0 0.7 - - - -
341B GLU* 3.3 17.9 + - + +
342B GLU* 3.1 20.8 + - - +
363B TYR* 3.5 50.9 - - + +
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Residues in contact with ILE 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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329B LEU* 4.3 4.3 - - + -
335B VAL* 2.9 28.2 + - + +
336B GLN* 3.6 7.2 - - - +
338B LYS* 1.3 76.4 - - - +
340B GLN* 1.3 58.0 + - - +
342B GLU* 3.4 10.4 + - - +
343B LEU* 2.9 41.9 + - + +
363B TYR* 3.8 20.4 - - + -
364B LEU* 4.1 32.1 - - + -
367B THR* 4.0 19.1 - - + +
467B LEU 5.5 0.2 - - - +
471B LEU* 3.5 33.2 - - + -
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 3.2 17.1 + - - +
337B ARG* 3.6 24.3 + - - +
338B LYS 3.0 0.4 - - - -
339B ILE* 1.3 74.9 - - - +
341B GLU* 1.3 64.3 + - - +
342B GLU 3.1 1.6 - - - -
343B LEU* 3.2 6.6 + - - +
344B ASP* 3.1 31.5 + - - +
471B LEU* 3.1 29.4 - - + +
474B PHE 2.7 28.1 - - - +
475B THR* 3.8 14.2 + - - -
507B ARG* 3.5 31.3 - - - +
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Residues in contact with GLU 341 (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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337B ARG* 3.4 28.4 + - - +
338B LYS* 3.3 18.5 + - - +
340B GLN* 1.3 78.7 - - - +
342B GLU* 1.3 58.6 + - - +
344B ASP* 3.7 4.8 + - - +
345B SER* 3.0 25.5 + - - -
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Residues in contact with GLU 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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338B LYS 3.1 12.2 + - - +
339B ILE* 3.4 9.9 - - - +
340B GLN 3.1 0.4 - - - -
341B GLU* 1.3 75.0 - - - +
343B LEU* 1.3 60.4 + - - +
344B ASP 3.2 0.2 - - - -
345B SER* 3.1 6.8 + - - +
346B LYS* 3.0 41.8 + - + +
360B ASN 3.9 3.3 - - - +
361B LEU* 3.5 30.1 - - + +
362B PRO* 3.1 16.5 - - - +
363B TYR* 3.0 28.8 + - + +
364B LEU* 3.3 24.8 + - - +
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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 ILE* 2.9 38.4 + - + +
340B GLN* 3.2 6.5 + - - +
342B GLU* 1.3 75.8 - - - +
344B ASP* 1.3 63.2 + - - +
347B ILE* 3.1 31.4 + - + +
348B GLY 3.0 22.9 + - - +
353B PRO* 4.4 11.9 - - + -
361B LEU* 3.4 28.9 - - + -
364B LEU* 5.2 1.6 - - + -
468B ALA* 3.7 26.5 - - + +
471B LEU* 4.1 5.2 - - + +
472B GLN* 3.9 25.9 + - + +
507B ARG* 5.5 0.2 - - - +
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Residues in contact with ASP 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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101A LYS* 4.7 2.3 + - - -
340B GLN 3.1 14.2 + - - +
341B GLU* 4.2 4.9 - - - +
343B LEU* 1.3 81.9 - - - +
345B SER* 1.3 64.9 + - - +
348B GLY* 3.1 30.0 + - - +
349B LYS* 4.1 32.4 + - - +
472B GLN* 5.0 5.2 - - - +
507B ARG* 2.6 35.8 + - - -
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Residues in contact with SER 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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101A LYS* 3.3 20.1 + - - +
341B GLU 3.0 18.0 + - - -
342B GLU* 3.1 11.4 + - - +
344B ASP* 1.3 80.2 - - - +
346B LYS* 1.3 71.9 + - - +
347B ILE 3.6 0.2 - - - -
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Residues in contact with LYS 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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93A HIS* 5.5 7.3 + - - -
96A LYS* 5.4 5.1 - - - +
101A LYS* 4.1 13.7 - - - +
342B GLU* 3.0 21.2 + - + +
343B LEU 4.3 0.2 - - - -
345B SER* 1.3 96.3 - - - +
347B ILE* 1.3 68.3 + - - +
357B ASP* 3.7 7.4 - - - +
360B ASN* 2.9 66.1 + - - +
361B LEU* 3.8 10.7 - - + +
362B PRO* 5.1 4.2 - - - +
434B ASP* 6.2 2.0 - - - +
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Residues in contact with ILE 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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101A LYS* 4.0 14.8 - - - +
343B LEU* 3.1 36.2 + - + +
344B ASP 4.1 0.2 - - - -
345B SER 3.6 0.2 - - - -
346B LYS* 1.3 86.7 - - - +
348B GLY* 1.3 66.7 + - - +
349B LYS 4.2 0.3 + - - -
350B GLU 5.1 0.5 + - - -
351B ARG* 3.6 46.8 + - + +
352B HIS 4.5 2.2 - - - +
353B PRO* 3.8 27.4 - - + -
357B ASP* 3.9 16.2 - - + +
361B LEU* 4.0 12.6 - - + -
472B GLN* 4.1 13.2 - - - +
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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