Contacts of the helix formed by residues 332 - 347 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A TYR* 2.9 28.7 + - - +
329A LEU 3.1 7.1 + - - +
331A HIS* 1.3 91.5 - - - +
333A PRO* 1.3 58.5 - - - +
334A GLN* 2.9 28.7 + - - +
335A VAL* 2.6 38.2 + - + +
336A GLN 3.2 7.6 + - - -
423A PHE* 4.1 29.2 - - + +
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Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU 3.6 3.2 - - - +
330A VAL 3.7 9.9 - - - +
331A HIS 3.2 9.9 - - - +
332A ASN* 1.3 89.3 - - - +
334A GLN* 1.3 66.1 + - - +
336A GLN* 3.4 14.6 + - + +
337A ARG* 3.0 24.6 + - - +
484A LEU* 6.2 0.2 - - + -
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Residues in contact with GLN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ASN* 2.9 41.4 + - - +
333A PRO* 1.3 75.2 - - - +
335A VAL* 1.3 72.9 + - + +
337A ARG* 3.8 2.6 - - - +
338A LYS* 3.1 45.5 + - + +
423A PHE 5.6 1.4 + - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 4.1 8.1 - - + -
332A ASN* 2.6 23.9 + - + +
334A GLN* 1.3 87.3 - - + +
336A GLN* 1.3 66.0 + - - +
338A LYS 3.3 0.3 + - - -
339A ILE* 3.0 28.3 + - + +
363A TYR* 3.4 24.1 - - + +
367A THR* 3.9 34.8 - - + +
423A PHE* 4.4 9.9 - - + +
425A PRO* 3.8 18.6 - - + -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 2.8 49.9 + - + +
330A VAL* 3.9 0.6 + - - +
332A ASN 3.2 3.2 + - - -
333A PRO* 3.5 15.3 - - + +
335A VAL* 1.3 79.8 - - - +
337A ARG* 1.3 56.0 + - - +
339A ILE* 3.2 4.9 + - - +
340A GLN* 2.9 39.5 + - - +
471A LEU* 3.6 26.2 - - + +
475A THR* 3.5 11.4 + - - -
476A LEU* 2.6 46.6 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PRO 3.0 16.9 + - - +
334A GLN* 3.8 5.6 - - - +
336A GLN* 1.3 76.3 - - - +
338A LYS* 1.3 82.5 + - - +
340A GLN* 3.2 15.6 + - + +
341A GLU* 3.0 54.7 + - + +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLN* 3.1 41.3 + - + +
336A GLN 3.3 0.2 - - - -
337A ARG* 1.3 108.3 - - - +
339A ILE* 1.3 64.6 + - - +
341A GLU* 3.3 21.8 + - - +
342A GLU* 3.0 22.9 + - - +
363A TYR* 3.4 41.6 - - + +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 4.3 5.4 - - + -
335A VAL* 3.0 21.4 + - + +
336A GLN 3.4 7.6 - - - +
338A LYS* 1.3 77.6 - - - +
340A GLN* 1.3 61.7 + - - +
342A GLU* 3.3 8.2 + - - +
343A LEU* 3.1 36.2 + - + +
363A TYR* 3.6 18.4 - - + -
364A LEU* 3.7 34.3 - - + -
367A THR* 3.6 27.1 - - + +
467A LEU* 6.3 0.2 - - + -
468A ALA* 6.0 0.4 - - - -
471A LEU* 3.7 31.0 - - + -
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLN* 2.9 26.0 + - - +
337A ARG* 3.7 17.9 - - + +
339A ILE* 1.3 76.3 - - - +
341A GLU* 1.3 58.6 + - - +
343A LEU* 3.2 8.8 + - - +
344A ASP* 2.9 34.3 + - - +
471A LEU* 3.1 26.2 - - + +
474A PHE 2.9 26.0 - - - +
475A THR* 3.6 17.9 - - - +
507A ARG* 3.4 30.2 - - - +
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Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.0 49.3 + - + +
338A LYS* 3.5 34.5 - - - +
340A GLN* 1.3 74.4 - - - +
342A GLU* 1.3 63.5 + - - +
344A ASP* 3.7 10.8 - - + +
345A SER* 3.4 22.0 + - - -
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LYS 3.0 13.2 + - - +
339A ILE* 3.4 11.6 - - - +
341A GLU* 1.3 76.6 - - - +
343A LEU* 1.3 60.4 + - - +
344A ASP 3.1 0.2 - - - -
345A SER* 3.2 3.8 + - - -
346A LYS* 3.0 48.0 + - + +
361A LEU* 3.4 35.0 - - + +
362A PRO* 3.0 14.4 - - - +
363A TYR* 3.0 33.7 + - + +
364A LEU* 3.4 17.8 + - - +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ILE* 3.1 30.2 + - + +
340A GLN* 3.5 7.9 - - - +
342A GLU* 1.3 77.9 - - - +
344A ASP* 1.3 69.1 + - - +
345A SER 3.3 0.2 - - - -
346A LYS 4.0 0.9 - - - +
347A ILE* 3.4 34.5 + - + +
348A GLY 3.2 20.6 + - - +
353A PRO* 5.0 2.0 - - + -
361A LEU* 4.1 20.4 - - + -
364A LEU* 5.2 3.6 - - + -
468A ALA* 3.8 23.1 - - + +
471A LEU* 3.9 8.1 - - + +
472A GLN* 3.6 39.3 - - + +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A GLN 2.9 16.5 + - - +
341A GLU* 4.0 10.2 - - + +
342A GLU 3.1 0.4 - - - -
343A LEU* 1.3 85.1 - - - +
345A SER* 1.3 60.3 + - - +
348A GLY* 3.4 27.3 - - - +
349A LYS* 6.0 1.8 - - - +
472A GLN* 5.4 2.6 - - - +
507A ARG* 2.8 40.6 + - - -
509A ASP* 6.0 1.8 - - - -
510A TRP* 5.7 1.6 + - - -
101B LYS* 4.9 1.2 + - - -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLU 3.4 12.3 + - - -
342A GLU* 3.2 6.9 + - - -
344A ASP* 1.3 80.3 - - - +
346A LYS* 1.3 80.2 + - - +
347A ILE 3.5 0.7 - - - -
101B LYS* 3.2 24.0 + - - +
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Residues in contact with LYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A GLU* 3.0 23.4 + - + +
345A SER* 1.3 96.7 - - - +
347A ILE* 1.3 68.1 + - - +
357A ASP* 4.1 5.4 - - - +
360A ASN* 3.0 61.7 + - + +
361A LEU* 4.0 6.1 - - + -
362A PRO* 5.7 2.5 - - + -
93B HIS* 5.2 11.5 + - - +
96B LYS* 5.1 6.1 - - - +
101B LYS* 3.6 20.6 - - - +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.4 29.1 + - + +
345A SER 3.5 0.8 + - - -
346A LYS* 1.3 86.6 - - - +
348A GLY* 1.3 61.6 + - - +
349A LYS 4.0 0.7 + - - -
350A GLU 5.1 0.3 + - - -
351A ARG* 3.9 36.0 + - + +
352A HIS 4.3 7.0 - - - -
353A PRO* 3.5 28.9 - - + -
357A ASP* 3.6 30.1 - - + +
361A LEU* 4.1 9.9 - - + -
472A GLN* 3.5 26.7 - - - +
101B LYS* 4.1 12.2 - - - +
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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