Contacts of the helix formed by residues 354 - 366 (chain A) in PDB entry 4RA2
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 LYS 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ARG* 4.6 2.1 - - - +
305A GLU* 3.2 28.5 + - - +
308A LEU* 3.9 12.2 - - + +
309A ASP* 2.6 30.4 + - - -
312A LEU* 3.6 18.8 - - + -
345A LEU* 4.0 13.2 - - + -
346A PRO* 3.7 35.0 - - + -
350A GLU 4.0 5.4 - - - +
351A LEU* 2.8 12.9 + - + +
353A SER* 1.3 82.9 + - - +
355A ARG* 1.3 64.7 + - - +
356A ASN 3.3 2.7 - - - -
357A VAL* 3.2 18.8 + - - +
358A ILE* 3.1 25.8 + - + +
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Residues in contact with ARG 355 (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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277A TYR* 3.4 48.1 + - + -
330A LEU* 3.4 25.1 - - + +
331A VAL* 5.7 7.5 - - - +
334A MET* 4.1 32.1 - - + +
351A LEU 3.3 3.1 + - - -
352A ALA* 3.3 18.6 + - - +
353A SER 3.5 0.2 - - - -
354A LYS* 1.3 79.0 - - - +
356A ASN* 1.3 58.3 + - - +
358A ILE* 3.7 7.8 - - - +
359A GLU* 2.5 61.8 + - + +
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Residues in contact with ASN 356 (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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270A GLU* 5.9 3.6 - - - +
273A ASP* 2.8 33.5 + - - +
277A TYR* 2.7 31.0 + - - -
353A SER 5.1 3.2 + - - +
354A LYS 3.3 0.8 - - - -
355A ARG* 1.3 76.3 - - - +
357A VAL* 1.3 59.5 + - + +
359A GLU* 3.9 6.7 - - - +
360A ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 357 (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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309A ASP* 3.6 55.0 - - + +
312A LEU* 4.5 10.5 - - + -
313A GLU* 4.6 9.6 - - + +
353A SER 5.8 0.4 - - - +
354A LYS* 3.2 23.1 + - - +
356A ASN* 1.3 78.2 - - + +
358A ILE* 1.3 63.8 + - - +
360A ALA* 3.4 6.6 + - - +
361A VAL* 3.2 23.0 + - - +
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Residues in contact with ILE 358 (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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312A LEU* 4.1 24.5 - - + -
316A VAL* 3.9 16.2 - - + +
330A LEU* 4.1 12.3 - - + -
333A VAL* 4.5 2.7 - - + -
334A MET* 3.7 31.4 - - + -
337A LEU* 3.6 32.1 - - + -
351A LEU* 3.8 22.0 - - + -
354A LYS 3.1 18.9 + - - +
355A ARG 3.3 5.1 + - - +
357A VAL* 1.3 77.0 - - - +
359A GLU* 1.3 57.3 + - - +
361A VAL* 3.3 5.4 + - - +
362A TYR* 2.9 27.1 + - + +
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Residues in contact with GLU 359 (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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277A TYR* 4.5 6.2 + - - -
330A LEU* 3.6 25.8 - - + +
355A ARG* 2.5 52.1 + - - +
356A ASN* 4.0 6.0 - - - +
358A ILE* 1.3 71.8 - - - +
360A ALA* 1.3 60.5 + - - +
362A TYR* 4.1 6.1 - - + -
363A ASN* 2.8 50.3 + - - +
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Residues in contact with ALA 360 (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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356A ASN 3.0 19.8 + - - +
357A VAL* 3.6 7.6 - - - +
358A ILE 3.3 0.2 - - - -
359A GLU* 1.3 76.8 - - - +
361A VAL* 1.3 62.6 + - + +
363A ASN* 3.4 8.3 + - - +
364A ARG* 3.1 39.5 + - - +
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Residues in contact with VAL 361 (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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313A GLU* 3.0 61.9 - - + +
316A VAL* 4.2 8.1 - - + -
317A GLU* 4.9 2.9 - - + -
357A VAL 3.2 16.0 + - - +
358A ILE* 3.7 5.6 - - - +
360A ALA* 1.3 72.4 - - + +
362A TYR* 1.3 69.0 + - - +
364A ARG* 3.0 30.0 + - - +
365A LEU* 3.1 31.8 + - + +
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Residues in contact with TYR 362 (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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316A VAL* 4.1 13.4 - - + +
320A ILE* 4.0 16.6 - - + -
328A PRO 2.8 29.8 + - - -
329A ASP* 3.3 9.9 - - - +
330A LEU* 3.6 38.8 - - + -
333A VAL* 3.7 25.4 - - + -
358A ILE* 2.9 18.3 + - + +
359A GLU 3.6 4.0 - - - +
361A VAL* 1.3 75.0 - - - +
363A ASN* 1.3 69.2 + - - +
365A LEU* 3.2 5.0 + - - +
366A ASN* 2.8 63.1 + - + +
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Residues in contact with ASN 363 (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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330A LEU* 5.8 0.3 - - - +
359A GLU* 2.8 40.1 + - - +
360A ALA* 3.6 7.7 - - - +
362A TYR* 1.3 90.4 - - - +
364A ARG* 1.3 60.4 + - + +
366A ASN 4.5 4.5 - - - +
367A PRO* 3.1 31.5 - - + +
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Residues in contact with ARG 364 (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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313A GLU* 3.3 29.9 + - - +
360A ALA* 3.1 36.1 + - - +
361A VAL* 3.0 26.5 + - + +
363A ASN* 1.3 76.4 - - + +
365A LEU* 1.3 66.5 + - + +
367A PRO* 3.6 11.5 - - - +
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Residues in contact with LEU 365 (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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316A VAL* 4.0 11.2 - - + -
317A GLU* 3.9 37.5 - - + +
320A ILE* 3.8 26.0 - - + +
361A VAL* 3.1 31.7 + - + +
362A TYR 3.8 0.4 - - - +
364A ARG* 1.3 79.4 - - + +
366A ASN* 1.3 60.4 + - - +
367A PRO* 3.3 7.4 - - - +
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Residues in contact with ASN 366 (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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320A ILE* 4.3 8.3 - - + -
327A VAL* 3.3 25.8 - - - +
362A TYR* 2.8 53.0 + - + +
363A ASN* 3.5 7.2 - - - +
365A LEU* 1.3 80.9 - - - +
367A PRO* 1.3 65.1 - - - +
368A TYR* 3.1 19.0 + - - +
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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