Contacts of the helix formed by residues 333 - 348 (chain J) in PDB entry 5A31
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 TYR 333 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J PRO* 4.7 9.5 - - + +
299J PRO* 4.2 24.5 - - + -
300J VAL* 3.3 33.5 - - + +
303J PHE* 4.1 27.1 - + + -
326J ALA* 4.7 3.8 - - + +
327J THR* 3.9 4.3 + - - -
330J GLU* 3.0 29.0 + - + +
332J THR* 1.3 74.6 - - - +
334J GLY* 1.3 64.6 + - - +
335J PRO* 3.7 19.0 - - + +
336J ALA* 3.5 36.8 + - + +
337J TRP* 3.4 21.9 + - - -
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Residues in contact with GLY 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.5 0.7 - - - -
174J HIS* 5.1 4.2 - - - -
332J THR 3.3 6.1 + - - -
333J TYR* 1.3 71.2 - - - +
335J PRO* 1.4 64.9 - - - +
337J TRP* 2.8 28.6 + - - +
338J ILE* 3.2 5.2 + - - +
363J LEU* 4.2 5.2 - - - -
364J MET* 3.3 37.9 - - - +
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Residues in contact with PRO 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.1 40.1 - - + +
2G LEU* 5.9 0.5 + - - +
174J HIS* 4.9 9.0 - - - +
269J PRO* 5.7 7.4 - - + -
303J PHE* 4.2 19.2 - - + -
333J TYR* 3.4 31.0 - - + +
334J GLY* 1.4 91.1 - - - +
336J ALA* 1.3 60.4 + - - +
338J ILE* 3.3 4.9 + - + +
339J ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J PHE* 4.1 14.3 - - + -
323J LEU* 3.8 15.6 - - + +
326J ALA* 4.1 18.6 - - + -
327J THR* 4.3 7.6 - - - -
333J TYR* 3.5 31.4 - - + +
334J GLY 3.2 0.4 - - - -
335J PRO* 1.3 77.9 - - - +
337J TRP* 1.3 66.1 + - - +
339J ALA* 3.7 3.8 + - - +
340J TYR* 3.1 22.0 + - - +
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Residues in contact with TRP 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327J THR* 2.7 37.6 + - + -
331J LYS* 5.3 3.2 - - + +
332J THR 4.8 1.8 - - - +
333J TYR 3.4 15.9 - - - -
334J GLY 2.8 12.2 + - - +
336J ALA* 1.3 72.1 - - - +
338J ILE* 1.3 67.7 + - - +
340J TYR* 3.0 39.6 + + - +
341J GLY* 3.0 18.5 + - - -
356J ALA* 4.2 13.7 - - + +
359J THR* 3.3 37.2 - - + -
360J ALA* 3.6 19.7 - - + -
363J LEU* 3.8 35.2 - - + +
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Residues in contact with ILE 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 3.5 31.2 - - + -
2G LEU* 4.1 14.1 - - + +
334J GLY 3.2 3.0 + - - +
335J PRO* 3.9 8.3 - - + +
336J ALA 3.3 0.2 - - - -
337J TRP* 1.3 78.6 - - - +
339J ALA* 1.3 65.7 + - - +
341J GLY* 3.0 12.1 + - - -
342J HIS* 3.0 36.6 + - + +
357J TYR* 3.6 19.5 - - + -
360J ALA* 4.1 13.0 - - + -
364J MET* 4.0 20.0 - - + -
369J LEU* 4.1 14.8 - - + -
370J PRO* 4.1 16.2 - - + -
373J TYR* 5.0 5.8 - - + -
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Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LEU* 4.8 9.0 - - + -
303J PHE* 4.2 15.7 - - + -
310J LEU* 4.5 14.8 - - + +
323J LEU* 4.0 19.1 - - + +
335J PRO 3.1 17.1 + - - +
336J ALA 3.7 6.1 - - - +
338J ILE* 1.3 78.8 - - - +
340J TYR* 1.3 62.4 + - - +
342J HIS* 3.1 24.3 + - - +
343J SER* 3.1 12.5 + - - -
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Residues in contact with TYR 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J ARG* 3.7 22.7 - - + +
323J LEU* 3.9 17.7 - - + +
324J SER* 3.6 29.9 + - - -
327J THR* 4.9 2.7 - - + -
336J ALA 3.1 14.8 + - - +
337J TRP* 3.0 46.1 + + + +
339J ALA* 1.3 75.3 - - - +
341J GLY* 1.3 60.0 + - - +
343J SER* 2.5 22.8 + - - -
344J PHE* 3.3 37.4 - + - -
356J ALA* 4.2 4.5 - - + -
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Residues in contact with GLY 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J TRP 3.0 6.9 + - - -
338J ILE 3.0 10.1 + - - -
340J TYR* 1.3 75.5 - - - +
342J HIS* 1.3 61.4 + - - +
344J PHE* 3.0 16.0 + - - +
345J ALA 3.1 9.5 + - - -
353J ALA* 3.7 8.9 - - - +
356J ALA* 3.6 18.9 - - - +
357J TYR* 3.4 22.1 + - - -
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Residues in contact with HIS 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LEU* 3.0 43.6 + - + +
3G ARG* 4.8 1.1 - - - -
4G ARG* 3.4 33.4 - - + +
310J LEU* 5.4 6.7 - - + -
338J ILE* 3.0 31.8 + - + +
339J ALA* 3.3 14.9 - - - +
341J GLY* 1.3 76.5 - - - +
343J SER* 1.3 60.9 + - - +
345J ALA* 3.7 2.6 - - - +
346J VAL* 2.9 27.5 + - - +
357J TYR* 2.8 28.2 + - - -
373J TYR* 4.3 9.0 - + - -
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Residues in contact with SER 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310J LEU* 4.2 21.4 - - - +
316J ASN* 3.9 8.5 - - - +
320J ARG* 3.6 33.7 + - - +
323J LEU* 4.3 2.8 - - - +
339J ALA 3.1 11.4 + - - -
340J TYR* 2.5 25.4 + - - -
342J HIS* 1.3 73.8 - - - +
344J PHE* 1.3 62.6 + - - +
346J VAL* 3.3 21.2 - - - +
347J ALA* 3.4 11.1 + - - +
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Residues in contact with PHE 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J ARG* 3.2 41.5 - - - -
340J TYR* 3.3 48.2 - + - -
341J GLY* 3.0 5.8 + - - +
343J SER* 1.3 80.2 - - - +
345J ALA* 1.3 53.5 + - - +
347J ALA* 3.2 5.3 + - - +
348J SER 2.7 30.0 + - - -
349J GLU* 3.0 41.9 + - - +
352J GLN* 3.2 51.8 - - + -
353J ALA* 3.6 7.6 - - - +
356J ALA* 4.8 2.7 - - + -
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Residues in contact with ALA 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 3.4 29.3 + - - +
341J GLY 3.1 11.2 + - - +
342J HIS 3.7 5.8 - - - +
344J PHE* 1.3 76.9 - - - +
346J VAL* 1.3 59.4 + - - +
348J SER* 2.9 22.7 + - - +
349J GLU 4.8 0.4 - - - +
350J HIS* 4.8 6.3 + - + -
353J ALA* 3.9 4.6 - - - +
357J TYR* 4.0 3.4 - - - +
377J GLU* 3.0 31.2 - - - +
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Residues in contact with VAL 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 4.1 6.6 - - - +
310J LEU* 5.6 2.9 - - + -
316J ASN* 3.9 17.7 - - - +
342J HIS* 2.9 15.9 + - + +
343J SER* 3.3 17.0 - - - +
345J ALA* 1.3 76.3 - - - +
347J ALA* 1.3 64.4 + - - +
348J SER* 3.3 3.6 + - - -
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Residues in contact with ALA 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316J ASN* 4.3 11.2 - - - +
320J ARG* 4.3 12.1 - - - +
343J SER 3.4 13.7 + - - +
344J PHE* 3.2 5.9 + - - +
346J VAL* 1.3 78.3 - - - +
348J SER* 1.3 69.1 + - - +
349J GLU* 3.4 17.0 + - - +
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Residues in contact with SER 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344J PHE 2.7 10.3 + - - -
345J ALA 2.9 15.9 + - - -
346J VAL 3.1 4.0 - - - -
347J ALA* 1.3 77.8 - - - +
349J GLU* 1.3 55.9 + - - +
350J HIS* 3.2 37.9 + - - -
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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