Contacts of the helix formed by residues 324 - 339 (chain A) in PDB entry 5ITZ
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 VAL 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A VAL* 4.7 1.8 - - - +
322A ASP* 4.2 10.0 + - - +
323A VAL* 1.3 75.7 - - - +
325A PRO* 1.3 79.3 - - + +
326A LYS* 4.1 24.2 - - + +
327A ASP* 2.9 35.4 + - - +
328A VAL* 3.3 9.5 + - - +
355A ILE* 4.5 0.7 - - - -
357A TYR* 5.3 0.2 - - - -
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Residues in contact with PRO 325 (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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323A VAL 3.7 2.5 - - - +
324A VAL* 1.3 88.9 - - + +
326A LYS* 1.3 61.1 - - - +
328A VAL* 3.0 14.7 + - - +
329A ASN* 3.1 21.2 + - - +
355A ILE* 3.8 19.5 - - + -
357A TYR* 3.4 27.6 - - + +
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Residues in contact with LYS 326 (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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324A VAL* 4.1 16.5 - - + +
325A PRO* 1.3 78.4 - - - +
327A ASP* 1.3 73.8 + - - +
329A ASN* 3.4 11.3 + - - +
330A ALA* 3.0 28.6 + - - +
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Residues in contact with ASP 327 (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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288A VAL* 3.6 24.2 - - + +
289A ALA* 5.3 0.5 + - - +
324A VAL* 2.9 32.3 + - - +
326A LYS* 1.3 86.7 - - - +
328A VAL* 1.3 60.3 + - - +
330A ALA* 3.5 6.1 + - - +
331A ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 3.8 9.0 - - + -
319A TYR* 3.6 38.1 - - + +
323A VAL* 3.4 33.2 - - + -
324A VAL 3.3 4.1 + - - +
325A PRO* 3.0 9.9 + - + +
327A ASP* 1.3 77.4 - - - +
329A ASN* 1.3 62.1 + - - +
331A ALA* 3.1 2.9 + - - +
332A ILE* 2.8 46.6 + - + +
353A VAL* 3.7 17.5 - - + -
355A ILE* 4.1 6.7 - - + -
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Residues in contact with ASN 329 (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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325A PRO* 3.1 21.1 + - - +
326A LYS* 3.8 9.9 - - - +
328A VAL* 1.3 82.0 - - - +
330A ALA* 1.3 57.9 + - - +
332A ILE* 3.4 8.7 + - - +
333A ALA* 2.9 31.2 + - - +
353A VAL* 5.1 4.2 - - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS 3.0 16.3 + - - +
327A ASP* 3.9 7.4 - - - +
329A ASN* 1.3 78.5 - - - +
331A ALA* 1.3 57.4 + - - +
333A ALA* 3.4 7.2 + - - +
334A THR* 2.9 32.9 + - - +
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Residues in contact with ALA 331 (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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288A VAL* 4.2 2.7 - - + -
289A ALA* 3.9 33.0 - - + +
292A THR* 3.9 20.9 - - + +
293A ASN* 5.1 2.0 - - - +
327A ASP 3.0 18.3 + - - +
328A VAL* 3.1 4.0 + - - +
330A ALA* 1.3 77.2 - - - +
332A ILE* 1.3 61.9 + - - +
334A THR* 3.2 9.2 + - - -
335A ILE* 3.0 26.0 + - - +
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Residues in contact with ILE 332 (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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292A THR* 4.9 2.0 - - + -
317A LEU* 3.7 24.2 - - + -
319A TYR* 4.5 3.8 - - - +
328A VAL* 2.8 28.2 + - + +
329A ASN* 3.9 7.9 - - - +
331A ALA* 1.3 75.3 - - - +
333A ALA* 1.3 65.6 + - - +
335A ILE* 3.0 10.6 + - - +
336A LYS* 3.0 43.3 + - + +
351A PHE* 3.7 26.9 - - + +
353A VAL* 3.5 32.1 - - + -
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Residues in contact with ALA 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 ASN 2.9 18.8 + - - +
330A ALA* 3.6 7.6 - - - +
332A ILE* 1.3 77.6 - - - +
334A THR* 1.3 61.4 + - - +
336A LYS* 3.3 10.1 + - - +
337A THR* 3.1 29.8 + - + +
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Residues in contact with THR 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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293A ASN* 4.9 12.8 - - - +
330A ALA* 2.9 16.2 + - - +
331A ALA* 3.4 11.6 - - - +
333A ALA* 1.3 78.3 - - - +
335A ILE* 1.3 65.2 + - + +
337A THR* 3.2 9.9 + - - +
338A LYS* 3.0 46.4 + - + +
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Residues in contact with ILE 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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292A THR* 4.1 10.3 - - + -
293A ASN* 3.2 30.7 - - + +
296A PHE* 3.8 43.3 - - + -
331A ALA 3.0 18.3 + - - +
332A ILE* 3.0 10.7 + - - +
334A THR* 1.3 77.7 - - + +
336A LYS* 1.3 57.9 + - + +
338A LYS* 5.0 1.3 - - + -
339A ARG* 2.6 61.9 + - + +
341A ILE* 4.2 9.4 - - + -
351A PHE* 4.6 7.9 - - + -
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Residues in contact with LYS 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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332A ILE* 3.0 38.1 + - + +
333A ALA* 3.8 10.1 - - - +
334A THR 3.3 0.2 - - - -
335A ILE* 1.3 81.6 - - + +
337A THR* 1.3 63.0 + - + +
339A ARG 3.6 11.7 - - - +
341A ILE* 5.0 8.7 - - + -
343A PHE* 6.2 0.2 - - - -
349A THR 4.2 15.8 + - - -
350A GLY* 4.6 2.8 - - - -
351A PHE* 4.2 31.6 - - + +
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Residues in contact with THR 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 ALA* 3.1 19.5 - - + +
334A THR* 3.2 11.8 + - - +
336A LYS* 1.3 79.1 - - + +
338A LYS* 1.3 71.1 + - - +
339A ARG 4.6 0.4 - - - +
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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
----------------------------------------------------------
334A THR* 3.0 31.0 + - + +
335A ILE* 5.0 0.7 - - + -
337A THR* 1.3 87.8 - - - +
339A ARG* 1.3 71.6 + - + +
340A SER* 5.0 2.1 + - - -
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Residues in contact with ARG 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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293A ASN 5.1 1.6 + - - -
296A PHE* 3.4 30.4 + - + +
297A GLU* 3.5 23.0 + - - -
307A PRO* 6.0 0.4 - - - +
308A ARG* 3.0 39.0 - - - +
335A ILE* 2.6 49.7 + - + +
336A LYS 3.6 16.3 - - - +
337A THR 4.6 0.5 - - - -
338A LYS* 1.3 82.9 - - + +
340A SER* 1.3 61.8 + - - +
341A ILE* 3.2 25.0 + - + +
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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