Contacts of the helix formed by residues 318 - 328 (chain A) in PDB entry 1ULH
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 ALA 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A THR* 1.3 85.6 + - - +
319A LYS* 1.3 62.3 + - - +
320A GLN 3.3 0.9 - - - -
321A ILE* 3.5 8.4 + - - +
322A LYS* 3.1 15.4 + - - +
392A GLN* 2.9 39.7 + - + +
396A ALA* 6.2 4.0 - - + -
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Residues in contact with LYS 319 (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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317A THR* 3.6 7.6 + - + +
318A ALA* 1.3 80.8 - - - +
320A GLN* 1.3 59.2 + - + +
322A LYS* 3.1 39.5 + - + +
323A THR* 2.7 42.6 + - + -
392A GLN* 5.3 2.6 - - - +
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Residues in contact with GLN 320 (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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315A THR 4.6 0.7 - - - +
316A ASP* 3.5 23.7 + - + +
317A THR* 2.8 45.5 + - + +
318A ALA 3.3 0.4 - - - -
319A LYS* 1.3 79.0 - - + +
321A ILE* 1.3 55.3 + - - +
323A THR* 3.0 9.0 + - - +
324A LYS* 2.9 41.7 + - - +
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Residues in contact with ILE 321 (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 ILE* 4.4 11.0 - - + -
316A ASP* 4.1 10.5 - - + -
317A THR 3.0 25.8 - - - +
318A ALA* 3.5 9.2 - - + +
319A LYS 3.2 0.2 - - - -
320A GLN* 1.3 75.7 - - - +
322A LYS* 1.3 62.7 + - - +
324A LYS* 3.3 5.0 + - - +
325A VAL* 3.3 27.2 + - + +
388A ILE* 4.8 3.8 - - + -
391A LEU* 4.0 33.0 - - + -
392A GLN* 4.0 24.7 - - + +
395A ILE* 3.5 39.5 - - + -
396A ALA* 5.3 1.1 - - + +
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Residues in contact with LYS 322 (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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318A ALA 3.1 11.7 + - - +
319A LYS* 3.3 43.3 - - + +
321A ILE* 1.3 79.4 - - - +
323A THR* 1.3 69.0 + - + +
325A VAL* 3.4 2.3 - - - +
326A ASN* 2.7 48.2 + - + +
388A ILE* 4.2 20.6 - - + -
392A GLN* 4.0 9.8 - - - +
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Residues in contact with THR 323 (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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319A LYS* 2.7 37.5 + - + +
320A GLN* 3.0 14.7 + - - +
322A LYS* 1.3 86.6 - - + +
324A LYS* 1.3 58.5 + - - +
326A ASN* 4.4 4.0 - - - -
327A LYS* 3.1 57.0 + - - +
328A HIS* 4.2 2.5 - - - -
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Residues in contact with LYS 324 (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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296A LEU* 4.5 11.6 - - + +
309A ASN* 3.4 40.5 - - + +
311A SER 2.9 21.9 + - - +
312A ILE* 3.8 26.9 - - + -
313A PHE* 4.0 13.3 - - - -
316A ASP* 2.7 34.4 + - - +
320A GLN* 2.9 24.8 + - - +
321A ILE 3.7 4.5 - - - +
322A LYS 3.2 0.4 - - - -
323A THR* 1.3 75.8 - - - +
325A VAL* 1.3 60.2 + - - +
326A ASN 3.1 1.6 - - - -
328A HIS* 2.7 35.2 + - + +
329A ALA 3.2 5.9 + - - -
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Residues in contact with VAL 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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296A LEU* 5.1 4.0 - - + -
312A ILE* 3.6 24.5 - - + -
321A ILE* 3.3 13.0 + - + +
322A LYS 3.4 10.1 - - - +
324A LYS* 1.3 75.3 - - - +
326A ASN* 1.3 60.9 + - - +
329A ALA* 3.1 18.8 - - + +
352A SER* 5.3 1.1 - - - +
355A TYR* 5.5 0.2 - - + -
384A LYS* 3.0 33.0 + - + +
387A LEU* 4.2 15.5 - - + -
388A ILE* 3.3 34.3 - - + -
391A LEU* 3.9 17.9 - - + -
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Residues in contact with ASN 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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322A LYS* 2.7 42.4 + - - +
323A THR* 4.3 4.7 - - - +
324A LYS 3.1 0.4 - - - -
325A VAL* 1.3 83.0 - - - +
327A LYS* 1.3 65.3 + - + +
328A HIS 3.7 0.2 - - - -
381A GLY* 4.7 6.4 - - - +
384A LYS* 3.2 38.5 + - - +
385A LYS* 5.1 1.1 + - - +
388A ILE* 3.5 19.5 - - - +
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Residues in contact with LYS 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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323A THR* 3.1 43.0 + - - +
326A ASN* 1.3 83.2 - - + +
328A HIS* 1.3 80.6 + - + +
329A ALA 5.1 0.7 - - - -
384A LYS* 5.4 0.4 - - - -
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Residues in contact with HIS 328 (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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296A LEU* 4.3 4.5 - - + -
297A GLN* 3.0 56.7 + - + +
309A ASN* 2.7 49.2 + - + +
323A THR 4.2 7.2 - - - -
324A LYS* 2.7 20.5 + - + +
327A LYS* 1.3 96.1 + - + +
329A ALA* 1.3 67.4 + - - +
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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