Contacts of the helix formed by residues 317 - 329 (chain B) 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 THR 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B THR 5.1 2.9 - - - +
316B ASP* 1.3 76.7 - - - +
318B ALA* 1.3 64.4 + - - +
319B LYS* 3.3 11.0 + - - +
320B GLN* 2.7 46.3 + - - +
321B ILE* 3.0 20.8 + - - +
399B GLN* 5.2 1.3 - - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B THR* 1.3 72.3 - - - +
319B LYS* 1.3 63.0 + - - +
321B ILE* 3.3 7.3 + - - +
322B LYS* 3.0 16.3 + - - +
392B GLN* 3.0 46.8 - - + +
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B THR* 3.3 9.3 + - - +
318B ALA* 1.3 78.2 - - - +
320B GLN* 1.3 54.9 + - + +
322B LYS* 3.2 33.4 + - - +
323B THR* 2.7 47.9 + - - +
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B THR 4.3 1.6 - - - +
316B ASP* 3.4 24.6 + - + +
317B THR* 2.7 56.0 + - - +
319B LYS* 1.3 74.2 - - + +
321B ILE* 1.3 53.3 + - - +
323B THR* 3.2 7.4 + - - -
324B LYS* 2.8 50.5 + - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ILE* 4.0 10.5 - - + +
316B ASP* 3.8 24.4 - - + +
317B THR 3.0 18.7 + - - +
318B ALA* 3.6 8.5 - - - +
320B GLN* 1.3 75.2 - - - +
322B LYS* 1.3 62.2 + - - +
324B LYS* 3.4 5.0 + - - +
325B VAL* 3.0 33.5 + - + +
388B ILE* 5.0 6.3 - - + -
391B LEU* 3.9 34.3 - - + -
392B GLN* 4.1 20.9 - - + +
395B ILE* 3.5 33.4 - - + -
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ALA 3.0 15.0 + - - +
319B LYS* 3.6 37.4 - - - +
321B ILE* 1.3 73.2 - - - +
323B THR* 1.3 66.2 + - - +
325B VAL* 3.4 0.5 + - - +
326B ASN* 3.1 48.3 + - - +
388B ILE* 3.8 32.3 - - + +
392B GLN* 4.0 6.8 + - - +
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Residues in contact with THR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LYS* 2.7 42.8 + - - +
320B GLN* 3.4 8.9 - - - -
322B LYS* 1.3 78.9 - - - +
324B LYS* 1.3 63.6 + - + +
326B ASN* 4.1 2.4 - - - +
327B LYS* 3.1 59.0 + - + +
328B HIS* 5.7 2.5 - - + -
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.9 11.9 - - + +
307B ASP* 5.5 0.9 + - - -
309B ASN* 6.2 2.0 - - - +
311B SER 3.2 25.5 + - - +
312B ILE* 4.2 14.8 - - + -
313B PHE* 3.7 12.9 - - - -
316B ASP* 2.7 41.3 + - - +
320B GLN* 2.8 30.6 + - - +
321B ILE 3.7 4.7 - - - +
323B THR* 1.3 77.6 - - + +
325B VAL* 1.3 57.6 + - - +
328B HIS* 3.0 42.7 + - + +
329B ALA 3.2 8.3 + - - -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 5.1 0.4 - - + -
312B ILE* 4.3 9.2 - - + -
321B ILE* 3.0 19.1 + - + +
322B LYS 4.0 0.2 - - - +
324B LYS* 1.3 75.2 - - - +
326B ASN* 1.3 64.6 + - - +
329B ALA* 3.3 18.5 + - + +
352B SER* 3.7 21.5 - - - +
355B TYR* 5.7 0.4 - - + -
384B LYS* 3.0 37.9 + - + +
387B LEU* 4.1 11.7 - - + -
388B ILE* 3.8 24.7 - - + -
391B LEU* 4.3 22.7 - - + -
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LYS* 3.1 40.7 + - - +
323B THR* 4.2 2.9 - - - +
325B VAL* 1.3 80.5 - - - +
327B LYS* 1.3 65.1 + - + +
381B GLY* 5.2 4.7 - - - +
384B LYS* 3.1 34.6 + - - +
385B LYS* 5.2 0.3 + - - -
388B ILE* 3.8 14.9 - - - +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B THR* 3.1 39.1 + - + +
326B ASN* 1.3 85.0 - - + +
328B HIS* 1.3 76.6 + - + +
329B ALA 3.7 2.4 - - - +
384B LYS* 5.0 0.9 + - - -
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Residues in contact with HIS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.5 30.0 - - + +
297B GLN* 4.0 12.6 + - - +
309B ASN* 3.1 40.8 + - + -
323B THR* 5.3 2.0 - - + -
324B LYS* 3.0 39.5 + - + +
327B LYS* 1.3 84.6 + - + +
329B ALA* 1.3 61.4 + - - +
330B PHE* 3.2 3.5 + - - -
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.6 24.2 - - + +
324B LYS 3.2 5.1 + - - -
325B VAL* 3.3 24.0 + - + +
327B LYS 4.9 1.4 - - - +
328B HIS* 1.3 74.8 - - - +
330B PHE* 1.3 66.8 + - - +
331B SER 3.2 1.0 + - - -
351B VAL* 4.2 10.1 - - + -
352B SER* 4.1 16.6 - - - +
355B TYR* 5.6 2.2 - - + -
384B LYS* 3.0 20.8 + - - -
387B LEU* 6.0 0.4 - - + -
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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