Contacts of the helix formed by residues 310 - 323 (chain B) in PDB entry 5ULM
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 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B ARG* 3.4 21.8 - - - +
308B VAL* 3.6 19.0 + - + +
309B LEU* 1.3 82.3 - - - +
311B ALA* 1.3 64.8 + - - +
312B ASP* 2.7 26.0 + - - -
313B ILE* 3.5 8.0 + - - +
314B VAL* 3.2 22.0 + - - +
343B PHE* 4.3 2.5 - - - -
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Residues in contact with ALA 311 (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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310B THR* 1.3 73.9 - - - +
312B ASP* 1.3 59.3 + - - +
314B VAL* 3.7 7.0 - - - +
315B ILE* 2.8 37.4 + - + +
343B PHE* 4.2 9.4 - - + -
348B HIS* 3.4 37.2 - - + +
351B VAL* 4.9 5.2 - - + -
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Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 3.5 21.6 + - - -
277B LEU* 3.8 22.0 - - + +
310B THR* 2.7 25.0 + - - -
311B ALA* 1.3 77.3 - - - +
313B ILE* 1.3 82.0 + - - +
315B ILE* 4.0 3.9 - - - +
316B ASN* 2.7 36.9 + - - +
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Residues in contact with ILE 313 (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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273B ARG* 4.0 24.2 - - + +
276B ILE* 3.6 35.2 - - + -
277B LEU* 3.9 11.9 - - + -
280B ILE* 4.3 2.6 - - + +
303B VAL* 4.0 23.6 - - + -
306B ILE* 5.3 10.8 - - + -
308B VAL 5.9 0.4 - - - +
309B LEU* 3.5 21.1 - - + -
310B THR* 3.5 16.1 + - - +
311B ALA 3.3 0.2 - - - -
312B ASP* 1.3 90.6 + - - +
314B VAL* 1.3 70.2 + - - +
316B ASN* 3.4 2.3 + - - +
317B LEU* 2.9 26.9 + - + +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.0 20.4 - - + -
310B THR 3.2 15.1 + - - +
311B ALA* 3.7 9.0 - - - +
313B ILE* 1.3 79.3 - - - +
315B ILE* 1.3 63.6 + - - +
317B LEU* 3.1 11.7 + - + +
318B LEU* 2.9 47.6 + - + +
333B LEU* 4.8 7.2 - - + -
334B VAL* 5.3 0.2 - - + -
337B LEU* 3.5 36.1 - - + -
343B PHE* 4.3 7.0 - - + -
351B VAL* 4.1 15.5 - - + -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA* 2.8 26.7 + - + +
312B ASP* 4.0 4.9 - - - +
314B VAL* 1.3 71.8 - - - +
316B ASN* 1.3 65.1 + - - +
318B LEU* 3.2 7.5 + - + +
319B LEU* 2.9 45.4 + - + +
350B HIS* 4.0 16.2 - - + -
351B VAL* 3.7 38.6 - - + +
354B HIS* 4.0 16.1 - - + +
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Residues in contact with ASN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.8 19.5 - - + +
280B ILE* 3.5 22.8 - - + +
284B ARG* 4.6 8.5 + - - +
312B ASP* 2.7 32.0 + - - +
313B ILE 4.1 2.2 - - - +
315B ILE* 1.3 81.5 - - - +
317B LEU* 1.3 63.8 + - - +
319B LEU* 3.9 14.9 - - - +
320B SER* 3.1 23.4 + - - -
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Residues in contact with LEU 317 (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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280B ILE* 4.1 21.7 - - + +
296B LEU* 4.6 8.5 - - + +
299B ILE* 4.9 7.2 - - + -
300B ARG* 3.6 35.0 - - + +
303B VAL* 3.8 20.9 - - + -
309B LEU* 5.9 0.7 - - + -
313B ILE* 2.9 18.5 + - + +
314B VAL* 3.3 9.9 - - - +
316B ASN* 1.3 74.5 - - - +
318B LEU* 1.3 59.6 + - - +
320B SER* 2.6 26.5 + - - +
321B TYR* 2.9 32.5 + - + +
333B LEU* 3.7 23.6 - - + -
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Residues in contact with LEU 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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314B VAL* 2.9 30.1 + - + +
315B ILE* 3.6 8.5 - - - +
317B LEU* 1.3 76.3 - - - +
319B LEU* 1.3 58.5 + - - +
321B TYR* 3.5 1.3 + - + -
322B ARG* 3.0 29.0 + - - +
330B ILE* 3.7 35.6 - - + +
333B LEU* 3.6 29.4 - - + -
334B VAL* 3.9 24.5 - - + -
351B VAL* 4.2 11.4 - - + +
354B HIS* 3.8 36.2 + - + -
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Residues in contact with LEU 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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284B ARG* 3.7 30.0 + - - +
315B ILE* 2.9 36.6 + - + +
316B ASN* 4.0 13.5 - - - +
317B LEU 3.3 0.2 - - - -
318B LEU* 1.3 75.4 - - - +
320B SER* 1.3 56.6 + - - +
322B ARG* 3.2 36.8 + - - +
323B ASP* 3.0 33.5 + - - +
354B HIS* 3.7 21.8 - - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 4.2 2.8 - - - +
284B ARG* 3.8 19.4 - - - +
292B LEU* 4.1 3.5 - - - +
296B LEU* 3.3 40.4 - - - +
316B ASN 3.1 16.0 + - - -
317B LEU* 2.6 24.8 + - - +
319B LEU* 1.3 76.1 - - - +
321B TYR* 1.3 60.0 + - - +
323B ASP* 3.2 28.2 + - - +
324B ILE* 3.8 5.0 + - - +
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Residues in contact with TYR 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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293B ALA* 5.8 2.0 - - + -
296B LEU* 3.7 29.5 + - + +
297B ALA* 5.2 0.9 + - - -
300B ARG* 2.8 49.9 + - - +
317B LEU* 2.9 41.9 + - + +
318B LEU* 4.6 2.0 - - + -
320B SER* 1.3 76.0 + - - +
322B ARG* 1.3 61.8 + - - +
324B ILE* 3.4 10.2 + - + +
325B GLN 3.2 2.8 + - - -
326B ASP* 2.9 49.7 + - + +
329B SER* 3.8 22.6 + - - -
330B ILE* 3.6 27.1 - - + -
333B LEU* 4.6 4.3 - - + -
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Residues in contact with ARG 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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284B ARG* 6.0 0.6 - - - +
318B LEU 3.0 17.4 + - - +
319B LEU* 3.2 36.6 + - - +
321B TYR* 1.3 75.1 - - - +
323B ASP* 1.3 59.4 + - - +
325B GLN* 2.8 26.2 + - - +
327B TYR* 3.8 13.2 - - + +
330B ILE* 4.0 11.0 - - + +
353B PHE* 5.1 5.3 - - - -
354B HIS* 4.0 20.7 + - - +
357B PHE* 4.0 26.2 - - - -
509B TRP* 3.4 69.8 + - + +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 2.6 56.4 + - - +
292B LEU* 4.1 13.5 - - + +
319B LEU 3.0 18.2 + - - +
320B SER* 3.2 9.0 + - - +
322B ARG* 1.3 78.2 + - - +
324B ILE* 1.3 60.0 + - - +
325B GLN* 5.4 1.4 - - - +
507B PRO* 5.8 4.8 - - - +
508B ALA* 5.7 5.7 + - - +
509B TRP* 5.2 10.2 + - - -
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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