Contacts of the helix formed by residues 319 - 330 (chain B) in PDB entry 5DTM
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 ARG 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ALA 2.8 30.9 + - - -
259B ASN* 4.2 1.6 - - - +
260B MET 2.8 29.1 + - - +
261B LYS* 4.4 0.6 - - - +
262B GLU* 2.8 51.3 + - - +
290B ILE* 3.8 35.1 - - + +
317B ILE* 3.5 18.3 - - + +
318B ASP* 1.3 67.4 - - - +
320B THR* 1.4 58.6 + - - +
321B ILE 3.2 2.0 - - - -
322B LEU* 3.3 9.6 + - + +
323B GLU* 3.1 40.1 + - + +
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Residues in contact with THR 320 (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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262B GLU* 4.7 1.8 + - - +
318B ASP* 2.7 28.7 + - - +
319B ARG* 1.4 74.4 - - - +
321B ILE* 1.4 57.6 + - - +
323B GLU* 3.7 23.3 - - - +
324B ASN* 3.0 48.5 + - - -
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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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277B PHE* 5.4 2.5 - - + -
279B ILE* 4.0 19.0 - - + +
288B GLY 4.0 8.5 - - - +
289B THR* 3.3 20.6 - - - +
291B MET 3.5 36.1 - - - +
292B ARG* 3.9 15.7 - - + +
318B ASP* 3.5 23.1 - - - +
319B ARG 3.2 0.4 - - - -
320B THR* 1.4 80.4 + - - +
322B LEU* 1.3 59.5 + - - +
324B ASN* 4.1 4.8 - - - +
325B TYR* 3.4 19.2 + - - +
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Residues in contact with LEU 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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279B ILE* 3.9 20.2 - - + -
284B LEU* 3.9 16.4 - - + +
289B THR* 3.2 24.0 + - - +
290B ILE* 4.2 17.5 - - + -
319B ARG* 3.3 10.2 + - + +
321B ILE* 1.3 78.2 - - - +
323B GLU* 1.4 61.6 + - + +
325B TYR* 3.3 4.9 + - - +
326B PHE* 3.3 55.0 + - + -
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Residues in contact with GLU 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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262B GLU* 5.4 1.7 - - - +
319B ARG* 3.1 35.7 + - + +
320B THR* 3.4 23.5 + - - +
322B LEU* 1.4 74.5 - - - +
324B ASN* 1.4 59.2 + - - +
326B PHE* 3.5 6.7 + - - +
327B SER* 3.2 28.9 + - - -
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Residues in contact with ASN 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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320B THR* 3.0 33.5 + - - +
321B ILE* 4.1 5.4 - - - +
323B GLU* 1.4 74.8 - - - +
325B TYR* 1.4 64.1 + - - +
327B SER* 3.4 8.1 + - - -
328B SER* 3.0 24.6 + - - -
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Residues in contact with TYR 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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279B ILE* 3.7 39.9 - - + -
280B ASN* 4.0 22.9 - - - -
281B SER* 3.4 27.8 + - - -
284B LEU* 3.6 32.6 - - + +
321B ILE 3.4 5.2 + - - +
322B LEU 3.3 9.2 + - - +
324B ASN* 1.4 76.5 - - - +
326B PHE* 1.4 73.7 + + - +
328B SER* 2.9 25.7 + - - -
329B LEU* 3.2 41.1 + - + +
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Residues in contact with PHE 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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284B LEU* 4.6 15.9 - - + -
322B LEU* 3.3 49.7 + - + +
323B GLU* 3.8 8.7 - - - +
324B ASN 3.3 0.2 - - - -
325B TYR* 1.4 88.5 - + - +
327B SER* 1.4 63.1 + - - +
329B LEU* 3.2 14.0 + - + +
330B LYS* 3.1 47.3 + - + +
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Residues in contact with SER 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 GLU 3.2 15.5 + - - -
324B ASN* 3.4 11.6 + - - -
326B PHE* 1.4 75.2 - - - +
328B SER* 1.4 60.7 + - - +
330B LYS* 3.4 8.6 + - - +
331B ASN* 3.3 31.4 + - - +
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Residues in contact with SER 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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324B ASN 3.0 13.2 + - - -
325B TYR* 2.9 23.9 + - - -
327B SER* 1.4 75.0 - - - +
329B LEU* 1.4 59.5 + - - +
331B ASN* 3.6 20.0 - - - +
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Residues in contact with LEU 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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284B LEU* 6.0 0.4 - - + -
325B TYR* 3.2 49.0 + - + +
326B PHE* 3.2 20.3 + - + +
328B SER* 1.4 73.6 + - - +
330B LYS* 1.4 61.6 + - + +
331B ASN 3.2 7.6 + - - -
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Residues in contact with LYS 330 (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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326B PHE* 3.1 38.0 + - + +
327B SER* 3.4 8.0 + - - +
329B LEU* 1.4 75.7 - - + +
331B ASN* 1.4 66.2 + - - +
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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