Contacts of the helix formed by residues 319 - 330 (chain X) in PDB entry 6JM9
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258X ALA 4.6 6.9 + - - -
259X ASN 5.3 0.8 + - - -
260X MET 3.2 24.9 + - - -
261X LYS* 4.5 4.4 - - - +
262X GLU* 3.1 44.3 + - + +
290X ILE* 4.0 31.3 - - - +
317X ILE* 3.8 16.7 - - - +
318X ASP* 1.4 68.8 - - - +
320X THR* 1.4 57.0 + - - +
321X ILE 3.2 2.7 - - - -
322X LEU* 3.2 24.8 + - + +
323X GLU* 3.0 39.3 + - + +
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Residues in contact with THR 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262X GLU* 4.5 3.8 + - - +
292X ARG* 3.2 29.8 + - - +
318X ASP* 3.3 10.3 - - + +
319X ARG* 1.4 73.1 - - - +
321X ILE* 1.4 64.5 + - - +
323X GLU* 3.3 10.5 + - + +
324X ASN* 3.1 39.6 + - - +
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Residues in contact with ILE 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277X PHE* 3.9 20.9 - - + -
279X ILE* 5.4 8.4 - - + +
283X ASN* 5.8 0.2 - - - +
288X GLY 3.8 7.2 - - - +
289X THR* 3.3 25.1 - - + +
291X MET 3.2 41.3 - - - +
292X ARG* 3.8 23.1 - - + +
318X ASP* 4.0 8.7 - - + +
319X ARG 3.2 0.2 - - - -
320X THR* 1.4 81.4 - - - +
322X LEU* 1.4 58.8 + - - +
324X ASN* 3.5 8.0 + - - +
325X TYR* 3.3 19.8 + - - +
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Residues in contact with LEU 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284X LEU* 6.0 2.7 - - + -
289X THR* 3.1 42.9 + - + +
290X ILE* 4.3 11.9 - - + -
319X ARG* 3.2 35.8 + - + +
321X ILE* 1.4 72.8 - - - +
323X GLU* 1.3 75.1 + - - +
325X TYR* 3.3 3.7 + - - +
326X PHE* 3.3 56.3 + - + -
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Residues in contact with GLU 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319X ARG* 3.0 27.8 + - + +
320X THR* 3.3 12.9 + - + +
322X LEU* 1.3 86.8 - - - +
324X ASN* 1.3 67.4 + - - +
326X PHE* 3.6 12.8 + - - +
327X SER* 3.1 28.0 + - - -
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Residues in contact with ASN 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279X ILE* 5.2 9.4 - - + +
320X THR* 3.1 24.1 + - - +
321X ILE* 3.8 7.3 - - - +
323X GLU* 1.3 78.3 - - - +
325X TYR* 1.4 64.4 + - - +
327X SER* 3.4 5.8 + - - -
328X SER* 3.2 23.6 + - - -
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Residues in contact with TYR 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279X ILE* 4.1 24.6 - - + +
280X ASN 3.3 17.7 - - - -
281X SER* 3.6 28.4 + - - -
282X ARG 4.1 0.3 + - - -
283X ASN* 3.1 25.2 + - - +
284X LEU* 3.9 30.9 - - + +
289X THR* 4.5 9.9 - - + -
321X ILE 3.3 11.4 + - - +
322X LEU* 3.3 10.7 + - - +
324X ASN* 1.4 78.3 - - - +
326X PHE* 1.4 79.4 - + - +
328X SER* 3.0 23.3 + - - -
329X LEU* 3.2 41.7 + - + +
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Residues in contact with PHE 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284X LEU* 4.3 16.8 - - + -
322X LEU* 3.3 48.5 + - + +
323X GLU* 4.2 14.1 - - - +
325X TYR* 1.4 102.8 - + - +
327X SER* 1.3 56.2 + - - +
329X LEU* 3.1 28.5 + - + +
330X LYS* 3.2 33.1 + - - +
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Residues in contact with SER 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323X GLU 3.1 18.2 + - - -
324X ASN* 3.8 6.7 - - - -
325X TYR 3.3 0.2 - - - -
326X PHE* 1.3 70.3 - - - +
328X SER* 1.3 65.9 + - - +
330X LYS* 3.2 25.0 + - - +
331X ASN* 3.0 24.7 + - - -
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Residues in contact with SER 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X ILE* 4.9 8.5 - - - +
324X ASN 3.2 14.2 + - - -
325X TYR* 3.0 26.5 + - - -
327X SER* 1.3 74.9 - - - +
329X LEU* 1.4 49.5 + - - +
331X ASN* 2.8 33.7 + - - +
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Residues in contact with LEU 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281X SER* 6.5 0.7 - - - -
284X LEU* 6.0 2.2 - - + -
325X TYR* 3.2 54.6 + - + +
326X PHE* 3.1 21.9 + - + +
328X SER* 1.4 72.6 - - - +
330X LYS* 1.3 55.4 + - + +
331X ASN 3.1 13.9 + - - +
332X PRO* 5.0 1.4 - - - +
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Residues in contact with LYS 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326X PHE* 3.2 31.0 + - - +
327X SER* 3.2 17.2 + - - +
329X LEU* 1.3 72.4 - - + +
331X ASN* 1.4 63.2 + - - +
332X PRO* 3.1 16.8 - - - +
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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