Contacts of the strand formed by residues 307 - 314 (chain X) in PDB entry 5Z58
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 GLN 307 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X GLY 4.0 5.6 + - - -
211X GLY* 3.3 14.3 - - - -
212X ASN* 3.0 44.7 + - - +
282X LEU* 5.3 15.4 - - + +
283X LEU 4.9 1.3 - - - -
284X GLY* 5.0 0.7 - - - -
294X ILE* 5.9 4.5 - - + +
305X VAL* 3.3 15.9 - - - +
306X PHE* 1.3 84.1 - - + +
308X TYR* 1.3 64.1 + - - +
331X LEU* 3.6 27.0 - - + +
332X GLY 5.4 0.2 - - - -
333X SER* 4.3 5.0 - - - -
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Residues in contact with TYR 308 (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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283X LEU* 3.5 22.8 + - + +
284X GLY* 4.2 2.4 - - - -
304X ALA* 4.0 30.3 - - + -
305X VAL 3.4 5.1 + - - +
306X PHE 4.1 0.2 - - - -
307X GLN* 1.3 72.7 - - - +
309X ARG* 1.3 66.8 + - + +
330X ASP* 3.2 20.1 - - - +
331X LEU* 3.3 10.6 + - - +
333X SER* 3.5 25.4 - - - -
336X GLY 5.4 0.9 - - - -
337X THR* 4.4 8.3 - - - -
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Residues in contact with ARG 309 (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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282X LEU* 4.0 0.7 - - - +
283X LEU* 2.7 41.1 + - + +
308X TYR* 1.3 83.6 - - + +
310X LEU* 1.3 71.8 + - - +
329X ILE 3.5 11.7 - - - +
330X ASP* 4.0 9.0 - - - +
331X LEU* 3.7 11.5 - - - +
337X THR* 4.9 10.8 - - + +
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Residues in contact with LEU 310 (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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213X ASN* 3.6 33.2 - - + +
280X ALA* 6.3 1.1 - - + -
281X TYR 3.6 9.9 - - - +
282X LEU* 3.6 23.1 - - + -
283X LEU* 4.2 2.5 - - - +
309X ARG* 1.3 83.3 - - - +
311X VAL* 1.3 68.1 + - - +
312X GLU* 4.1 3.4 - - + -
328X ILE* 4.4 0.7 - - - +
329X ILE* 2.9 37.3 + - + +
331X LEU* 3.7 14.1 - - + -
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Residues in contact with VAL 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280X ALA* 3.3 3.2 - - - -
281X TYR* 2.8 48.0 + - + +
283X LEU* 5.2 4.9 - - + +
310X LEU* 1.3 77.2 - - - +
312X GLU* 1.3 60.0 + - - +
313X TYR* 4.2 1.5 + - - -
327X TYR 3.3 12.1 - - - +
328X ILE* 4.1 14.4 - - + -
352X LEU* 5.0 4.3 - - + -
358X LEU* 4.9 12.8 - - + -
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Residues in contact with GLU 312 (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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213X ASN* 6.3 2.9 - - - -
215X GLU* 5.3 4.7 - - + -
216X LYS* 4.8 6.1 - - + +
219X PRO* 4.1 14.8 - - + -
280X ALA* 3.7 20.9 - - + -
310X LEU* 4.1 3.9 - - + -
311X VAL* 1.3 73.1 - - - +
313X TYR* 1.3 75.2 + - - +
314X THR* 3.6 12.5 + - - +
327X TYR* 2.9 39.7 + - - +
329X ILE* 5.5 1.9 - - + +
349X TYR* 4.5 20.6 - - + +
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Residues in contact with TYR 313 (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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219X PRO* 3.5 20.8 - - - +
220X ALA 3.8 19.5 + - - +
222X GLU* 3.8 26.2 - - + -
239X PHE* 6.3 1.6 - + - -
264X PHE* 4.9 11.7 - - + -
280X ALA* 4.6 10.4 + - - +
281X TYR* 6.4 1.8 - + - -
311X VAL 4.2 1.7 + - - -
312X GLU* 1.3 77.3 - - - +
314X THR* 1.3 59.0 - - - +
324X VAL* 4.8 7.4 - - + -
325X LYS 3.3 10.3 - - - +
326X PRO* 4.2 17.3 - - + -
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Residues in contact with THR 314 (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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216X LYS* 4.3 5.2 - - - +
218X VAL* 3.7 24.2 - - - +
219X PRO* 4.6 1.6 - - - -
220X ALA 5.7 1.1 - - - -
312X GLU* 3.6 15.2 + - - +
313X TYR* 1.3 75.5 + - - +
315X ARG* 1.3 62.3 + - - +
316X ALA 4.1 0.8 + - - -
323X ARG 3.5 0.9 - - - +
324X VAL* 3.7 3.8 - - - +
325X LYS* 2.9 32.9 + - - +
327X TYR* 3.5 27.7 - - - +
349X TYR* 4.8 4.7 - - - -
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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