Contacts of the strand formed by residues 285 - 290 (chain P) in PDB entry 1ZD2
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 285 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252P GLU* 2.7 38.7 + - + +
254P GLY 3.5 20.0 - - - +
255P SER* 3.7 2.2 - - - +
256P GLY 3.3 28.7 - - - +
257P PRO 3.1 5.4 + - - +
258P ALA* 3.4 11.5 - - - -
259P VAL 3.0 21.4 + - - -
284P TYR* 1.3 73.3 - - - +
286P VAL* 1.3 61.0 + - - +
287P LEU* 3.5 9.1 + - + +
322P LEU* 3.7 25.1 + - - +
324P LEU* 3.6 26.2 - - - +
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Residues in contact with VAL 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P VAL 3.4 0.9 - - - +
252P GLU* 3.2 6.8 - - - -
253P LEU 3.0 34.9 + - - +
259P VAL* 3.5 7.4 - - + +
261P LEU* 3.6 31.4 - - + -
276P ILE* 3.8 25.4 - - + +
279P LEU* 3.5 37.7 - - + -
280P ALA 3.8 12.1 - - - +
284P TYR* 4.8 4.5 - - + -
285P ARG* 1.3 72.0 - - - +
287P LEU* 1.3 65.1 + - - +
288P ALA 3.9 6.5 - - - +
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Residues in contact with LEU 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250P PHE* 3.7 23.6 - - + -
251P VAL 3.5 3.1 - - - -
252P GLU* 2.9 45.5 - - + +
258P ALA* 5.0 5.4 - - + -
259P VAL 2.9 12.8 + - - +
260P CYS* 3.4 16.4 - - + -
261P LEU 2.9 22.8 + - - -
285P ARG* 4.1 14.4 - - - +
286P VAL* 1.3 76.7 - - - +
288P ALA* 1.3 62.5 + - - +
289P MET* 3.3 2.8 + - - +
318P PHE* 4.0 17.5 - - + -
319P LEU* 5.9 0.4 - - + -
322P LEU* 4.0 3.8 - - + -
324P LEU* 4.0 27.6 - - + -
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Residues in contact with ALA 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250P PHE* 3.2 3.3 - - - -
251P VAL* 2.9 38.9 + - + +
261P LEU* 3.8 17.7 - - + -
269P TRP* 3.7 19.5 - - + +
272P TRP* 4.7 0.7 - - + -
276P ILE* 3.5 35.7 - - + -
286P VAL* 3.8 2.2 - - + +
287P LEU* 1.3 69.1 - - - +
289P MET* 1.3 64.4 + - - +
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Residues in contact with MET 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P LEU* 3.8 24.7 - - + -
249P HIS 3.9 1.3 - - - +
250P PHE* 3.7 11.0 - - + -
260P CYS* 3.2 25.8 - - - -
261P LEU 2.8 17.9 + - - +
263P HIS* 3.3 9.2 - - - -
269P TRP* 3.1 23.9 - - - +
272P TRP* 5.3 0.2 - - - -
287P LEU 4.0 1.8 - - - +
288P ALA* 1.3 74.4 - - - +
290P ASP* 1.3 63.9 + - - +
291P MET* 3.5 18.8 - - - -
315P MET* 3.4 32.5 - - + -
318P PHE* 3.4 41.5 - - + -
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Residues in contact with ASP 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P LEU* 4.4 5.2 - - - +
249P HIS* 2.8 39.3 + - - +
263P HIS* 3.7 2.3 + - - -
268P SER* 3.8 11.4 - - - -
269P TRP* 3.5 26.0 + - - -
289P MET* 1.3 73.2 - - - +
291P MET* 1.3 64.9 + - - +
292P LYS 3.4 1.0 + - - -
294P TYR 3.9 2.2 - - - -
295P GLY* 3.4 15.6 + - - -
296P GLU* 2.9 25.1 + - - +
297P SER* 2.5 31.4 + - - +
452P GLN* 4.3 1.2 - - - +
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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