Contacts of the strand formed by residues 285 - 291 (chain D) in PDB entry 3VZC
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 MET 285 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 3.8 18.4 - - + -
262D ALA* 3.1 36.8 - - + -
263D LEU 3.3 13.5 - - - +
264D LEU* 3.2 39.3 - - + +
280D CYS* 3.7 9.6 - - - -
284D VAL* 1.3 77.9 - - - +
286D HIS* 1.3 61.3 + - - +
323D PRO* 3.5 5.5 - - - +
324D VAL* 3.0 48.2 + - + +
325D VAL 5.4 0.9 - - - +
326D ALA* 6.0 0.2 - - - -
327D PHE* 4.8 5.6 - - - -
354D VAL* 3.5 26.2 - - + -
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Residues in contact with HIS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D LEU 3.7 0.4 - - - +
262D ALA* 3.4 2.9 - - - -
263D LEU* 2.6 47.2 + - + +
265D HIS 3.6 21.3 + - - -
266D SER* 4.9 0.7 - - - -
275D ALA* 3.6 20.8 - - + +
277D MET* 3.9 9.0 - - - +
278D GLY 3.6 20.7 + - - -
279D ARG* 5.4 1.1 - - - -
280D CYS* 3.0 32.5 + - - -
284D VAL* 6.2 0.4 - - + -
285D MET* 1.3 75.5 - - - +
287D LEU* 1.3 60.3 + - - +
288D PHE* 3.7 15.3 - - + -
321D TYR* 2.8 43.4 + + + -
322D VAL 4.3 0.4 - - - -
323D PRO* 5.8 0.4 - - + -
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D LEU* 4.3 17.5 - - + -
212D TYR* 3.7 45.1 - - + -
260D VAL* 4.1 18.2 - - + -
261D LEU 3.3 20.0 - - - +
262D ALA* 4.1 11.4 - - + +
286D HIS* 1.3 74.3 - - - +
288D PHE* 1.3 65.4 + - - +
289D TYR* 5.0 4.5 - - + -
320D VAL 3.8 0.9 - - - +
321D TYR* 3.4 5.3 - - - -
322D VAL* 2.9 47.6 + - + +
324D VAL* 3.8 15.7 - - + -
327D PHE* 4.8 11.0 - - + -
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D LEU* 4.8 5.2 - - + -
260D VAL* 3.5 3.8 - - - +
261D LEU* 2.7 58.3 + - + +
263D LEU* 4.1 14.1 - - + -
274D ALA 3.4 24.0 - - - -
275D ALA* 4.0 5.2 - - + -
277D MET* 4.0 9.4 - - + -
286D HIS* 3.7 20.6 - - + -
287D LEU* 1.3 76.7 - - - +
289D TYR* 1.3 65.5 + - - +
312D MET* 4.1 13.2 - - - -
319D LEU* 4.2 12.8 - - + -
320D VAL 3.3 5.4 - - - -
321D TYR* 3.5 35.0 - + + -
1001D UUL 3.3 26.7 - - + -
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Residues in contact with TYR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D LEU* 3.7 22.9 - - + -
212D TYR* 4.5 13.4 + + - -
252D VAL* 4.0 32.6 - - + +
253D PRO* 5.5 1.7 - - - +
254D ASP* 4.2 7.1 + - - -
257D PHE* 3.6 19.1 - + + -
259D LEU* 3.1 15.9 - - - +
260D VAL* 4.1 13.9 - - + -
287D LEU* 5.0 6.7 - - + -
288D PHE* 1.3 77.6 - - - +
290D VAL* 1.3 64.0 + - - +
291D ARG* 4.4 14.6 + - - -
318D TYR 3.6 1.0 - - - +
319D LEU* 3.5 3.6 - - - +
320D VAL* 2.9 75.8 + - + +
322D VAL* 5.1 2.9 - - + -
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PHE* 3.3 6.1 - - - +
258D VAL* 2.8 50.6 + - + -
259D LEU* 2.9 28.9 + - + -
289D TYR* 1.3 77.9 - - - +
291D ARG* 1.3 58.8 + - - +
294D VAL* 3.6 33.2 - - + -
299D LEU* 4.9 4.9 - - + -
302D LEU* 5.1 8.5 - - + -
318D TYR 3.1 10.8 - - - +
319D LEU* 3.7 27.8 - - + +
1001D UUL 5.1 3.4 - - + -
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Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PRO* 6.2 1.6 - - - +
254D ASP* 3.1 44.7 + - + +
256D ASP 3.7 6.3 - - - +
257D PHE* 4.4 2.9 - - + +
258D VAL* 4.4 1.1 - - - -
289D TYR* 4.0 11.4 + - + -
290D VAL* 1.3 75.3 - - - +
292D ALA* 1.3 69.8 + - - +
293D GLY 3.7 0.5 + - - -
294D VAL* 3.8 7.3 - - - +
317D PRO 4.0 16.2 + - - -
318D TYR* 2.8 49.0 + - + +
320D VAL* 4.0 24.0 - - - +
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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