Contacts of the strand formed by residues 297 - 302 (chain D) in PDB entry 2UZ1
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 297 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D LEU* 3.5 26.7 - - + +
271D ASP 2.9 11.2 + - - +
272D LEU* 3.2 20.6 - - + +
273D VAL 3.0 23.6 + - - -
295D SER 3.9 2.6 + - - +
296D ALA* 1.3 73.8 - - - +
298D VAL* 1.3 60.3 + - - +
315D ALA* 4.1 23.0 - - + +
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Residues in contact with VAL 298 (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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273D VAL* 3.4 12.8 - - + +
275D MET* 3.5 29.4 - - + -
280D PHE* 4.2 2.2 - - + -
292D ILE* 3.7 26.7 - - + -
296D ALA* 3.7 10.7 + - + +
297D GLN* 1.3 77.7 - - - +
299D ILE* 1.3 68.5 + - - +
300D GLN* 4.3 1.1 - - + +
312D GLN* 4.5 9.9 - - - +
313D GLY 4.7 4.9 - - - +
314D ILE* 3.6 28.2 - - + +
315D ALA* 2.8 33.7 + - - +
316D LEU 3.3 5.5 + - - -
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Residues in contact with ILE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ALA* 3.6 39.3 - - + +
200D LEU* 3.9 19.7 - - + -
201D LEU* 5.5 0.9 - - + -
272D LEU* 3.9 30.3 - - + -
273D VAL 2.9 7.8 + - - +
274D LEU* 3.4 26.7 - - + +
275D MET* 2.8 26.9 + - - +
297D GLN 4.1 0.2 + - - -
298D VAL* 1.3 76.0 - - - +
300D GLN* 1.3 62.0 + - - +
301D VAL* 4.6 1.6 - - + -
316D LEU* 3.5 29.4 - - + +
318D ILE* 4.3 10.5 - - + -
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Residues in contact with GLN 300 (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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275D MET* 3.6 17.3 - - + +
278D ALA 4.0 14.2 + - - +
279D ARG* 4.5 4.6 - - - +
280D PHE* 3.3 23.5 - - - -
298D VAL* 4.0 8.6 - - + -
299D ILE* 1.3 73.8 - - - +
301D VAL* 1.3 68.9 + - - +
302D ASP* 4.6 4.6 + - - +
307D GLU* 3.1 32.7 + - - +
308D LEU* 3.5 15.8 - - + +
309D GLY 2.8 26.1 + - - -
314D ILE* 3.8 9.1 - - + +
316D LEU 3.0 9.2 + - - +
318D ILE* 2.9 27.2 + - - +
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 4.3 10.8 - - + -
275D MET 2.9 8.2 + - - +
276D LEU* 3.8 27.1 - - + -
277D GLY 2.9 27.7 + - - -
299D ILE* 4.6 0.9 - - + -
300D GLN* 1.3 77.8 - - - +
302D ASP* 1.3 65.2 + - - +
318D ILE* 3.3 33.9 - - + +
320D ALA* 4.2 11.7 - - + +
321D ASP 4.6 1.6 - - - +
322D VAL* 4.0 5.9 - - + +
325D THR* 3.4 37.2 - - + +
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Residues in contact with ASP 302 (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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92D ARG* 2.8 43.1 + - - -
277D GLY* 3.7 16.8 - - - +
279D ARG* 4.0 6.4 + - - +
300D GLN* 4.6 6.1 + - + +
301D VAL* 1.3 75.0 - - - +
303D PRO* 1.3 72.9 - - - +
304D ASP* 2.9 27.7 + - - +
307D GLU* 3.7 11.6 - - + +
308D LEU* 4.1 15.2 - - + +
318D ILE 3.1 6.4 + - - +
319D VAL* 3.3 23.6 - - - +
320D ALA 3.5 4.9 - - - -
322D VAL* 4.8 0.9 - - - -
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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
------------------------------------------------------------
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