Contacts of the strand formed by residues 382 - 386 (chain B) in PDB entry 2P2Q
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 ILE 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.0 14.1 - - + -
293B PHE* 3.8 31.4 - - + +
294B ASP* 4.4 6.7 - - + +
352B ASN 3.2 2.3 + - - +
353B ILE* 3.4 29.1 - - + -
354B LEU 3.0 23.7 + - - -
380B LEU* 4.6 1.6 - - - +
381B ARG* 1.3 92.1 - - + +
383B LEU* 1.3 78.1 + - - +
407B CYS* 3.8 0.6 - - - -
408B PRO* 3.9 9.9 - - + +
410B VAL* 4.5 5.6 - - + -
427B PRO* 3.5 35.9 - - + -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PHE* 5.4 0.2 - - - -
354B LEU* 3.2 23.6 - - + -
380B LEU* 4.0 21.1 - - + -
382B ILE* 1.3 83.8 - - - +
384B GLY* 1.3 54.2 + - - +
398B TYR* 3.6 41.5 - - + +
399B TRP* 4.2 1.8 - - - -
402B ILE* 4.1 7.2 - - + -
403B GLY* 3.6 23.8 - - - +
407B CYS* 3.9 11.9 - - + -
408B PRO 2.8 14.7 + - - +
409B VAL* 4.0 17.9 - - + -
410B VAL* 2.7 36.9 + - - +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 4.7 0.9 - - - -
354B LEU 2.6 14.6 + - - -
355B TYR* 3.7 17.5 - - - -
356B THR 3.2 13.2 + - - +
383B LEU* 1.3 77.0 - - - +
385B SER* 1.3 59.3 + - - -
398B TYR* 2.8 23.2 + - - -
409B VAL* 4.7 0.4 - - - -
410B VAL* 3.2 15.9 - - - -
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B TYR* 3.9 2.1 - - - -
356B THR 3.3 5.6 - - - -
358B PRO* 3.2 29.3 - - - +
361B ILE* 4.4 1.7 - - - +
384B GLY* 1.3 74.8 - - - -
386B VAL* 1.3 59.3 + - - +
388B GLU 5.0 0.3 + - - -
390B ILE* 3.8 20.4 - - - +
398B TYR* 4.7 4.5 - - - -
409B VAL* 4.6 10.1 - - - -
410B VAL 2.9 6.5 + - - +
411B ASP* 3.5 16.9 + - - +
412B THR* 3.0 30.1 + - - -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ALA* 5.9 1.3 - - + -
311B THR* 4.1 15.9 - - + +
355B TYR* 3.2 28.7 - - + +
356B THR* 2.9 21.1 + - - +
357B ALA* 3.5 12.7 - - + +
358B PRO* 3.2 18.3 - - - +
385B SER* 1.3 74.9 + - - +
387B GLY* 1.3 62.3 + - - +
388B GLU 3.5 2.9 - - - -
412B THR* 3.6 10.5 - - - +
414B TRP* 3.4 30.5 - - + +
998B PRX 3.6 19.3 - - + -
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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