Contacts of the strand formed by residues 390 - 395 (chain B) in PDB entry 2A8I
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 LYS 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B GLY* 3.0 3.6 - - - -
381B TYR* 2.8 84.9 + - + +
386B ASP* 4.6 13.2 + - - -
388B LYS* 3.8 21.3 + - - +
389B ALA* 1.3 78.6 - - - +
391B THR* 1.3 63.7 + - - +
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Residues in contact with THR 391 (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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62B LYS* 3.1 62.6 + - - +
65B CYS* 4.2 8.1 - - + -
66B LYS* 3.8 25.8 - - + +
379B VAL 3.4 5.2 - - - -
380B GLY* 4.3 0.9 - - - -
381B TYR* 5.6 0.7 - - - -
389B ALA 4.3 1.1 - - - -
390B LYS* 1.3 81.5 - - - +
392B HIS* 1.3 65.3 + - - +
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Residues in contact with HIS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.9 6.8 - - - +
370B TRP* 3.7 23.3 - + + -
377B MSE 3.8 0.3 - - - +
378B CYS* 3.6 1.9 - - - -
379B VAL* 2.8 43.4 + - + +
381B TYR* 5.2 6.7 - - + +
391B THR* 1.3 80.3 - - - +
393B ILE* 1.3 82.7 + - - +
394B SER* 3.6 10.4 + - - -
395B ARG 5.6 0.2 - - - -
409B GLU* 2.7 35.3 + - - -
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Residues in contact with ILE 393 (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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53B HIS* 4.1 13.9 - - + -
58B ALA* 3.3 45.1 - - + +
61B TYR* 5.0 0.7 - - + -
62B LYS* 3.9 18.8 - - + +
376B SER* 4.0 11.2 - - - +
377B MSE 3.4 9.2 - - - +
378B CYS* 4.1 12.3 - - + -
392B HIS* 1.3 91.9 + - - +
394B SER* 1.3 60.6 + - - +
395B ARG* 3.6 44.9 + - + +
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Residues in contact with SER 394 (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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370B TRP* 3.6 20.2 + - - -
372B HIS* 2.8 28.2 + - - -
376B SER* 2.9 6.4 - - - -
377B MSE 2.7 42.1 + - - -
379B VAL* 5.9 0.4 - - - -
392B HIS* 3.6 10.8 + - - -
393B ILE* 1.3 69.9 - - - +
395B ARG* 1.3 61.0 + - - +
407B ALA* 4.4 7.3 - - - +
409B GLU* 3.3 22.9 + - - +
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Residues in contact with ARG 395 (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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52B TYR* 3.8 19.0 + - - -
53B HIS 2.9 29.5 + - - -
55B GLU* 2.9 38.8 + - - +
372B HIS* 4.4 3.4 - - - -
375B GLU 3.4 6.1 - - - +
376B SER* 3.8 14.4 - - - -
393B ILE* 3.6 36.6 + - + +
394B SER* 1.3 82.7 + - - +
396B LEU* 1.3 68.8 + - - +
397B PRO* 3.2 12.3 - - - +
407B ALA* 4.9 2.6 - - - +
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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