Contacts of the strand formed by residues 352 - 356 (chain B) in PDB entry 2J4S
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 GLU 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ARG* 5.7 2.8 + - - +
48B VAL 4.0 11.4 + - - +
49B THR* 3.9 23.9 - - - +
50B ARG* 3.0 36.4 + - - +
70B ASN* 3.5 17.9 + - - +
72B SER* 4.3 8.8 - - - -
332B SER* 2.6 32.7 + - - +
333B LEU 3.1 7.6 - - - +
334B TYR* 4.3 0.9 - - - +
350B GLY 3.3 5.1 + - - +
351B ASP* 1.3 72.5 - - - +
353B LEU* 1.3 68.2 + - - +
354B MET* 3.6 9.1 - - - +
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Residues in contact with LEU 353 (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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39B ILE* 5.0 0.2 - - + -
50B ARG* 3.5 30.1 - - + -
52B LEU* 3.9 25.1 - - + -
61B ALA* 3.8 20.6 - - + -
67B PHE* 3.4 38.6 - - + -
332B SER* 3.4 2.8 + - - -
333B LEU* 2.6 49.4 + - + +
341B LEU* 4.1 7.2 - - + -
347B LEU* 4.0 21.8 - - + -
351B ASP 4.6 4.5 - - - +
352B GLU* 1.3 76.5 - - - +
354B MET* 1.3 60.5 + - - +
355B VAL 4.1 0.9 + - - -
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Residues in contact with MET 354 (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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49B THR* 3.4 20.9 - - - +
50B ARG 2.7 10.2 + - - +
51B TYR* 3.6 36.3 - - + +
52B LEU* 2.9 29.7 + - - +
72B SER* 4.8 7.6 - - - -
330B ALA* 3.0 37.2 - - + -
331B PHE* 3.6 7.6 - - - +
332B SER* 3.6 24.2 - - - -
352B GLU* 3.6 15.3 - - - +
353B LEU* 1.3 73.6 - - - +
355B VAL* 1.3 62.9 + - - +
356B LEU 3.4 1.0 + - - -
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Residues in contact with VAL 355 (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 LEU* 3.9 9.6 - - + -
58B ILE* 3.8 39.7 - - + -
61B ALA* 5.0 0.9 - - + -
62B CYS* 5.3 0.2 - - - -
330B ALA* 3.2 27.9 - - - +
331B PHE* 2.8 58.4 + - + +
333B LEU* 4.0 18.2 - - + -
353B LEU 4.1 0.2 - - - -
354B MET* 1.3 69.7 - - - +
356B LEU* 1.3 59.6 + - - +
357B ILE* 3.2 15.4 + - + +
360B LEU* 4.6 4.7 - - + -
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Residues in contact with LEU 356 (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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26B VAL* 4.3 26.0 - - + +
29B LEU* 3.8 44.6 - - + +
30B MET* 4.0 6.3 - - + +
33B ALA* 4.1 3.1 - - + -
40B PHE* 4.8 3.6 - - + -
51B TYR* 4.5 23.8 - - + -
52B LEU 2.9 19.7 + - - +
53B SER* 3.7 16.8 - - - +
329B PRO 4.1 3.4 - - - +
330B ALA* 4.8 5.8 - - + -
354B MET 3.4 0.4 + - - -
355B VAL* 1.3 71.6 - - - +
357B ILE* 1.3 63.3 + - - +
358B PRO* 3.4 4.5 - - + -
359B GLN* 2.9 24.2 + - + +
360B LEU* 3.0 11.3 + - - +
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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