Contacts of the strand formed by residues 244 - 248 (chain A) in PDB entry 2XJC
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS 2.9 12.6 + - - +
48A CYS* 3.2 15.8 - - - -
49A PHE* 2.7 32.3 + - - -
243A GLY* 1.3 75.7 - - - -
245A VAL* 1.3 59.9 + - - +
284A ASP* 3.2 24.0 - - + +
321A LEU* 6.5 0.2 - - - -
338A LEU 5.0 1.2 + - - -
339A LEU* 3.1 51.2 + - + +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.2 12.6 - - + +
51A PHE* 4.0 14.6 - - + -
236A LEU* 4.1 11.9 - - + +
239A MET* 3.8 29.8 - - + -
240A LYS* 3.8 18.8 - - + +
244A LYS* 1.3 79.7 - - - +
246A PHE* 1.3 62.2 + - - +
282A TYR 3.6 21.3 - - - +
283A PHE* 3.5 19.8 - - + -
284A ASP* 2.7 43.3 + - - +
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A CYS* 4.2 9.9 - - + -
49A PHE 2.9 12.5 + - - +
50A GLY* 3.4 28.0 - - - -
51A PHE* 2.8 30.8 + - - +
245A VAL* 1.3 74.8 - - - +
247A LEU* 1.3 67.2 + - - +
248A ALA* 4.3 9.2 - - + -
283A PHE* 3.6 6.5 - - - -
285A LEU* 3.2 27.4 - - + +
335A ILE* 3.6 39.3 - - + -
339A LEU* 3.7 20.2 - - + -
346A ILE* 3.9 17.0 - - + -
348A TYR* 4.2 11.0 - + - -
366A TRP* 3.9 22.7 - + - -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.5 14.1 - - + +
52A ASN 4.3 7.0 - - - -
53A MET* 4.4 5.8 - - + +
57A LEU* 3.6 31.6 - - + -
246A PHE* 1.3 79.4 - - - +
248A ALA* 1.3 60.0 + - - +
249A THR* 4.4 11.2 - - + -
256A THR* 3.8 30.1 - - + -
260A MET* 4.5 5.8 - - + -
279A TRP* 3.9 19.7 - - + -
283A PHE* 3.6 16.1 - - + -
285A LEU* 3.0 9.6 + - - +
286A ILE* 3.7 14.4 - - + -
287A LEU* 2.9 27.9 + - - +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE 2.9 16.6 + - - +
52A ASN* 3.6 5.0 + - - -
246A PHE* 4.3 19.3 - - + -
247A LEU* 1.3 74.2 - - - +
249A THR* 1.3 61.0 + - - +
287A LEU* 3.3 11.7 - - + -
290A ALA* 4.5 1.3 - - + -
292A LYS* 3.5 10.2 - - - -
295A PHE* 4.6 23.1 - - + -
335A ILE* 4.8 0.7 - - + -
348A TYR* 3.4 25.2 + - + +
366A TRP* 6.2 0.2 - - + -
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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