Contacts of the strand formed by residues 52 - 55 (chain A) in PDB entry 2XFN
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 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.4 24.4 - - - +
48A ASN 2.8 16.0 + - - +
49A GLN* 4.0 2.3 + - - +
50A LYS 3.7 1.2 - - - -
51A VAL* 1.3 76.0 - - - +
53A TYR* 1.3 83.8 + - + +
332A LYS* 4.1 8.9 - - - +
334A GLU* 4.8 14.8 + - - +
336A ASN* 5.0 6.3 + - - +
337A TYR* 3.8 36.3 + - + +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.8 14.8 - - + -
46A LEU 3.2 8.3 - - - +
47A ARG* 4.1 7.4 - - + -
51A VAL* 2.9 7.7 + - - +
52A LYS* 1.3 98.6 - - + +
54A VAL* 1.3 66.2 + - - +
55A ASP* 5.2 1.8 - - - -
80A TYR* 4.2 8.5 - + - -
209A LYS* 5.7 5.4 - - - -
210A PHE 4.2 4.3 - - - -
211A VAL* 3.9 13.0 - - + +
212A GLY* 3.1 49.7 + - - +
213A GLY* 3.7 9.2 - - - -
332A LYS* 2.7 58.8 + - + +
333A PRO* 4.1 13.0 - - - +
334A GLU* 5.3 0.7 + - - -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.4 4.4 - - - +
46A LEU* 2.9 55.4 + - + +
51A VAL* 3.9 13.5 - - + -
53A TYR* 1.3 79.4 - - - +
55A ASP* 1.3 75.3 + - - +
56A LEU* 3.4 10.2 + - + -
298A ILE* 3.8 15.3 - - + -
300A TYR* 3.3 26.9 - - - +
330A ASP* 3.8 20.0 - - - +
332A LYS* 5.0 1.1 - - - +
384A GLU* 4.5 4.9 - - + -
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Residues in contact with ASP 55 (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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44A TYR 3.6 3.7 - - - +
45A THR* 2.7 29.1 + - - +
53A TYR* 5.2 2.6 - - - -
54A VAL* 1.3 81.7 - - - +
56A LEU* 1.3 61.1 + - - +
57A GLY 3.5 0.7 - - - +
58A GLY 4.2 4.7 - - - +
59A SER* 2.8 39.7 + - - +
209A LYS* 4.1 14.0 + - - +
210A PHE 5.0 2.9 + - - +
213A GLY* 3.7 7.6 - - - -
214A SER* 3.0 32.3 + - - -
296A LYS* 3.3 19.0 + - - +
298A ILE* 4.2 1.0 - - - +
330A ASP* 5.3 0.7 - - - +
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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