Contacts of the strand formed by residues 253 - 258 (chain A) in PDB entry 3UJK
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 ARG 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A VAL* 3.9 7.9 - - - +
252A SER* 1.3 80.1 - - - +
254A ALA* 1.3 68.3 + - - +
255A VAL* 3.7 17.9 - - + -
264A ALA* 4.8 2.9 - - + -
266A SER* 3.3 21.5 - - - +
268A ASP* 2.8 35.1 + - - +
334A LEU* 3.5 2.3 - - - -
335A ALA 3.1 29.5 + - - +
340A TRP* 3.4 52.4 + - + +
343A MET 5.1 1.2 + - - -
344A THR* 5.7 0.6 - - - +
345A ASN* 2.8 37.7 + - - +
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Residues in contact with ALA 254 (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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235A VAL* 3.8 13.9 - - + +
246A VAL* 3.8 26.7 - - + -
253A ARG* 1.3 73.9 - - - +
255A VAL* 1.3 65.5 + - - +
264A ALA* 3.8 0.9 - - - -
265A LEU* 2.9 27.3 + - + -
266A SER* 3.1 10.5 + - - +
332A LEU* 4.7 1.6 - - + -
333A ILE 3.4 5.4 - - - -
334A LEU* 3.6 22.9 - - + -
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Residues in contact with VAL 255 (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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253A ARG* 3.7 12.3 - - - -
254A ALA* 1.3 79.5 - - - +
256A LEU* 1.3 66.2 + - - +
262A PRO* 4.0 6.1 - - + -
263A LEU 3.7 15.3 - - - +
264A ALA* 4.3 3.6 - - - +
332A LEU* 3.6 5.2 - - - +
333A ILE* 2.9 44.2 + - + +
340A TRP* 3.5 28.3 - - + -
345A ASN* 3.6 25.4 - - + +
349A CYS* 3.6 27.8 - - - -
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Residues in contact with LEU 256 (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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244A ILE* 4.4 7.6 - - + -
254A ALA 4.3 0.4 - - - -
255A VAL* 1.3 74.4 - - - +
257A CYS* 1.3 63.1 + - - +
258A ARG* 3.6 23.4 + - + +
261A THR 3.5 1.0 - - - +
262A PRO* 3.5 1.4 - - - +
263A LEU* 2.6 55.8 + - + +
265A LEU* 4.0 27.3 - - + +
323A VAL* 4.7 10.3 - - + -
329A ASP* 3.7 25.1 - - - +
331A CYS 3.7 9.0 - - - +
332A LEU* 4.3 4.9 - - + +
411A LEU* 3.4 33.7 - - + -
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Residues in contact with CYS 257 (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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255A VAL 4.1 0.8 + - - -
256A LEU* 1.3 73.1 - - - +
258A ARG* 1.3 58.5 + - - +
259A GLY 3.5 21.1 - - - -
260A LYS* 4.0 11.2 - - - -
261A THR 3.7 3.1 - - - -
329A ASP* 3.8 1.4 - - - -
330A ASP* 2.8 31.6 + - - +
331A CYS* 2.8 30.7 + - - +
333A ILE* 5.0 0.2 - - + -
349A CYS* 3.8 33.4 - - + -
353A ARG* 3.8 20.2 - - - -
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Residues in contact with ARG 258 (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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256A LEU* 3.6 12.6 + - + +
257A CYS* 1.3 69.6 - - - +
259A GLY* 1.3 60.6 + - - +
260A LYS 3.1 0.5 + - - -
261A THR* 3.0 32.8 + - - +
263A LEU* 3.6 30.3 - - + +
323A VAL* 3.6 19.1 - - - +
324A ARG 3.0 26.5 + - - -
325A ARG* 4.3 0.2 - - - +
326A VAL* 3.2 27.1 - - + +
328A GLU* 4.1 8.3 - - + -
329A ASP* 2.7 37.4 + - - +
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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