Contacts of the strand formed by residues 254 - 259 (chain A) in PDB entry 5KJH
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 LEU 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.4 6.4 - - - -
251A TYR* 2.8 39.1 + - + +
253A ASP* 1.3 84.8 - - + +
255A ILE* 1.3 60.0 + - - +
267A LEU* 3.8 30.3 - - + -
268A TRP 3.8 3.6 - - - +
269A ARG* 3.9 25.1 - - + -
315A LEU* 3.9 9.9 - - + -
224B LEU* 4.0 35.7 - - + +
225B LEU* 4.3 13.2 - - + -
228B THR* 3.6 21.5 - - - +
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Residues in contact with ILE 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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203A LEU* 3.9 27.8 - - + -
248A VAL* 4.2 6.5 - - + -
249A ALA 3.5 9.9 - - - +
250A PHE* 4.2 7.9 - - + -
253A ASP 4.3 5.6 - - - +
254A LEU* 1.3 78.8 - - - +
256A LEU* 1.3 70.8 + - - +
266A VAL 3.6 0.7 - - - +
267A LEU* 3.3 7.4 - - - +
268A TRP* 2.9 76.0 + - + +
270A ILE* 3.5 44.6 - - + +
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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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248A VAL* 3.5 0.3 - - - -
249A ALA* 2.9 39.3 + - + +
250A PHE* 5.0 0.6 - - - +
251A TYR* 3.8 17.3 - - + +
255A ILE* 1.3 75.4 - - - +
257A SER* 1.3 61.9 + - - +
265A ILE* 3.9 14.1 - - + -
266A VAL 3.3 5.4 - - - +
267A LEU* 3.9 26.0 - - + -
318A PHE* 3.9 25.4 - - + -
331A PHE* 3.5 28.1 - - + -
333A MET* 3.6 34.3 - - + -
343A LEU* 4.6 4.9 - - + -
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Residues in contact with SER 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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211A ILE* 3.5 16.9 - - - +
241A HIS* 2.7 30.0 + - - -
245A VAL* 4.4 1.8 - - - -
247A CYS 3.1 12.6 - - - -
248A VAL* 4.1 6.5 - - - -
256A LEU* 1.3 76.1 - - - +
258A ARG* 1.3 60.0 + - - +
265A ILE* 3.7 0.9 - - - +
266A VAL 2.8 31.7 + - - +
268A TRP* 2.9 26.1 + - - -
331A PHE* 4.0 6.4 - - - -
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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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241A HIS* 4.0 5.4 - - - -
245A VAL* 3.4 7.8 - - - +
246A ASP* 2.7 76.8 + - - +
247A CYS* 3.1 22.4 + - + -
257A SER* 1.3 73.4 - - - +
259A ALA* 1.3 81.6 + - - +
260A CYS* 4.4 1.2 - - - +
261A HIS 5.6 0.8 - - - +
263A ASP 5.4 2.6 - - - +
264A THR 3.5 20.4 + - - +
265A ILE* 4.3 8.3 - - + -
320A THR* 4.7 3.6 - - - +
323A CYS* 3.5 38.4 - - - +
326A GLN 3.8 16.2 + - - -
327A PHE* 4.1 0.8 - - - +
329A MET* 3.2 25.2 - - - +
331A PHE* 3.9 12.6 - - + -
345A PHE* 3.8 15.8 - - + -
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Residues in contact with ALA 259 (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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241A HIS* 3.5 38.6 + - + +
243A ASN* 3.8 4.5 - - + +
244A LEU 3.1 15.7 - - - +
246A ASP* 4.5 0.7 - - - -
258A ARG* 1.3 95.2 + - - +
260A CYS* 1.3 65.8 + - - +
261A HIS 3.9 0.5 + - - -
262A GLU* 3.6 24.9 + - - +
263A ASP 5.0 0.5 + - - -
264A THR 4.6 3.5 + - - +
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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