Contacts of the strand formed by residues 256 - 262 (chain A) in PDB entry 4KZK
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 MET 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ARG* 3.9 2.4 + - - -
160A TRP* 3.9 0.2 - - - -
168A LEU* 5.3 0.2 - - + -
220A PHE* 3.9 25.8 - - + -
229A TRP* 3.3 29.2 - - + +
231A ALA* 3.8 32.8 - - + -
242A ALA 4.5 9.6 - - - +
243A VAL* 4.6 9.2 - - + -
246A GLY* 5.2 2.9 - - - -
251A ILE* 4.1 14.6 - - + +
252A GLY 3.1 13.8 + - - +
253A THR 3.2 13.5 - - - +
254A ASP 3.6 1.2 - - - -
255A ASP* 1.3 80.6 - - - +
257A ILE* 1.3 72.3 + - - +
258A ALA* 4.2 4.7 - - + +
278A GLY* 3.6 31.0 - - - +
280A PHE* 5.6 0.3 - - - +
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Residues in contact with ILE 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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151A ILE* 4.2 23.2 - - + +
154A GLU* 3.7 21.1 - - + -
155A ALA* 3.5 37.0 - - + +
158A ARG* 3.7 24.7 - - - +
160A TRP* 3.7 19.7 - - + -
229A TRP 3.0 8.1 + - - -
230A VAL* 3.1 15.0 - - + +
231A ALA 3.1 20.5 + - - +
256A MET* 1.3 77.0 - - - +
258A ALA* 1.3 60.5 + - - +
259A VAL* 4.7 0.2 - - + -
278A GLY 3.9 1.1 - - - -
280A PHE* 4.1 19.7 - - + -
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Residues in contact with ALA 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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231A ALA* 3.2 15.5 - - + +
239A THR* 3.8 11.7 - - + -
243A VAL* 3.5 25.1 - - + -
256A MET* 4.2 9.4 - - - -
257A ILE* 1.3 74.2 - - - +
259A VAL* 1.3 66.3 + - - +
278A GLY 2.9 16.7 + - - +
279A PHE* 3.7 2.6 - - - -
280A PHE* 2.8 26.2 + - - +
281A GLY 3.5 1.2 + - - +
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Residues in contact with VAL 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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147A VAL* 3.7 25.1 - - + +
150A ALA* 4.3 15.7 - - + -
151A ILE* 3.5 27.9 - - + +
231A ALA 3.2 6.7 + - - -
232A PHE* 3.6 21.7 - - - +
233A GLY 4.6 0.2 + - - -
239A THR* 3.7 5.8 + - - +
257A ILE* 4.7 0.9 - - + -
258A ALA* 1.3 80.3 - - - +
260A GLY* 1.3 72.9 + - - +
280A PHE* 4.0 24.0 - - + -
281A GLY* 3.2 17.7 - - - +
282A SER* 4.0 4.0 - - - +
283A ILE* 4.6 0.7 - - + +
318A LEU* 4.4 4.3 - - + -
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Residues in contact with GLY 260 (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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147A VAL* 3.9 0.5 - - - +
233A GLY 5.7 0.4 - - - -
235A ASN 4.3 0.7 - - - -
236A ASP* 3.4 16.2 - - - -
239A THR* 3.6 22.3 - - - +
259A VAL* 1.3 80.3 - - - +
261A ILE* 1.3 67.7 + - - +
279A PHE* 4.1 1.7 - - - -
281A GLY 3.0 11.3 + - - -
282A SER* 3.3 3.0 - - - -
283A ILE* 2.9 20.3 + - - +
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Residues in contact with ILE 261 (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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138A ILE* 4.2 7.2 - - + -
143A ILE* 3.7 30.5 - - + -
144A GLY* 5.0 1.1 - - - +
147A VAL* 3.7 20.0 - - + -
181A ARG* 3.8 26.0 - - + +
233A GLY 4.4 6.1 - - - +
234A SER 3.7 25.6 - - - +
235A ASN* 3.2 3.4 - - - +
236A ASP* 2.8 25.9 + - - +
260A GLY* 1.3 78.6 - - - +
262A ASN* 1.3 76.6 + - - +
283A ILE* 3.8 6.5 - - + +
285A LEU* 3.8 23.6 - - + -
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Residues in contact with ASN 262 (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 ASP* 4.0 5.7 + - - -
46A TRP* 3.7 28.0 - - + +
235A ASN* 3.7 6.9 - - - +
236A ASP* 3.4 9.6 + - - +
237A ASP* 4.6 3.6 + - - -
261A ILE* 1.3 80.9 + - - +
263A GLY* 1.3 62.3 + - - +
264A SER* 3.2 9.0 + - - +
283A ILE 2.8 14.8 + - - -
284A LEU* 3.6 3.5 - - - +
285A LEU* 3.0 40.3 + - - +
600A GAL 2.6 48.3 + - - -
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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