Contacts of the strand formed by residues 260 - 265 (chain K) in PDB entry 5GJQ
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 ALA 260 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185K LEU* 4.9 0.7 - - - -
226K ALA* 3.1 32.8 - - + +
228K ILE* 4.6 7.2 - - + -
254K ALA* 4.1 23.6 - - + +
257K ASN* 4.4 1.8 - - + -
258K ALA 2.4 18.6 + - - +
259K PRO* 1.3 75.3 - - - +
261K ILE* 1.3 61.0 + - - +
262K ILE 3.7 1.7 + - - -
304K ASN 3.2 3.5 + - - +
305K VAL* 3.5 6.0 - - + +
306K LYS* 3.2 23.4 + - - +
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Residues in contact with ILE 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K VAL* 3.7 28.9 - - + -
185K LEU* 4.1 9.6 - - + -
219K VAL* 3.4 32.3 - - + -
223K THR* 4.0 12.3 - - - +
225K ALA* 5.4 1.6 - - + -
226K ALA 2.9 8.7 + - - +
227K PHE* 3.1 33.7 - - + -
228K ILE* 2.7 33.0 + - - -
259K PRO 4.2 0.2 + - - -
260K ALA* 1.3 75.8 - - - +
262K ILE* 1.3 65.4 + - - +
263K PHE 3.5 0.3 + - - -
306K LYS* 3.8 7.6 - - + +
308K ILE* 3.5 20.6 - - + -
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Residues in contact with ILE 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ILE* 3.6 26.7 - - + +
230K VAL* 5.9 2.5 - - + -
250K VAL* 3.8 18.6 - - + -
251K PHE* 3.2 43.5 - - + -
254K ALA* 4.0 4.3 - - + -
260K ALA 3.7 1.6 + - - -
261K ILE* 1.3 73.8 - - - +
263K PHE* 1.3 63.7 + - - +
264K ILE* 4.1 22.4 - - + -
305K VAL* 3.7 22.9 - - + -
306K LYS 3.0 13.3 + - - +
307K VAL* 3.3 10.8 - - + +
308K ILE 2.8 24.4 + - - -
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Residues in contact with PHE 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K MET* 4.8 2.5 - - + -
212K LYS 4.9 1.1 - - - -
213K THR* 5.1 2.9 - - - -
216K ALA* 2.9 36.3 - - + -
227K PHE* 3.7 24.0 - + + -
228K ILE 2.9 14.2 + - - +
229K ARG* 4.5 13.2 - - + -
230K VAL 3.2 24.1 + - - +
261K ILE* 4.3 1.1 - - + -
262K ILE* 1.3 77.0 - - - +
264K ILE* 1.3 62.9 + - - +
265K ASP* 3.2 49.6 - - + -
308K ILE* 3.1 37.9 - - + -
310K ALA* 4.3 11.2 - - + -
267L PHE* 4.9 7.9 - + - -
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Residues in contact with ILE 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K VAL* 3.5 16.2 - - + +
232K GLY* 4.0 20.6 - - - +
235K PHE* 5.1 14.8 - - + -
251K PHE* 6.0 1.1 - - + -
262K ILE* 4.1 14.6 - - + -
263K PHE* 1.3 76.9 - - - +
265K ASP* 1.3 62.9 + - - +
266K GLU 3.3 1.0 + - - -
267K ILE* 3.3 22.7 - - + +
270K ILE* 5.6 2.0 - - + -
292K LEU* 4.4 16.6 - - + -
307K VAL* 4.4 6.7 - - + -
308K ILE 2.6 11.5 + - - +
309K MET* 3.2 35.5 - - + +
310K ALA 3.0 21.7 + - - -
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Residues in contact with ASP 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K THR* 3.5 27.9 + - - +
230K VAL 4.0 4.2 + - - -
231K VAL* 4.0 14.4 - - + +
232K GLY 3.9 13.5 + - - -
263K PHE* 3.2 35.7 + - + -
264K ILE* 1.3 72.3 - - - +
266K GLU* 1.3 98.1 + - - +
310K ALA* 3.9 11.5 - - - +
501K ADP 5.0 0.9 + - - -
262L ASN* 4.9 12.3 - - - +
266L GLY* 4.9 3.5 - - - -
267L PHE* 5.0 3.1 - - - -
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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