Contacts of the strand formed by residues 305 - 310 (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 VAL 305 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200K ARG* 3.5 22.2 + - - +
254K ALA* 3.8 31.0 - - + +
255K LYS* 4.7 0.2 - - - -
258K ALA 4.7 1.3 - - - +
260K ALA 3.5 9.4 - - - +
262K ILE* 3.7 32.8 - - + -
299K PHE* 3.8 21.6 - - + -
303K VAL* 2.5 40.5 + - + +
304K ASN* 1.3 76.8 - - - +
306K LYS* 1.3 67.3 + - - +
307K VAL* 4.5 3.5 - - + +
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Residues in contact with LYS 306 (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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180K ALA 4.2 12.9 + - - +
181K VAL* 3.8 27.4 - - + -
184K PRO* 4.4 6.5 + - - +
185K LEU* 3.7 46.9 - - + +
188K PHE* 5.2 7.0 - - - -
198K PRO* 3.8 24.4 - - - +
199K PRO* 3.3 30.0 + - + +
200K ARG* 3.4 3.5 - - - +
201K GLY* 5.8 0.4 - - - -
260K ALA 3.2 7.8 + - - +
261K ILE* 3.8 6.4 - - + -
262K ILE* 3.0 29.3 + - - +
304K ASN* 5.3 2.8 - - - +
305K VAL* 1.3 79.7 - - - +
307K VAL* 1.3 62.2 + - - +
308K ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K VAL* 5.7 0.5 - - - +
200K ARG* 2.8 18.0 + - + +
201K GLY* 3.7 7.4 - - - -
202K VAL* 2.4 36.3 + - - +
251K PHE* 5.4 4.0 - - + -
262K ILE* 3.3 22.0 - - + +
264K ILE* 4.4 11.4 - - + -
292K LEU* 5.6 1.3 - - + -
296K MET* 3.7 28.0 - - + -
299K PHE* 5.6 4.9 - - + -
305K VAL* 4.5 4.9 - - + +
306K LYS* 1.3 77.6 - - - +
308K ILE* 1.3 63.1 + - - +
309K MET* 4.1 30.1 - - + -
327K LEU* 4.7 1.3 - - + -
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Residues in contact with ILE 308 (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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177K VAL* 4.7 13.7 - - + -
181K VAL* 4.4 20.2 - - + -
202K VAL* 3.5 16.2 - - + -
204K MET* 3.4 28.0 - - + -
216K ALA* 6.0 0.7 - - + -
219K VAL* 5.0 4.7 - - + -
227K PHE* 4.4 7.9 - - + -
261K ILE* 3.5 29.2 - - + -
262K ILE 2.8 11.4 + - - +
263K PHE* 3.1 26.7 - - + -
264K ILE 2.6 34.0 + - - +
306K LYS 5.4 0.2 - - - -
307K VAL* 1.3 78.9 - - - +
309K MET* 1.3 57.8 + - - +
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Residues in contact with MET 309 (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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202K VAL 2.9 7.4 + - - +
203K LEU* 2.8 9.9 - - + +
204K MET* 2.6 33.9 + - - +
264K ILE* 3.2 20.0 - - + -
267K ILE* 2.9 46.0 - - + -
292K LEU* 3.7 32.1 - - + -
296K MET* 5.1 2.2 - - - -
307K VAL* 4.1 10.8 - - + -
308K ILE* 1.3 79.7 - - - +
310K ALA* 1.3 56.9 + - - +
321K LEU* 3.9 12.8 - - + -
327K LEU* 3.0 39.5 - - + -
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Residues in contact with ALA 310 (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* 3.0 14.6 - - + +
212K LYS* 4.6 17.5 - - + +
213K THR* 5.4 1.6 - - - +
263K PHE* 4.3 15.5 - - + -
264K ILE 3.0 6.9 + - - -
265K ASP* 3.9 22.0 - - - +
266K GLU* 2.5 31.5 + - - +
308K ILE* 5.6 0.2 - - + -
309K MET* 1.3 74.2 - - - +
311K THR* 1.3 67.1 + - - +
501K ADP 6.0 0.4 - - - +
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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