Contacts of the strand formed by residues 249 - 256 (chain x) 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 GLU 249 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238x LYS* 3.9 21.6 + - - -
247x GLY 4.3 1.0 + - - -
248x VAL* 1.3 71.7 - - - +
250x PHE* 1.3 75.5 + - - +
268x LYS* 5.9 6.7 - - + +
269x GLU 3.3 2.9 - - - +
270x ASN* 2.8 22.7 - - - +
316x ILE 3.7 0.9 - - - -
317x SER* 2.9 33.3 + - - +
318x ARG* 3.4 40.9 + - + +
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Residues in contact with PHE 250 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248x VAL* 4.1 22.7 - - + -
249x GLU* 1.3 98.7 - - - +
251x GLU* 1.3 54.0 + - - +
252x THR* 5.8 1.1 - - + -
268x LYS* 2.6 39.5 - - - +
269x GLU* 2.6 40.5 + - + +
270x ASN 6.2 0.2 - - - -
271x GLN* 4.9 10.1 - - + -
274x LEU* 4.6 12.3 - - + -
292x ARG* 6.5 1.1 - - + -
293x LEU* 4.9 11.2 - - + -
314x SER* 4.1 27.8 - - - -
315x LYS 4.2 4.5 - - - -
316x ILE* 3.7 31.0 - - + -
317x SER* 3.5 6.6 - - - +
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Residues in contact with GLU 251 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250x PHE* 1.3 75.9 - - - +
252x THR* 1.3 63.3 + - - +
253x THR* 5.3 9.9 - - + +
266x LYS* 6.2 3.1 - - + -
267x GLY 3.5 4.7 - - - +
268x LYS* 3.9 25.2 + - - -
313x SER 3.3 5.4 - - - +
314x SER* 3.3 2.0 - - - -
315x LYS* 3.0 39.6 + - + +
317x SER* 4.5 6.1 + - - -
359x THR* 3.6 25.9 + - - +
360x PRO* 5.3 1.0 - - - +
361x GLU* 3.4 20.5 - - - +
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Residues in contact with THR 252 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250x PHE* 5.3 0.9 - - + -
251x GLU* 1.3 77.1 - - - +
253x THR* 1.3 63.1 + - - +
254x MET* 4.6 6.2 + - - +
265x THR 3.5 1.7 + - - +
266x LYS* 2.8 12.0 - - - +
267x GLY* 2.4 80.0 + - - +
268x LYS* 3.6 5.4 - - - +
269x GLU* 3.9 26.0 + - + +
312x LYS* 4.7 11.2 - - - +
313x SER 3.1 6.8 + - - -
314x SER* 4.2 11.4 + - - -
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Residues in contact with THR 253 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251x GLU* 5.3 9.6 - - + +
252x THR* 1.3 80.2 - - - +
254x MET* 1.3 60.9 + - - +
255x LYS* 4.3 1.0 + - - +
264x VAL* 4.6 5.8 - - - -
265x THR 3.6 4.3 - - - -
266x LYS* 3.7 36.3 - - + +
311x ILE 3.9 0.7 - - - +
312x LYS* 3.6 0.5 - - - -
313x SER* 2.8 50.6 + - - +
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Residues in contact with MET 254 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252x THR* 4.8 5.6 - - - +
253x THR* 1.3 75.8 - - - +
255x LYS* 1.3 59.2 + - - +
263x GLU 4.1 2.4 - - - +
264x VAL* 3.6 8.1 - - - +
265x THR* 3.0 48.8 + - - +
297x ILE* 3.7 26.5 - - + -
299x LYS* 3.0 42.6 - - - +
310x TYR* 4.1 15.6 - - + -
311x ILE 3.1 24.0 - - - +
312x LYS* 4.4 5.4 - - + -
4y PHE* 5.8 1.8 - - + -
64y GLU* 4.3 8.5 - - - +
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Residues in contact with LYS 255 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253x THR* 4.3 0.6 - - - +
254x MET* 1.3 75.2 - - - +
256x CYS* 1.3 65.9 + - - +
262x GLU 5.5 1.6 - - - +
264x VAL* 3.8 27.8 - - + +
310x TYR* 4.5 2.2 - - - -
311x ILE* 2.7 49.7 + - + +
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Residues in contact with CYS 256 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255x LYS* 1.3 84.2 - - - +
257x THR* 1.3 61.9 + - - +
258x GLU* 2.9 58.6 + - - +
259x SER* 4.7 1.6 + - - -
261x GLU 6.0 0.2 - - - +
262x GLU* 4.0 30.2 + - + +
304x LEU* 4.4 4.3 - - - -
308x ALA* 4.6 2.5 - - - -
309x LEU 3.8 9.4 - - - -
310x TYR* 3.8 29.5 - - + +
311x ILE* 5.3 0.6 - - - +
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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