Contacts of the strand formed by residues 449 - 456 (chain K) in PDB entry 3GHG
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 LYS 449 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254K ASN* 5.8 0.7 - - - +
255K ARG 3.5 4.3 - - - +
256K GLN* 2.4 56.0 + - + +
257K ASP* 5.3 1.0 + - - +
313K GLU 6.2 0.2 - - - -
314K MET* 3.3 6.7 - - - +
315K GLU* 3.0 59.3 + - + +
435K VAL* 5.7 0.2 - - - -
447K MET* 3.7 4.8 - - - +
448K ARG* 1.3 99.5 - - + +
450K MET* 1.3 63.4 + - - +
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Residues in contact with MET 450 (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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253K GLN* 3.4 18.9 + - - +
254K ASN* 3.1 5.5 - - - +
255K ARG* 2.7 49.9 + - + +
312K ILE* 4.2 10.3 - - + -
313K GLU 3.5 8.1 - - - +
314K MET* 3.2 38.1 - - + -
412K PRO* 3.1 42.8 - - + -
435K VAL* 4.3 21.5 - - + -
436K VAL 4.5 9.2 - - - +
437K TRP* 4.2 7.6 - - + -
447K MET* 5.0 2.5 - - + -
449K LYS* 1.3 75.4 - - - +
451K SER* 1.3 63.2 + - - +
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Residues in contact with SER 451 (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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251K VAL* 5.3 3.1 - - - -
253K GLN* 3.3 11.4 - - - +
254K ASN* 3.5 15.0 - - - -
312K ILE* 3.0 21.4 - - - +
313K GLU* 3.0 43.9 + - - +
450K MET* 1.3 75.9 - - - +
452K MET* 1.3 60.6 + - - +
453K LYS* 3.7 13.4 + - - -
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Residues in contact with MET 452 (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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251K VAL* 3.4 5.1 - - - +
252K ILE* 2.7 49.3 + - + +
253K GLN* 2.8 42.5 + - + +
293K TRP* 4.3 15.0 - - + -
299K ILE* 6.6 0.2 - - + -
310K LEU* 4.1 19.7 - - + -
311K LEU 3.7 4.0 - - - -
312K ILE* 3.7 25.8 - - + -
329K PHE* 4.9 8.7 - - + -
402K TRP* 4.3 28.5 - - + -
403K TRP* 5.0 6.7 - - + -
412K PRO* 5.1 2.2 - - + -
451K SER* 1.3 76.4 - - - +
453K LYS* 1.3 56.1 + - - +
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Residues in contact with LYS 453 (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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241K ASP* 3.0 26.6 + - + +
244K THR* 4.6 1.5 - - - +
249K TRP* 3.5 36.7 - - + -
250K THR 3.1 16.4 - - - +
251K VAL* 3.7 20.3 - - + +
252K ILE* 3.0 2.5 - - - +
310K LEU* 3.0 5.4 - - - +
311K LEU* 2.9 38.9 + - + +
313K GLU* 2.9 34.2 + - - +
451K SER* 3.7 18.1 + - - -
452K MET* 1.3 73.9 - - - +
454K ILE* 1.3 64.3 + - - +
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Residues in contact with ILE 454 (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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248K GLY 3.7 1.4 - - - +
249K TRP* 3.1 7.3 - - - -
250K THR* 2.8 39.7 + - - +
252K ILE* 3.4 26.0 - - + -
299K ILE* 5.1 1.6 - - + -
302K LEU* 3.2 46.9 - - + -
303K THR* 4.3 7.6 - - + -
308K THR* 3.8 16.6 - - + -
309K GLU 3.5 9.6 - - - +
310K LEU* 4.2 1.3 - - + -
329K PHE* 3.8 23.6 - - + -
453K LYS* 1.3 80.8 - - - +
455K ARG* 1.3 68.5 + - - +
456K PRO* 6.0 0.2 - - + -
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Residues in contact with ARG 455 (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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210K GLU* 5.6 0.2 - - - -
212K GLU* 4.1 13.9 + - + -
245K GLU* 3.0 20.0 + - - +
246K ASN* 4.3 9.1 + - - +
247K GLY 3.0 28.0 + - - -
248K GLY* 3.8 17.3 - - - +
249K TRP* 3.4 31.2 - - + +
250K THR* 5.6 0.4 - - - -
308K THR* 3.4 7.8 - - - +
309K GLU* 2.7 57.4 + - + +
325K HIS* 5.4 2.0 + - - -
454K ILE* 1.3 81.4 - - - +
456K PRO* 1.3 82.8 + - + +
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Residues in contact with PRO 456 (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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210K GLU* 3.9 36.8 - - + +
212K GLU* 4.2 9.9 - - + -
302K LEU* 6.4 1.6 - - + -
305K MET* 5.0 10.1 - - + -
307K PRO 3.4 8.7 - - - +
308K THR* 4.6 1.1 - - - +
309K GLU* 3.6 12.7 - - - +
455K ARG* 1.3 103.6 + - + +
457K PHE* 1.3 65.1 + - - +
458K PHE* 3.9 21.5 - - + -
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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