Contacts of the strand formed by residues 449 - 455 (chain H) in PDB entry 2HPC
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254H ASN* 4.0 9.7 + - - -
255H ARG 2.8 19.1 + - - +
256H GLN* 3.0 46.9 - - + +
289H PRO* 5.9 1.2 - - - +
314H MET* 3.3 24.5 - - - +
315H GLU* 3.3 34.3 + - - +
435H VAL* 5.3 0.2 - - - -
447H MET* 4.7 2.4 - - - +
448H ARG* 1.3 87.4 - - + +
450H MET* 1.3 61.0 - - - +
451H SER* 4.3 4.6 + - - -
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Residues in contact with MET 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253H GLN* 2.9 26.6 + - - +
255H ARG* 3.1 18.6 + - - +
312H ILE* 4.4 9.9 - - + -
313H GLU 3.4 17.3 - - - +
314H MET* 3.3 30.3 - - + +
411H ASN 4.5 0.9 - - - -
412H PRO* 3.0 54.3 - - + -
435H VAL* 3.9 25.6 - - + -
436H VAL 5.1 3.4 - - - +
437H TRP* 4.2 11.2 - - - -
447H MET* 5.5 2.7 - - + -
449H LYS* 1.3 75.8 - - - +
451H SER* 1.3 59.4 + - - +
452H MET* 5.5 0.2 - - + -
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Residues in contact with SER 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H VAL* 5.3 5.6 - - - -
253H GLN* 3.2 12.6 - - - -
254H ASN* 3.0 27.6 + - - -
312H ILE* 3.4 4.0 - - - +
313H GLU* 3.1 31.4 + - - +
449H LYS* 4.3 4.2 + - - -
450H MET* 1.3 75.3 - - - +
452H MET* 1.3 65.2 + - - +
453H LYS* 3.2 26.2 + - - -
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Residues in contact with MET 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H ILE* 2.7 43.8 + - + +
253H GLN* 3.0 47.3 + - + +
293H TRP* 3.5 20.6 - - + -
310H LEU* 4.5 9.2 - - + -
311H LEU 3.9 3.8 - - - -
312H ILE* 4.2 29.8 - - + +
329H PHE* 5.6 6.5 - - + -
402H TRP* 3.6 34.3 - - + -
403H TRP* 4.1 10.8 - - + -
412H PRO* 4.4 3.4 - - + -
450H MET* 5.5 0.4 - - + -
451H SER* 1.3 75.2 - - - +
453H LYS* 1.3 53.7 + - - +
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Residues in contact with LYS 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241H ASP* 3.4 32.1 - - + +
244H THR* 5.0 0.9 - - - -
249H TRP* 3.2 23.6 - - + -
250H THR 3.5 4.5 - - - +
251H VAL* 3.8 23.8 - - + +
311H LEU* 2.7 58.0 + - + +
313H GLU* 3.6 32.1 - - - +
451H SER* 3.2 29.7 + - - +
452H MET* 1.3 74.1 - - - +
454H ILE* 1.3 58.0 + - - +
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Residues in contact with ILE 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H GLY 4.0 0.2 - - - +
249H TRP* 3.3 8.6 - - - -
250H THR* 2.9 33.4 + - - +
252H ILE* 3.5 32.1 - - + -
299H ILE* 4.8 4.3 - - + -
302H LEU* 4.7 13.5 - - + -
303H THR* 4.0 17.5 - - + -
308H THR* 4.1 9.2 - - + -
309H GLU 3.0 17.7 - - - +
310H LEU* 3.4 25.1 - - + +
329H PHE* 3.5 24.2 - - + -
452H MET* 4.9 0.4 - - + +
453H LYS* 1.3 74.4 - - - +
455H ARG* 1.3 66.7 + - - +
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Residues in contact with ARG 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLU* 5.5 0.2 - - - -
212H GLU* 3.1 28.0 + - - +
245H GLU* 3.0 34.1 + - - +
246H ASN* 3.3 21.1 - - - +
247H GLY 3.5 5.5 + - - -
248H GLY 4.0 12.1 - - - +
249H TRP* 2.9 44.1 - - + +
250H THR* 6.0 0.2 - - - -
308H THR* 2.9 8.6 - - - +
309H GLU* 2.6 60.0 + - + -
454H ILE* 1.3 81.0 - - - +
456H PRO* 1.3 76.4 - - + +
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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