Contacts of the strand formed by residues 309 - 315 (chain K) 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 GLU 309 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249K TRP* 3.6 19.6 - - + -
308K THR* 1.3 73.7 - - - +
310K LEU* 1.3 61.0 + - - +
325K HIS* 2.7 27.8 + - + -
326K TYR 3.2 14.6 - - - +
327K GLY* 4.0 8.3 - - - +
329K PHE* 4.6 2.5 - - - -
346K ARG* 3.9 7.3 + - - -
454K ILE* 3.5 6.8 - - - +
455K ARG* 2.5 64.6 + - - +
457K PHE* 2.6 29.5 - - - +
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Residues in contact with LEU 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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252K ILE* 5.6 0.4 - - + -
309K GLU* 1.3 74.1 - - - +
311K LEU* 1.3 61.0 + - - +
312K ILE* 3.4 37.2 - - + -
324K ALA 3.9 0.5 - - - +
325K HIS* 3.2 5.9 + - - -
326K TYR* 2.6 62.5 + - + -
329K PHE* 3.9 37.6 - - + +
353K LEU* 4.3 7.9 - - + -
452K MET* 4.2 22.7 - - + -
453K LYS 3.7 6.7 - - - +
454K ILE* 3.8 21.5 - - + -
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Residues in contact with LEU 311 (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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244K THR* 3.6 16.6 - - + -
245K GLU* 4.4 9.0 - - + +
249K TRP* 3.5 41.5 - - + -
310K LEU* 1.3 74.3 - - - +
312K ILE* 1.3 61.5 + - - +
313K GLU* 2.8 32.3 + - + +
323K LYS* 3.9 24.2 - - + -
324K ALA 4.0 2.9 - - - +
325K HIS* 3.7 22.0 - - + +
451K SER 3.7 2.3 - - - +
453K LYS* 2.9 39.6 + - + +
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Residues in contact with ILE 312 (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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310K LEU* 3.4 33.2 - - + -
311K LEU* 1.3 71.4 - - - +
313K GLU* 1.3 60.2 + - - +
314K MET* 4.0 3.6 - - + +
323K LYS* 3.6 0.7 - - - -
324K ALA* 2.9 39.1 + - - +
326K TYR* 4.5 3.6 - - + -
353K LEU* 3.8 14.1 - - + -
402K TRP* 5.2 2.2 - - + -
412K PRO* 5.4 0.7 - - + -
437K TRP* 3.5 34.8 - - + -
450K MET* 3.5 30.7 - - - -
451K SER 3.3 9.9 - - - +
452K MET* 3.5 26.9 - - + -
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Residues in contact with GLU 313 (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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244K THR* 3.0 9.1 + - - +
311K LEU* 2.8 35.8 - - + +
312K ILE* 1.3 76.6 - - - +
314K MET* 1.3 64.7 + - - +
321K LYS* 5.7 0.9 - - - -
322K VAL 3.9 0.4 - - - -
323K LYS* 2.7 52.9 + - + -
449K LYS 4.6 0.2 - - - -
450K MET* 3.4 2.4 - - - +
451K SER* 3.0 33.9 + - - +
453K LYS* 3.6 28.5 + - - +
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Residues in contact with MET 314 (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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312K ILE* 4.0 19.1 - - + +
313K GLU* 1.3 76.3 - - - +
315K GLU* 1.3 64.9 + - - +
321K LYS* 3.5 5.5 - - - +
322K VAL* 3.1 42.6 + - + +
349K ALA* 3.2 29.8 - - + -
437K TRP* 3.5 49.8 - - + -
440K TRP* 4.0 13.0 - - + -
447K MET* 4.1 4.9 - - + -
449K LYS* 3.0 15.0 - - - +
450K MET* 3.7 19.7 - - + -
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Residues in contact with GLU 315 (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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314K MET* 1.3 79.1 - - - +
316K ASP* 1.3 64.7 + - - +
319K GLY* 3.7 14.8 - - - +
320K ASP 3.1 19.7 - - - +
321K LYS* 3.6 24.0 - - + +
440K TRP* 4.1 5.4 - - - -
447K MET* 3.7 4.1 - - - +
448K ARG* 2.4 69.8 + - - +
449K LYS* 2.9 33.8 + - + +
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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