Contacts of the helix formed by residues 315 - 325 (chain K) in PDB entry 6T9L
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 315 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314K LYS* 1.3 82.8 - - + +
316K LEU* 1.3 64.8 - - - +
317K TYR* 4.1 13.2 - - + +
318K GLU* 3.2 35.7 + - + +
319K CYS* 3.2 19.9 + - - -
380K ILE* 4.0 2.9 - - - -
381K GLU* 3.3 29.8 - - + +
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Residues in contact with LEU 316 (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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308K LEU* 5.5 3.7 - - + +
315K LYS* 1.3 72.3 - - - +
317K TYR* 1.3 66.5 + - + +
319K CYS* 3.4 8.0 + - + +
320K LEU* 3.2 23.1 + - + +
360K LEU* 4.5 17.0 - - + -
362K LEU* 4.5 20.4 - - + -
380K ILE* 4.4 14.4 - - + -
381K GLU* 2.6 15.9 + - - +
382K PHE* 3.7 18.4 - - + -
383K PRO* 4.3 10.5 - - + -
386K LEU* 4.5 13.2 - - + -
463K LEU* 4.0 15.5 - - + -
465K TYR* 3.6 30.1 - - + +
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Residues in contact with TYR 317 (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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315K LYS* 3.3 12.5 - - + -
316K LEU* 1.3 77.3 - - - +
318K GLU* 1.3 61.6 + - + +
320K LEU* 4.5 1.1 - - - -
321K ASP* 2.8 41.0 + - - +
381K GLU* 5.2 3.8 - - - -
383K PRO* 3.9 23.3 - - + +
385K TYR 3.9 10.2 + - - -
386K LEU* 3.6 23.7 - - + +
387K ASN* 3.6 34.7 + - + +
390K ASN* 5.7 8.1 - - - -
391K TYR* 3.2 20.4 + + - +
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Residues in contact with GLU 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313K LYS* 3.3 23.7 - - + +
314K LYS* 2.6 35.1 + - - +
315K LYS* 3.5 38.1 - - + +
316K LEU 3.2 0.8 - - - -
317K TYR* 1.3 78.4 - - + +
319K CYS* 1.3 61.8 + - - +
321K ASP* 3.5 8.1 + - - +
322K SER* 3.2 21.8 + - - -
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Residues in contact with CYS 319 (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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308K LEU* 4.3 21.0 - - + +
309K ASP* 3.4 23.6 - - - +
310K ILE* 4.0 17.5 - - + -
313K LYS* 3.6 16.6 - - - -
315K LYS 3.2 18.4 - - - -
316K LEU* 3.4 9.8 + - + +
317K TYR 3.3 0.6 - - - -
318K GLU* 1.3 76.2 - - - +
320K LEU* 1.3 59.8 + - - +
322K SER* 2.6 20.9 + - - -
323K PHE* 3.3 10.4 + - - +
362K LEU* 5.1 2.5 - - + -
380K ILE* 4.1 11.9 - - - -
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Residues in contact with LEU 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306K LEU* 5.3 10.8 - - + -
308K LEU* 3.7 30.7 - - + +
316K LEU* 3.2 17.1 + - + +
317K TYR* 4.5 0.9 - - - -
319K CYS* 1.3 75.5 - - - +
321K ASP* 1.3 64.3 + - - +
323K PHE* 3.3 13.3 + - + +
324K HIS 3.2 16.3 + - - -
360K LEU* 5.3 7.2 - - + -
386K LEU* 4.8 13.0 - - + -
388K MET* 3.7 31.2 - - + -
391K TYR* 3.2 48.8 - - + +
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Residues in contact with ASP 321 (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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317K TYR* 2.8 31.5 + - - +
318K GLU* 3.8 8.2 - - - +
319K CYS 3.3 0.2 - - - -
320K LEU* 1.3 75.0 - - - +
322K SER* 1.3 53.8 + - - +
324K HIS* 3.2 4.2 + - - +
325K LYS* 2.7 35.1 + - - +
390K ASN* 5.6 2.3 - - - +
391K TYR* 2.8 27.6 + - - -
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Residues in contact with SER 322 (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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309K ASP* 3.8 17.7 + - - -
313K LYS* 3.9 13.6 - - - +
318K GLU 3.2 14.3 + - - -
319K CYS* 2.6 26.9 + - - -
321K ASP* 1.3 75.8 - - - +
323K PHE* 1.3 61.3 + - - +
325K LYS* 3.3 39.3 + - - +
327K GLU* 5.1 3.6 - - - +
6O LYS* 5.2 3.5 + - - -
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Residues in contact with PHE 323 (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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283K LEU* 4.6 13.0 - - + -
306K LEU* 4.4 20.2 - - + -
307K SER 4.5 6.7 - - - -
308K LEU* 3.7 32.1 - - + -
309K ASP* 5.4 1.5 + - - +
319K CYS 3.3 1.1 + - - +
320K LEU* 3.3 17.8 + - + +
321K ASP 3.2 0.6 - - - -
322K SER* 1.3 83.6 + - - +
324K HIS* 1.3 62.1 + + + +
325K LYS 3.6 3.8 + - - +
349K LEU* 3.8 53.2 + - + +
351K ILE* 4.5 22.2 - - + -
391K TYR* 6.4 0.4 - + - -
6O LYS* 4.1 33.3 + - + +
68O HIS* 5.1 9.0 - + - -
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Residues in contact with HIS 324 (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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320K LEU 3.2 15.2 + - - +
321K ASP* 3.2 4.9 + - - +
323K PHE* 1.3 77.9 - + + +
325K LYS* 1.3 64.4 + - - +
326K LYS* 3.5 2.4 + - - +
348K GLN* 3.2 37.6 + - - +
349K LEU 3.4 24.9 + - - -
350K GLY* 4.5 6.5 - - - -
351K ILE* 5.7 1.3 - - + -
390K ASN 4.7 8.8 + - - -
391K TYR* 3.9 46.9 + + + -
392K CYS 4.5 8.0 + - - -
393K SER* 5.6 1.2 - - - -
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Residues in contact with LYS 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321K ASP 2.7 19.1 + - - +
322K SER* 3.3 29.4 + - - +
323K PHE 4.2 3.3 - - - +
324K HIS* 1.3 75.6 - - - +
326K LYS* 1.3 77.7 + - - +
327K GLU* 3.7 26.2 + - - +
347K LYS 4.4 2.3 - - - +
348K GLN* 5.2 2.6 - - - -
349K LEU 5.6 0.3 + - - -
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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