Contacts of the strand formed by residues 346 - 353 (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 ILE 346 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286K SER 3.4 1.9 - - - +
287K ILE* 3.2 3.8 - - - -
288K VAL* 2.4 67.3 + - + +
290K PRO* 4.9 9.4 - - + -
326K LYS* 3.6 37.0 - - + -
327K GLU 3.4 9.4 - - - +
328K GLN* 3.7 29.6 - - + +
344K ASP 4.3 3.1 - - - +
345K ALA* 1.3 77.5 - - - +
347K LYS* 1.3 62.9 + - - +
348K GLN* 5.6 0.7 - - + -
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Residues in contact with LYS 347 (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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285K SER* 5.3 2.0 - - - -
286K SER 3.4 3.8 - - - +
287K ILE* 4.0 14.6 - - + -
325K LYS 4.4 1.2 - - - +
326K LYS* 3.5 3.6 - - - -
327K GLU* 2.5 42.2 + - + +
329K LEU* 4.1 15.0 - - + +
345K ALA 4.2 1.0 + - - -
346K ILE* 1.3 72.3 - - - +
348K GLN* 1.3 63.3 + - - +
349K LEU* 3.4 37.7 - - + +
4O PHE* 3.8 44.4 - - + -
12O THR* 3.7 30.2 + - + +
66O THR* 4.1 12.1 + - - +
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Residues in contact with GLN 348 (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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284K GLU 3.9 0.5 - - - +
285K SER* 3.6 2.4 - - - -
286K SER* 2.9 44.2 + - - +
288K VAL* 4.9 10.7 - - + +
324K HIS* 3.2 38.5 + - - +
325K LYS 5.2 1.6 - - - -
326K LYS* 3.4 46.4 + - + +
346K ILE* 5.2 1.6 - - + +
347K LYS* 1.3 75.8 - - - +
349K LEU* 1.3 71.4 + - - +
350K GLY* 4.1 0.4 + - - -
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Residues in contact with LEU 349 (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* 5.7 11.7 - - + -
284K GLU 3.4 3.6 - - - +
285K SER* 3.8 26.0 - - - +
323K PHE* 3.8 55.0 + - + +
324K HIS* 3.4 28.0 + - - -
325K LYS 5.6 0.8 + - - -
347K LYS* 3.4 31.0 - - - +
348K GLN* 1.3 77.6 - - - +
350K GLY* 1.3 58.7 + - - +
351K ILE* 5.8 0.2 - - - +
6O LYS* 5.1 11.2 - - + +
66O THR* 4.5 17.3 - - + +
68O HIS* 6.1 1.1 - - - +
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Residues in contact with GLY 350 (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* 3.5 5.4 - - - +
284K GLU* 2.5 45.0 + - - -
324K HIS* 4.5 11.4 - - - -
348K GLN* 4.1 0.8 + - - -
349K LEU* 1.3 74.5 - - - +
351K ILE* 1.3 62.4 + - - +
391K TYR 4.9 0.2 - - - -
393K SER* 3.2 18.2 - - - -
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Residues in contact with ILE 351 (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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282K SER 4.4 3.4 - - - +
283K LEU* 3.7 25.6 - - + -
303K PHE* 5.2 6.3 - - + -
306K LEU* 4.9 12.6 - - + -
323K PHE* 4.5 15.5 - - + -
324K HIS* 5.7 2.0 - - + -
349K LEU 5.9 0.2 - - - +
350K GLY* 1.3 72.9 - - - -
352K HIS* 1.3 62.5 + - - +
353K LYS 4.2 9.9 - - - +
354K LEU* 3.6 34.9 - - + +
355K PRO* 6.0 0.2 - - + -
388K MET* 5.5 8.3 - - + -
391K TYR* 3.4 31.2 + - + +
392K CYS* 4.2 2.7 - - - +
393K SER* 2.7 30.0 + - - -
57N TYR* 6.0 1.4 - - - -
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Residues in contact with HIS 352 (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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282K SER* 3.2 21.4 + - - +
283K LEU 4.1 12.3 - - - +
284K GLU* 3.6 20.9 + - + +
300K ILE* 4.0 24.6 - - + +
350K GLY 3.8 2.0 + - - -
351K ILE* 1.3 75.3 - - - +
353K LYS* 1.3 105.7 + - + +
354K LEU* 5.0 1.7 - - - +
393K SER* 5.0 0.8 - - - -
56N LYS 4.6 1.0 - - - +
57N TYR* 4.1 15.6 - - - +
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Residues in contact with LYS 353 (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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281K GLY* 3.9 1.1 - - - -
282K SER* 3.2 39.4 + - - +
303K PHE* 4.5 1.4 - - - -
351K ILE* 4.2 4.5 - - - +
352K HIS* 1.3 111.4 - - + +
354K LEU* 1.3 64.8 + - - +
355K PRO* 3.9 4.3 - - - +
55N LYS 3.0 22.2 + - - -
56N LYS* 2.9 26.4 + - - +
57N TYR 3.3 15.2 - - - +
58N PHE 3.8 9.0 + - - +
59N ASN* 3.6 23.6 - - - +
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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