Contacts of the helix formed by residues 354 - 364 (chain E) in PDB entry 1XSK
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 SER 354 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314E GLN* 3.7 13.2 - - - +
317E ASP* 2.9 43.3 + - - +
350E ILE* 4.4 2.9 - - - -
351E GLY 3.4 14.0 + - - -
352E GLN 3.0 4.6 + - - +
353E LYS* 1.3 78.2 - - - +
355E PRO* 1.3 66.2 - - - +
356E VAL* 2.9 16.6 + - - +
357E PHE* 2.9 23.4 + - - +
358E LYS 4.3 0.9 + - - -
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Residues in contact with PRO 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU* 6.2 0.2 - - - +
314E GLN* 3.6 18.8 - - - +
317E ASP* 4.5 0.4 - - - +
319E GLU* 5.7 4.3 - - + -
353E LYS 3.6 5.8 - - - +
354E SER* 1.3 87.5 - - - +
356E VAL* 1.3 62.6 + - + +
358E LYS* 4.2 9.8 + - + +
359E GLU* 4.5 6.1 + - - +
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Residues in contact with VAL 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ASP* 3.7 24.2 - - + +
319E GLU* 4.2 14.6 - - + +
350E ILE* 4.1 3.8 - - + -
354E SER* 2.9 13.2 + - - +
355E PRO* 1.3 83.3 - - + +
357E PHE* 1.3 65.4 + - - +
359E GLU* 3.0 25.5 + - - +
360E LEU* 3.1 21.8 + - + +
397E TRP* 3.3 40.6 - - + -
401E LYS* 5.2 1.8 - - - -
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Residues in contact with PHE 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLN* 4.8 9.2 - - + -
350E ILE* 3.7 19.4 - - + +
351E GLY 3.2 21.3 - - - +
352E GLN* 3.3 28.7 - - + +
354E SER* 2.9 17.1 + - - +
356E VAL* 1.3 77.3 - - - +
358E LYS* 1.3 65.4 + - - +
360E LEU* 3.2 6.9 + - - +
361E GLN* 2.9 38.9 + - - +
366E LEU* 4.2 3.8 - - + +
374E LEU* 3.9 21.3 - - + -
376E GLN* 3.3 25.4 - - - -
383E GLY 3.6 12.1 - - - -
385E ALA* 3.6 23.8 - - + -
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Residues in contact with LYS 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLN* 5.7 6.1 - - - +
354E SER 4.3 1.2 + - - +
355E PRO 4.2 8.2 + - - +
356E VAL 3.3 0.8 - - - -
357E PHE* 1.3 83.6 - - + +
359E GLU* 1.3 57.8 + - - +
361E GLN* 3.4 11.4 + - - +
362E GLU* 3.0 63.6 + - + +
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Residues in contact with GLU 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E PRO 4.5 3.7 + - - +
356E VAL* 3.0 27.5 + - - +
358E LYS* 1.3 80.3 - - - +
360E LEU* 1.3 63.5 + - + +
362E GLU* 3.4 6.4 + - - +
363E LYS* 3.1 58.4 + - + +
397E TRP* 3.7 22.8 + - - +
401E LYS* 5.8 0.2 + - - -
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Residues in contact with LEU 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E ILE* 3.5 32.1 - - + -
356E VAL* 3.1 23.7 + - + +
357E PHE* 3.2 5.6 + - - +
359E GLU* 1.3 75.2 - - + +
361E GLN* 1.3 61.2 + - - +
363E LYS 3.2 0.9 + - - -
364E GLY 2.9 23.0 + - - -
365E TYR* 2.9 47.3 + - + -
366E LEU* 3.8 21.3 + - + -
387E TYR* 3.5 20.6 - - + -
397E TRP* 3.7 30.3 - - + +
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Residues in contact with GLN 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLN* 3.2 30.0 + - - +
74C GLY* 3.4 17.2 + - - -
75C ALA 4.9 2.2 + - - -
357E PHE* 2.9 29.0 + - + +
358E LYS* 3.6 12.3 - - - +
360E LEU* 1.3 78.4 - - - +
362E GLU* 1.3 66.7 + - + +
364E GLY* 3.3 11.7 + - - -
366E LEU* 4.1 7.4 - - + +
368E LYS* 5.5 2.1 - - - -
374E LEU* 3.7 31.5 - - + +
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Residues in contact with GLU 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358E LYS* 3.0 54.2 + - + +
359E GLU* 4.0 6.2 - - - +
360E LEU 3.2 0.2 - - - -
361E GLN* 1.3 82.6 - - + +
363E LYS* 1.3 63.0 + - + +
364E GLY 3.6 0.2 + - - -
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Residues in contact with LYS 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E GLU* 3.1 50.1 + - + +
360E LEU 3.2 0.6 + - - +
362E GLU* 1.3 80.5 - - + +
364E GLY* 1.3 63.4 + - - +
365E TYR* 3.5 47.9 + - + +
391E ASN* 5.1 0.7 + - - -
397E TRP* 4.8 8.3 - - - -
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Residues in contact with GLY 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E LEU 2.9 4.3 + - - -
361E GLN* 3.3 9.3 + - - -
362E GLU 3.2 3.6 - - - -
363E LYS* 1.3 80.5 - - - +
365E TYR* 1.3 61.6 + - - +
366E LEU 3.4 7.8 + - - +
368E LYS* 4.3 23.8 + - - -
374E LEU* 6.2 0.4 - - - -
388E ASP* 5.5 0.7 - - - +
391E ASN* 3.0 20.6 + - - -
428E PHE* 5.1 1.6 - - - -
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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