Contacts of the helix formed by residues 346 - 363 (chain E) in PDB entry 1ZUM
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 ASP 346 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E VAL* 6.5 0.9 - - + -
196E GLN* 3.1 33.0 - - + +
344E GLN* 3.3 1.9 + - - +
345E VAL* 1.3 86.8 - - + +
347E GLU* 1.3 60.3 - - - +
348E THR* 3.7 14.3 + - - -
349E GLN* 2.8 30.0 + - - +
350E PHE* 3.0 23.9 + - - +
379E TYR* 3.7 17.5 - - + +
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Residues in contact with GLU 347 (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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346E ASP* 1.3 75.7 - - - +
348E THR* 1.3 64.5 + - - +
350E PHE* 3.2 8.8 - - + +
351E LYS* 3.0 61.6 + - + +
379E TYR* 3.6 35.1 + - + +
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Residues in contact with THR 348 (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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346E ASP* 3.3 14.7 + - - -
347E GLU* 1.3 79.5 + - - +
349E GLN* 1.3 67.0 + - - +
351E LYS* 3.5 6.1 + - - +
352E LYS* 3.1 33.2 + - + +
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Residues in contact with GLN 349 (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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168E TRP* 4.0 18.6 - - + +
196E GLN* 6.1 0.2 - - - +
300E GLN* 5.0 2.5 - - - +
344E GLN* 4.7 8.3 - - + -
345E VAL* 4.0 19.3 - - + -
346E ASP* 2.8 25.8 + - - +
348E THR* 1.3 78.2 - - - +
350E PHE* 1.3 66.3 + - - +
352E LYS* 3.7 26.1 - - - +
353E ILE* 2.9 35.8 + - + +
400E ILE 3.7 19.4 - - - +
401E PHE* 4.6 12.6 - - - +
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Residues in contact with PHE 350 (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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344E GLN* 4.6 4.6 - - - +
346E ASP 3.0 13.9 + - - +
347E GLU* 3.2 17.3 - - + +
349E GLN* 1.3 76.3 - - - +
351E LYS* 1.3 69.6 + - + +
353E ILE 3.6 0.3 + - - -
354E LEU* 3.2 38.9 + - + +
373E ILE* 3.8 35.2 - - + -
378E GLY 4.5 7.0 - - - -
379E TYR* 3.7 38.1 - + + -
380E PHE 3.7 12.3 - - - -
381E ILE* 3.7 37.0 - - + +
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Residues in contact with LYS 351 (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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347E GLU* 3.0 51.1 + - - +
348E THR* 4.0 5.6 - - - +
350E PHE* 1.3 82.3 - - + +
352E LYS* 1.3 61.3 + - - +
354E LEU* 3.3 10.3 + - + +
355E GLY* 2.9 26.7 + - - -
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Residues in contact with LYS 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E THR* 3.1 21.9 + - + +
349E GLN* 3.2 33.1 + - - +
351E LYS* 1.3 76.9 - - - +
353E ILE* 1.3 58.1 + - + +
355E GLY* 3.3 2.9 + - - -
356E TYR* 3.0 27.2 + - - +
398E GLU* 4.0 18.3 + - - +
399E GLU 5.1 5.1 + - - -
400E ILE* 4.4 13.3 - - + +
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Residues in contact with ILE 353 (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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344E GLN* 3.5 40.8 - - + +
349E GLN* 2.9 26.8 + - + +
352E LYS* 1.3 75.3 - - + +
354E LEU* 1.3 58.2 + - - +
356E TYR* 3.1 8.6 + - - +
357E ILE* 2.9 31.9 + - + +
381E ILE* 3.5 23.3 - - + -
400E ILE* 3.8 21.1 - - + +
401E PHE 3.8 4.0 - - - +
402E GLY* 3.6 15.3 - - - -
403E PRO* 4.6 2.2 - - + -
404E VAL* 4.0 24.7 - - + -
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Residues in contact with LEU 354 (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 PHE* 3.2 35.5 + - + +
351E LYS* 3.3 11.2 + - + +
353E ILE* 1.3 75.8 - - - +
355E GLY* 1.3 62.8 + - - +
357E ILE* 3.3 11.7 + - + +
358E ASN* 3.1 22.2 + - - +
371E GLY 4.7 5.8 - - - +
372E GLY* 4.5 17.3 - - - -
373E ILE* 3.9 33.7 - - + -
381E ILE* 4.0 15.0 - - + -
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Residues in contact with GLY 355 (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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351E LYS 2.9 14.9 + - - -
352E LYS 3.8 4.0 - - - -
353E ILE 3.2 0.2 - - - -
354E LEU* 1.3 75.9 - - - +
356E TYR* 1.3 55.9 + - - +
358E ASN* 3.4 8.4 + - - +
359E THR* 3.0 30.9 + - - -
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Residues in contact with TYR 356 (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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272E LYS* 2.9 20.8 + - - -
352E LYS 3.0 13.7 + - - +
353E ILE 3.4 9.4 - - - +
355E GLY* 1.3 74.8 - - - +
357E ILE* 1.3 67.5 + - - +
359E THR* 3.2 9.1 + - - -
360E GLY 3.0 17.7 + - - -
386E PHE* 5.3 0.2 - + - -
394E THR* 4.5 6.5 - - + -
395E ILE* 3.0 34.0 + - + +
398E GLU* 3.4 27.4 - - + +
400E ILE* 3.2 49.8 - - + +
404E VAL* 3.6 29.6 - - + -
406E GLN* 2.9 19.2 + - - -
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Residues in contact with ILE 357 (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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353E ILE* 2.9 25.5 + - + +
354E LEU* 3.3 12.5 + - + +
356E TYR* 1.3 76.3 - - - +
358E ASN* 1.3 64.1 + - - +
360E GLY 3.0 9.5 + - - -
361E LYS* 3.1 23.7 + - + +
367E LEU* 5.0 0.2 - - + -
371E GLY* 3.6 35.9 - - - +
381E ILE* 4.3 10.3 - - + -
384E THR* 3.7 22.7 - - + +
386E PHE* 3.4 19.8 - - + -
404E VAL* 3.8 29.8 - - + -
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Residues in contact with ASN 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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354E LEU 3.1 12.8 + - - +
355E GLY* 3.5 12.6 - - - +
356E TYR 3.2 0.2 - - - -
357E ILE* 1.3 78.3 - - - +
359E THR* 1.3 62.5 + - - +
361E LYS* 3.2 25.2 + - - +
362E GLN* 2.7 57.6 + - - +
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Residues in contact with THR 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 GLY 3.0 16.0 + - - -
356E TYR* 3.2 12.2 + - - -
358E ASN* 1.3 75.0 - - - +
360E GLY* 1.3 62.6 + - - +
362E GLN* 3.3 11.0 + - + +
363E GLU* 3.0 46.9 + - + +
394E THR* 3.7 25.1 - - + +
395E ILE* 5.1 0.7 - - + -
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Residues in contact with GLY 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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356E TYR 3.0 10.5 + - - -
357E ILE 3.0 5.3 + - - -
359E THR* 1.3 80.6 - - - +
361E LYS* 1.3 59.8 + - - +
363E GLU* 3.4 7.6 + - - +
365E ALA* 3.2 25.3 + - - +
386E PHE* 3.8 13.7 - - - -
395E ILE* 3.6 27.3 - - - +
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Residues in contact with LYS 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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357E ILE* 3.1 27.8 + - + +
358E ASN* 3.6 21.9 - - - +
360E GLY* 1.3 76.8 - - - +
362E GLN* 1.3 62.2 + - + +
364E GLY* 3.3 12.8 + - - -
365E ALA 4.3 8.3 + - - +
367E LEU* 4.1 30.5 - - + +
371E GLY 5.3 4.9 + - - -
386E PHE* 3.9 13.7 - - + -
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Residues in contact with GLN 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 ASN* 2.7 45.5 + - - +
359E THR* 3.8 8.5 + - - +
361E LYS* 1.3 76.5 - - + +
363E GLU* 1.3 62.6 + - + +
364E GLY 3.2 1.5 + - - -
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Residues in contact with GLU 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 THR* 3.0 32.4 + - + +
360E GLY* 3.4 5.4 + - - +
361E LYS 3.3 0.4 - - - -
362E GLN* 1.3 78.1 - - + +
364E GLY* 1.3 59.4 + - - +
365E ALA 3.6 0.9 - - - -
392E GLY 5.4 0.5 - - - +
393E MET* 3.6 29.5 - - + +
394E THR* 2.7 50.5 + - - -
395E ILE 4.0 2.4 + - - -
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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