Contacts of the helix formed by residues 346 - 363 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I VAL* 6.3 2.7 - - + -
196I GLN* 3.3 30.8 - - + +
344I GLN* 3.2 1.7 + - - +
345I VAL* 1.3 85.6 - - + +
347I GLU* 1.3 60.0 + - - +
348I THR* 3.8 15.1 + - - -
349I GLN* 2.9 36.4 + - - +
350I PHE* 3.0 27.5 + - - +
379I TYR* 3.7 19.1 - - + +
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Residues in contact with GLU 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346I ASP* 1.3 73.2 - - - +
348I THR* 1.3 66.8 + - - +
350I PHE* 3.3 6.4 + - + +
351I LYS* 3.1 56.1 + - + +
379I TYR* 3.7 37.4 + - + +
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Residues in contact with THR 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346I ASP* 3.3 14.5 + - - -
347I GLU* 1.3 79.3 + - - +
349I GLN* 1.3 65.0 + - - +
351I LYS* 3.6 7.1 + - - +
352I LYS* 3.1 35.9 + - + +
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Residues in contact with GLN 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I TRP* 4.0 22.1 - - + +
300I GLN* 4.7 1.3 - - - +
344I GLN* 4.5 9.4 - - + -
345I VAL* 3.6 20.9 - - + -
346I ASP* 2.9 25.3 + - - +
348I THR* 1.3 79.3 - - - +
350I PHE* 1.3 60.5 + - - +
352I LYS* 3.6 25.8 + - - +
353I ILE* 3.0 40.7 + - + +
400I ILE 3.6 20.6 - - - +
401I PHE* 4.3 11.2 - - - +
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Residues in contact with PHE 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344I GLN* 4.7 3.6 - - - +
346I ASP 3.0 18.7 + - - +
347I GLU* 3.3 11.7 - - + +
349I GLN* 1.3 78.1 - - - +
351I LYS* 1.3 72.9 + - + +
353I ILE 3.5 0.3 + - - -
354I LEU* 3.3 37.6 + - + +
373I ILE* 4.0 34.1 - - + -
375I ALA 5.3 0.2 - - - -
378I GLY 4.2 9.2 - - - -
379I TYR* 3.5 52.3 - + + -
380I PHE 3.5 13.2 - - - -
381I ILE* 3.6 23.8 - - + +
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Residues in contact with LYS 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347I GLU* 3.1 45.9 + - + +
348I THR* 4.2 5.8 - - - +
350I PHE* 1.3 86.5 - - + +
352I LYS* 1.3 64.3 + - - +
354I LEU* 3.3 12.2 + - + +
355I GLY* 3.0 21.0 + - - -
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Residues in contact with LYS 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I THR* 3.1 24.1 + - + +
349I GLN* 3.3 30.2 + - - +
351I LYS* 1.3 76.0 - - - +
353I ILE* 1.3 59.1 + - + +
355I GLY* 3.3 2.9 + - - -
356I TYR* 3.0 27.2 + - - +
398I GLU* 4.1 17.4 + - - +
399I GLU 4.8 6.3 + - - -
400I ILE* 4.3 20.2 + - + +
401I PHE* 6.3 0.6 - - - -
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Residues in contact with ILE 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344I GLN* 3.6 42.4 - - + +
349I GLN* 3.0 32.2 + - + +
350I PHE 3.8 0.2 - - - +
352I LYS* 1.3 75.0 - - + +
354I LEU* 1.3 59.1 + - - +
356I TYR* 3.2 8.2 + - - +
357I ILE* 2.9 32.5 + - + +
381I ILE* 3.5 22.4 - - + -
400I ILE* 4.1 22.9 - - + +
401I PHE 4.0 4.3 - - - +
402I GLY* 3.7 12.1 - - - -
403I PRO* 4.3 2.7 - - + -
404I VAL* 4.0 24.0 - - + -
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Residues in contact with LEU 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I PHE* 3.3 32.6 + - + +
351I LYS* 3.7 12.6 - - + +
352I LYS 3.3 0.4 - - - -
353I ILE* 1.3 76.7 - - - +
355I GLY* 1.3 62.5 + - - +
357I ILE* 3.3 18.6 + - + +
358I ASN* 3.1 29.0 + - - +
371I GLY 4.9 1.6 - - - +
372I GLY* 4.5 12.8 - - - -
373I ILE* 4.1 31.6 - - + -
381I ILE* 4.1 19.7 - - + -
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Residues in contact with GLY 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I LYS 3.0 14.7 + - - -
352I LYS* 3.3 3.6 + - - -
353I ILE 3.3 0.2 - - - -
354I LEU* 1.3 75.9 - - - +
356I TYR* 1.3 56.6 + - - +
358I ASN* 3.3 12.9 + - - +
359I THR* 3.0 31.6 + - - -
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Residues in contact with TYR 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LYS* 3.1 10.7 + - - -
306I SER* 5.6 0.2 - - - -
352I LYS 3.0 14.0 + - - +
353I ILE* 3.2 10.5 - - - +
355I GLY* 1.3 74.1 - - - +
357I ILE* 1.3 67.0 + - - +
359I THR* 3.3 8.7 + - - -
360I GLY 3.0 17.2 + - - -
394I THR* 5.3 1.3 - - + -
395I ILE* 3.0 48.6 + - + +
398I GLU* 3.4 31.2 - - - +
400I ILE* 3.2 51.1 - - + +
404I VAL* 3.7 21.0 + - + -
406I GLN* 2.9 28.3 + - - -
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Residues in contact with ILE 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I ILE* 2.9 26.8 + - + +
354I LEU* 3.5 14.1 - - + +
356I TYR* 1.3 75.7 - - + +
358I ASN* 1.3 64.9 + - - +
360I GLY 3.2 2.1 + - - -
361I LYS* 3.2 28.8 + - + +
367I LEU* 5.4 0.4 - - + -
371I GLY* 3.5 37.9 - - - +
381I ILE* 4.2 11.2 - - + -
384I THR* 3.9 19.1 - - + +
386I PHE* 3.4 23.5 - - + -
404I VAL* 3.9 26.2 - - + -
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Residues in contact with ASN 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I LEU* 3.1 20.8 + - - +
355I GLY* 3.5 11.7 - - - +
356I TYR 3.2 0.2 - - - -
357I ILE* 1.3 78.6 - - - +
359I THR* 1.3 62.4 + - - +
361I LYS* 3.1 26.8 + - - +
362I GLN* 2.9 33.7 + - + +
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Residues in contact with THR 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I GLY 3.0 15.8 + - - -
356I TYR* 3.3 12.3 + - - -
358I ASN* 1.3 75.2 - - - +
360I GLY* 1.3 63.2 + - - +
362I GLN* 3.4 7.1 + - + +
363I GLU* 3.0 53.0 + - + +
394I THR* 3.7 24.2 - - + +
395I ILE* 5.0 1.6 - - + -
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Residues in contact with GLY 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356I TYR 3.0 10.1 + - - -
357I ILE 3.2 4.9 + - - -
358I ASN 3.2 0.4 - - - -
359I THR* 1.3 78.6 - - - +
361I LYS* 1.3 60.0 + - - +
363I GLU* 3.5 7.0 + - - +
365I ALA* 3.1 31.1 + - - +
386I PHE* 4.0 5.6 - - - -
395I ILE* 3.8 31.4 - - - +
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Residues in contact with LYS 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I ILE* 3.2 26.9 + - + +
358I ASN* 3.1 25.7 + - - +
360I GLY* 1.3 75.9 - - - +
362I GLN* 1.3 63.4 + - + +
364I GLY* 3.2 14.2 + - - -
365I ALA 4.3 8.2 + - - +
367I LEU* 4.4 24.1 - - + +
371I GLY 5.2 5.7 + - - -
386I PHE* 4.0 13.2 - - + -
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Residues in contact with GLN 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I ASN* 2.9 29.2 + - + +
359I THR* 3.8 7.9 - - + +
361I LYS* 1.3 76.3 - - + +
363I GLU* 1.3 62.5 + - + +
364I GLY 3.3 0.9 + - - -
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Residues in contact with GLU 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359I THR* 3.0 25.5 + - + +
360I GLY* 4.1 3.8 - - - +
361I LYS 3.2 0.6 - - - -
362I GLN* 1.3 78.3 - - + +
364I GLY* 1.3 59.5 + - - +
365I ALA 3.5 1.1 - - - -
392I GLY 5.6 0.2 - - - -
393I MET* 3.3 30.8 - - + +
394I THR* 2.7 52.3 + - - -
395I ILE* 4.2 2.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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