Contacts of the helix formed by residues 346 - 364 (chain D) in PDB entry 3SZ9
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D GLN* 3.7 29.0 + - + +
344D GLN* 3.1 2.1 + - - +
345D VAL* 1.3 93.0 - - + +
347D GLU* 1.3 63.4 + - - +
348D THR* 3.9 13.9 + - - -
349D GLN* 2.9 30.7 + - - +
350D PHE* 3.2 19.1 + - - +
379D TYR* 3.4 20.3 - - + +
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Residues in contact with GLU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ASP* 1.3 72.9 - - - +
348D THR* 1.3 69.0 + - - +
350D PHE* 2.9 20.6 - - + +
351D LYS* 3.0 39.3 + - + +
379D TYR* 3.5 35.5 + - + +
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Residues in contact with THR 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ASP* 3.5 13.4 + - - -
347D GLU* 1.3 78.6 + - - +
349D GLN* 1.3 71.2 + - - +
351D LYS* 3.0 7.8 + - + +
352D LYS* 2.8 35.8 + - + +
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Residues in contact with GLN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D TRP* 3.9 25.6 - - + +
300D GLN* 4.9 3.1 - - - +
344D GLN* 4.7 5.8 - - + -
345D VAL* 3.9 18.2 - - + -
346D ASP* 2.9 27.3 + - - +
348D THR* 1.3 81.0 - - - +
350D PHE* 1.3 57.7 + - - +
352D LYS* 3.7 20.0 + - - +
353D ILE* 2.8 49.1 + - + +
400D ILE 4.6 3.6 - - - +
401D PHE* 4.3 17.7 - - - +
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Residues in contact with PHE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D GLN* 4.4 4.0 - - - +
346D ASP 3.2 14.7 + - - +
347D GLU* 2.9 20.2 + - + +
349D GLN* 1.3 78.5 - - - +
351D LYS* 1.3 69.5 + - + -
353D ILE 3.4 0.2 + - - -
354D LEU* 3.1 35.5 + - + +
373D ILE* 3.5 33.2 - - + -
375D ALA 5.3 0.2 - - - -
378D GLY 4.4 4.7 - - - -
379D TYR* 3.6 41.7 - + + -
380D PHE 3.3 23.8 - - - -
381D ILE* 3.5 28.7 - - + +
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Residues in contact with LYS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D GLU* 3.0 52.4 + - + +
348D THR* 3.6 6.5 - - - +
350D PHE* 1.3 81.2 - - + +
352D LYS* 1.3 69.4 + - - +
354D LEU* 2.8 13.3 + - + +
355D GLY* 2.8 22.3 + - - -
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Residues in contact with LYS 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D THR* 2.8 27.4 + - + +
349D GLN* 3.7 27.4 - - - +
351D LYS* 1.3 71.7 - - - +
353D ILE* 1.3 63.9 + - - +
355D GLY* 3.3 2.5 + - - -
356D TYR* 3.0 58.5 + - + -
399D GLU 5.5 3.2 + - - -
400D ILE 5.1 5.6 - - - +
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Residues in contact with ILE 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D GLN* 3.4 41.5 - - + +
349D GLN* 2.8 31.6 + - + +
350D PHE 3.7 3.6 - - - +
352D LYS* 1.3 72.3 - - + +
354D LEU* 1.3 58.6 + - - +
356D TYR* 3.3 3.6 + - - +
357D ILE* 3.0 32.2 + - + +
381D ILE* 3.7 14.8 - - + -
400D ILE* 4.1 22.2 - - + +
401D PHE 3.6 4.7 - - - +
402D GLY* 3.5 17.7 - - - -
403D PRO* 4.3 4.9 - - + -
404D VAL* 3.9 25.1 - - + -
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D PHE* 3.1 37.6 + - + +
351D LYS* 2.8 14.4 + - + +
353D ILE* 1.3 68.7 - - - +
355D GLY* 1.3 60.9 - - - +
357D ILE* 3.2 9.6 + - + +
358D ASN* 3.0 27.1 + - - +
371D GLY 4.7 3.6 - - - +
372D GLY* 3.9 32.8 - - - -
373D ILE* 3.8 27.8 - - + +
381D ILE* 4.3 16.8 - - + -
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Residues in contact with GLY 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D LYS 2.8 11.9 + - - -
352D LYS* 3.6 4.5 - - - -
354D LEU* 1.3 76.4 - - - +
356D TYR* 1.3 55.8 + - - +
358D ASN* 3.0 10.0 + - - +
359D THR* 2.9 31.9 + - - -
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Residues in contact with TYR 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D LYS* 3.0 60.1 + - + -
353D ILE 3.6 7.6 - - - +
355D GLY* 1.3 71.1 - - - +
357D ILE* 1.3 65.6 + - + +
359D THR* 3.5 6.6 + - - -
360D GLY* 3.0 19.1 + - - -
386D PHE* 5.4 0.2 - - - -
394D THR* 3.9 18.8 - - + -
395D ILE* 3.5 15.9 - - + +
398D GLU* 2.6 47.3 + - + +
399D GLU 4.3 14.4 + - - -
400D ILE* 3.9 39.5 - - + -
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Residues in contact with ILE 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D ILE* 3.0 24.0 + - + +
354D LEU* 3.2 13.2 + - + +
356D TYR* 1.3 77.2 - - - +
358D ASN* 1.3 60.7 + - - +
361D LYS* 3.1 27.0 + - - +
371D GLY* 3.3 37.2 - - - +
381D ILE* 4.3 10.8 - - + -
384D THR* 3.5 24.9 - - + +
386D PHE* 3.3 25.2 - - + -
404D VAL* 3.8 26.9 - - + -
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Residues in contact with ASN 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D LEU 3.0 12.0 + - - +
355D GLY* 3.0 13.5 + - - +
357D ILE* 1.3 73.8 - - - +
359D THR* 1.3 59.0 + - - +
361D LYS* 2.8 41.7 + - - +
362D GLN* 2.9 41.8 + - - +
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Residues in contact with THR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D GLY 2.9 15.8 + - - -
356D TYR* 3.6 13.8 - - - +
358D ASN* 1.3 75.8 + - - +
360D GLY* 1.3 56.1 + - - +
362D GLN* 3.3 10.2 + - - +
363D GLU* 3.0 39.3 + - + +
394D THR* 3.9 34.3 - - + -
395D ILE* 4.9 1.8 - - + -
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Residues in contact with GLY 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TYR 3.0 17.0 + - - -
357D ILE 3.8 1.8 - - - -
359D THR* 1.3 77.2 - - - +
361D LYS* 1.3 61.5 + - - +
363D GLU* 3.4 8.4 + - - +
364D GLY 3.6 0.3 + - - -
365D ALA* 3.2 27.4 + - - +
386D PHE* 3.9 13.2 - - - -
393D MET* 6.4 0.2 - - - -
395D ILE* 3.9 22.9 - - - +
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Residues in contact with LYS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ILE* 3.1 31.5 + - - +
358D ASN* 2.8 31.0 + - - +
360D GLY* 1.3 73.9 - - - +
362D GLN* 1.3 62.7 + - + +
363D GLU 3.4 0.5 + - - -
364D GLY* 3.8 7.6 + - - -
365D ALA 4.5 6.7 - - - +
367D LEU* 3.8 42.8 - - + -
371D GLY* 4.6 7.4 + - - -
386D PHE* 3.9 5.8 - - + -
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Residues in contact with GLN 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D ASN* 2.9 38.0 + - - +
359D THR* 3.6 12.0 - - - +
360D GLY 3.3 0.2 - - - -
361D LYS* 1.3 77.9 - - + +
363D GLU* 1.3 59.4 + - + +
364D GLY 3.4 0.6 + - - -
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Residues in contact with GLU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D THR* 3.0 25.6 + - + +
360D GLY* 3.4 5.5 + - - +
361D LYS 3.2 0.4 - - - -
362D GLN* 1.3 81.1 - - + +
364D GLY* 1.3 57.6 + - - +
365D ALA 3.7 1.3 - - - -
392D GLY 5.6 0.2 - - - -
393D MET* 3.3 30.1 - - + +
394D THR* 2.8 48.6 + - - -
395D ILE 4.4 1.0 + - - -
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Residues in contact with GLY 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D GLY 3.6 0.8 + - - -
361D LYS 3.8 4.5 + - - -
362D GLN 3.4 3.8 + - - -
363D GLU* 1.3 80.1 - - - +
365D ALA* 1.3 68.0 + - - +
366D LYS* 3.5 2.6 + - - +
388D ASP* 5.2 2.8 - - - +
393D MET* 4.1 9.2 - - - +
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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