Contacts of the helix formed by residues 350 - 368 (chain N) in PDB entry 3H1J
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 THR 350 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N SER 3.5 13.2 - - - +
349N THR* 1.3 73.3 - - - +
351N GLU* 1.3 66.4 + - - +
352N SER* 3.4 10.2 + - - -
353N GLU* 2.6 50.2 + - + +
354N VAL* 3.3 13.0 + - - +
404N ALA* 3.9 2.5 - - - -
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Residues in contact with GLU 351 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N THR* 1.3 72.4 - - - +
352N SER* 1.3 63.8 + - - +
354N VAL* 2.8 31.4 - - - +
355N LYS* 2.9 8.6 + - - +
403N ASP* 3.8 18.5 - - - +
404N ALA* 3.1 37.7 + - + +
405N ARG* 4.2 1.0 + - - +
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Residues in contact with SER 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LYS 4.6 0.6 + - - -
110F LYS* 2.8 37.5 + - - -
350N THR* 3.1 9.5 + - - -
351N GLU* 1.3 77.2 - - - +
353N GLU* 1.3 62.3 + - - +
355N LYS* 3.3 11.0 + - - +
356N ARG* 3.2 22.9 + - - +
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Residues in contact with GLU 353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N ILE* 3.9 32.0 - - + +
293N ARG* 4.1 20.1 - - - -
344N ARG* 6.0 1.2 - - - +
348N SER 4.0 1.1 - - - +
349N THR* 3.1 14.7 - - - +
350N THR* 2.6 53.0 + - + +
352N SER* 1.3 75.3 - - - +
354N VAL* 1.3 58.2 + - - +
356N ARG* 3.1 22.8 + - - +
357N ALA* 2.8 29.3 + - - +
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Residues in contact with VAL 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272N VAL* 4.5 5.4 - - + -
276N ILE* 4.5 2.7 - - + -
349N THR* 3.6 26.2 - - + -
350N THR 3.6 2.9 - - - +
351N GLU* 2.8 41.5 + - - +
353N GLU* 1.3 76.0 - - - +
355N LYS* 1.3 54.7 + - + +
357N ALA* 3.8 8.7 - - - -
358N LYS* 2.7 52.1 + - + +
402N VAL 4.9 0.2 - - - +
403N ASP* 4.2 7.4 - - - -
404N ALA* 3.6 21.5 - - - +
407N VAL* 3.9 13.7 - - + -
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Residues in contact with LYS 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N GLU 2.9 13.1 + - - +
352N SER* 3.4 15.0 - - - +
354N VAL* 1.3 79.6 - - + +
356N ARG* 1.3 63.1 + - - +
358N LYS* 3.7 9.3 - - - +
359N ASN* 3.1 37.5 + - - +
91O ALA 5.2 3.8 - - - +
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Residues in contact with ARG 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275N ALA 4.4 4.8 + - - -
276N ILE* 3.1 44.2 + - - +
291N SER* 3.5 48.4 + - - -
292N SER* 4.4 0.6 - - - +
352N SER 3.2 8.9 + - - +
353N GLU* 3.1 27.5 + - - +
355N LYS* 1.3 79.4 - - - +
357N ALA* 1.3 54.1 + - - +
359N ASN* 3.1 3.8 + - - +
360N HIS* 2.8 36.4 + - + +
90O GLU* 3.0 32.0 - - - +
91O ALA* 4.0 17.5 - - - +
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Residues in contact with ALA 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272N VAL* 3.2 33.7 - - + +
275N ALA* 3.5 18.7 - - + +
276N ILE* 3.6 16.2 - - + +
353N GLU 2.8 15.8 + - - +
354N VAL* 3.5 5.4 - - - +
356N ARG* 1.3 78.5 - - - +
358N LYS* 1.3 57.0 + - - +
360N HIS* 3.5 1.9 + - - +
361N LEU* 2.9 30.7 + - - +
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Residues in contact with LYS 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272N VAL* 3.9 16.6 - - + -
354N VAL* 2.7 40.8 + - + +
355N LYS* 3.7 7.8 - - - +
357N ALA* 1.3 73.0 - - - +
359N ASN* 1.3 64.0 + - - +
361N LEU* 3.1 5.1 + - - +
362N ARG* 2.9 42.7 + - - +
399N ILE* 3.2 38.5 - - + +
400N SER* 3.1 21.5 + - - +
402N VAL* 2.8 26.5 + - + +
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Residues in contact with ASN 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355N LYS* 3.1 26.7 + - - +
356N ARG 3.1 6.1 + - - +
358N LYS* 1.3 77.8 - - - +
360N HIS* 1.3 64.7 + - - +
362N ARG* 2.8 32.3 + - - +
363N SER* 3.1 23.7 + - - -
91O ALA 3.2 21.2 + - - +
92O VAL* 3.3 29.4 - - - +
93O GLY* 3.8 2.7 - - - +
112O LEU* 4.4 4.9 - - + +
115O HIS* 4.2 17.3 + - - -
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Residues in contact with HIS 360 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275N ALA* 4.1 27.4 - - + +
278N GLY* 5.7 5.8 - - - -
279N ARG* 6.4 0.2 - - - +
356N ARG* 2.8 21.7 + - + +
357N ALA* 3.8 5.2 - - - +
359N ASN* 1.3 71.7 - - - +
361N LEU* 1.3 64.7 + - - +
363N SER* 3.2 8.1 + - - -
364N ALA* 3.1 27.5 + - + +
90O GLU 5.3 2.7 - - - +
93O GLY* 3.7 19.5 - - - -
94O GLY 5.8 1.2 + - - -
71V ASN* 5.3 11.6 + - + -
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Residues in contact with LEU 361 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N VAL* 4.3 2.9 - - + +
271N HIS* 3.8 32.8 - - + +
272N VAL* 3.7 30.7 - - + +
275N ALA* 4.7 5.6 - - + -
357N ALA 2.9 18.7 + - - +
358N LYS* 3.4 5.4 - - - +
360N HIS* 1.3 76.0 - - - +
362N ARG* 1.3 56.5 + - - +
364N ALA* 2.9 15.1 + - + +
365N MET* 2.7 36.8 + - + +
399N ILE* 3.8 25.1 - - + -
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Residues in contact with ARG 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N TYR* 3.4 14.9 - - - +
355N LYS 5.0 0.2 + - - -
358N LYS* 2.9 40.7 + - - +
359N ASN* 2.8 45.5 + - - +
361N LEU* 1.3 75.0 - - - +
363N SER* 1.3 57.0 + - - +
365N MET* 3.0 16.7 + - + +
366N VAL* 2.9 32.1 + - - +
396N ASP* 3.3 29.1 + - - +
399N ILE* 4.2 18.4 - - + +
400N SER* 3.3 23.8 + - - +
112O LEU* 3.8 19.9 - - + +
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Residues in contact with SER 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359N ASN 3.1 8.8 + - - -
360N HIS* 3.4 12.8 - - - -
361N LEU 3.1 0.2 - - - -
362N ARG* 1.3 77.1 - - - +
364N ALA* 1.3 61.5 + - - +
366N VAL* 3.4 5.1 + - - +
367N ALA* 3.1 21.3 + - - +
93O GLY* 2.7 29.4 + - - -
111O CYS* 5.0 1.9 - - - -
112O LEU* 3.7 26.0 + - - +
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Residues in contact with ALA 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360N HIS* 3.1 20.0 + - + +
361N LEU* 2.9 18.2 + - + +
363N SER* 1.3 75.2 - - - +
365N MET* 1.3 64.3 + - - +
367N ALA* 3.0 18.8 + - - +
368N GLN* 3.1 22.7 + - + +
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Residues in contact with MET 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N TYR* 3.7 22.7 - - - +
8N LEU* 5.4 0.4 - - + -
361N LEU* 2.7 16.0 + - + +
362N ARG* 3.1 28.0 - - + +
364N ALA* 1.3 77.9 - - - +
366N VAL* 1.3 64.1 + - + +
368N GLN* 3.2 24.5 - - - +
369N LEU* 4.1 2.4 + - - +
392N LEU* 3.5 44.0 - - + +
395N TRP* 3.4 37.0 - - + -
396N ASP* 4.3 6.5 - - + +
399N ILE* 4.1 12.6 - - + -
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Residues in contact with VAL 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N TYR* 5.0 2.5 - - + -
8N LEU* 5.7 0.2 - - + -
362N ARG 2.9 17.9 + - - +
363N SER* 3.7 7.0 - - - +
364N ALA 3.2 0.2 - - - -
365N MET* 1.3 78.8 - - + +
367N ALA* 1.3 58.6 + - - +
368N GLN 3.0 5.2 - - - -
369N LEU* 3.0 27.8 + - - +
370N ASP* 4.7 1.2 - - - +
392N LEU* 4.2 22.4 - - + -
42O SER* 5.2 2.0 - - - +
43O PRO* 4.2 19.7 - - + -
44O ALA* 3.9 25.4 - - + -
112O LEU* 4.2 15.5 - - + -
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Residues in contact with ALA 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363N SER 3.1 13.1 + - - +
364N ALA* 3.0 12.4 + - - +
366N VAL* 1.3 73.6 - - - +
368N GLN* 1.3 61.9 + - - +
369N LEU 3.0 6.8 + - - -
370N ASP* 3.5 24.8 + - + +
374N PRO* 5.0 2.8 - - - +
110O GLU* 6.1 0.7 - - - +
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Residues in contact with GLN 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364N ALA* 3.1 20.6 + - - +
365N MET* 3.2 18.8 - - - +
366N VAL 3.0 0.8 - - - -
367N ALA* 1.3 80.1 + - - +
369N LEU* 1.3 70.5 + - + +
370N ASP 3.6 0.7 - - - -
374N PRO* 3.3 19.2 - - - +
378N THR* 3.6 10.0 + - + +
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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
------------------------------------------------------------
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