Contacts of the helix formed by residues 265 - 277 (chain N) in PDB entry 3H1I
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 PRO 265 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263N ALA 3.9 5.6 - - - +
264N ASP* 1.3 94.5 - - - +
266N ASP* 1.3 64.1 + - - +
267N ASN 3.3 0.4 - - - -
268N VAL* 3.2 26.9 - - + +
269N VAL* 4.4 3.3 + - - +
398N ARG* 4.2 23.1 + - - +
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Residues in contact with ASP 266 (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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260N PRO* 5.1 1.1 - - + -
264N ASP* 2.6 23.2 - - + +
265N PRO* 1.3 76.9 - - - +
267N ASN* 1.3 68.3 + - - +
268N VAL 2.7 4.6 + - - -
269N VAL* 2.7 22.1 + - - +
270N LEU* 3.0 12.6 + - + -
410N VAL* 4.3 24.0 - - + +
413N LYS* 3.1 21.5 + - - +
414N TYR* 3.1 28.5 + - + +
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Residues in contact with ASN 267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260N PRO* 3.7 18.5 - - - +
261N GLY 3.1 27.5 + - - -
262N TRP* 3.2 10.2 + - - +
264N ASP* 3.0 21.7 + - - +
266N ASP* 1.3 77.2 - - - +
268N VAL* 1.3 67.2 + - + +
270N LEU* 3.3 8.5 + - - +
271N HIS* 3.0 31.4 + - + +
311N ASN* 3.1 14.3 + - - +
313N SER* 3.0 23.0 + - - -
386N TYR* 4.7 11.2 - - + +
395N TRP* 6.4 0.9 - - + -
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Residues in contact with VAL 268 (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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265N PRO* 3.2 23.1 - - + +
266N ASP 2.7 3.2 + - - -
267N ASN* 1.3 78.8 - - + +
269N VAL* 1.3 68.9 + - + +
271N HIS* 2.7 16.2 + - - +
272N VAL* 3.1 10.5 + - + +
361N LEU* 4.5 1.5 - - + +
395N TRP* 4.3 21.8 - - + -
398N ARG* 3.5 49.8 - - + +
399N ILE* 4.0 17.7 - - + -
402N VAL* 4.2 7.2 - - + -
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Residues in contact with VAL 269 (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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265N PRO 4.6 3.4 - - - +
266N ASP* 2.7 22.0 + - - +
268N VAL* 1.3 74.8 - - + +
270N LEU* 1.3 64.8 + - + +
272N VAL* 2.7 24.9 + - - +
273N ALA* 2.9 10.4 + - - +
402N VAL* 4.0 7.0 - - + -
406N MET* 3.6 31.2 - - + -
407N VAL* 3.7 29.8 - - + +
410N VAL* 3.3 36.1 - - + -
411N CYS* 5.3 0.9 - - - -
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Residues in contact with LEU 270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260N PRO* 3.9 29.4 - - + -
266N ASP* 3.0 10.6 + - + +
267N ASN* 3.5 8.7 - - - +
269N VAL* 1.3 77.3 - - - +
271N HIS* 1.3 58.2 + - - +
273N ALA* 3.1 8.1 + - - +
274N ASN* 2.8 27.8 + - - +
311N ASN* 3.7 16.8 - - - +
320N PHE* 3.6 40.1 - - + -
410N VAL* 3.5 27.6 - - + +
411N CYS* 4.9 9.2 - - - +
414N TYR* 4.3 19.1 - - + -
415N ILE* 6.1 0.4 - - + -
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Residues in contact with HIS 271 (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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262N TRP* 6.4 2.5 - + - -
267N ASN* 3.0 25.7 + - + +
268N VAL* 2.7 16.5 + - - +
270N LEU* 1.3 70.4 - - - +
272N VAL* 1.3 63.7 + - - +
274N ASN* 3.3 12.4 + - + +
275N ALA* 3.0 21.1 + - - +
311N ASN* 3.5 43.9 + - + +
313N SER* 5.1 2.0 - - - -
361N LEU* 3.7 26.9 - - + +
386N TYR* 5.8 3.1 - - - -
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Residues in contact with VAL 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N VAL* 3.1 12.4 + - + +
269N VAL* 2.7 18.8 + - - +
271N HIS* 1.3 67.7 - - - +
273N ALA* 1.3 68.1 + - - +
275N ALA* 2.8 21.2 + - - +
276N ILE* 3.3 1.4 + - + +
354N VAL* 4.6 8.3 - - + +
357N ALA* 3.2 25.8 - - + +
358N LYS* 4.5 19.1 - - + +
361N LEU* 3.9 18.2 - - + -
399N ILE* 5.1 4.0 - - + -
402N VAL* 4.0 35.0 - - + -
407N VAL* 4.4 10.8 - - + -
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Residues in contact with ALA 273 (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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269N VAL 2.9 9.6 + - - +
270N LEU* 3.2 11.0 - - - +
272N VAL* 1.3 75.3 - - - +
274N ASN* 1.3 53.5 + - - +
275N ALA 2.5 13.3 + - - -
276N ILE* 2.5 35.3 + - - +
277N ILE* 3.5 4.0 + - - +
320N PHE* 4.7 6.1 - - + -
345N LEU* 4.4 15.0 - - + -
407N VAL* 4.0 8.0 - - + +
411N CYS* 3.8 28.3 - - - -
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Residues in contact with ASN 274 (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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270N LEU 2.8 12.2 + - - +
271N HIS* 3.6 17.4 - - + +
272N VAL 3.3 0.2 - - - -
273N ALA* 1.3 71.1 - - - +
275N ALA* 1.3 56.4 + - - +
277N ILE* 4.2 3.9 - - - +
278N GLY* 3.2 16.1 + - - -
309N THR* 3.1 44.5 + - - +
310N PHE* 3.3 30.0 + - - +
311N ASN* 3.4 11.8 + - - +
320N PHE* 3.4 31.0 - - - -
321N GLY 4.4 3.6 + - - -
342N TRP* 5.3 2.2 - - - +
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Residues in contact with ALA 275 (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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271N HIS 3.0 10.2 + - - +
272N VAL* 2.8 15.6 + - - +
273N ALA 2.5 5.7 + - - -
274N ASN* 1.3 74.7 - - - +
276N ILE* 1.3 60.8 + - - +
278N GLY* 3.3 11.0 + - - -
292N SER* 5.7 0.3 - - - -
356N ARG* 4.6 6.6 + - - -
357N ALA* 3.3 32.6 - - + +
360N HIS* 4.1 23.5 - - + +
361N LEU* 4.7 4.9 - - + +
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Residues in contact with ILE 276 (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* 3.7 7.4 - - + +
273N ALA* 2.5 24.9 + - - +
275N ALA* 1.3 73.2 - - - +
277N ILE* 1.3 62.1 + - + +
292N SER* 3.8 13.2 - - - -
293N ARG* 4.6 6.8 + - + -
345N LEU* 4.0 22.0 - - + -
349N THR* 3.7 28.9 - - + -
353N GLU* 3.8 34.5 - - + +
354N VAL* 4.2 14.6 - - + -
356N ARG* 3.4 25.1 + - - +
357N ALA* 3.7 12.3 - - + -
407N VAL* 4.6 2.9 - - + -
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Residues in contact with ILE 277 (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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273N ALA 3.5 5.1 + - - +
274N ASN* 5.2 3.1 - - - +
276N ILE* 1.3 79.5 - - + +
278N GLY* 1.3 65.3 + - - +
292N SER* 2.9 18.7 + - - -
293N ARG* 5.7 1.1 - - - +
294N LEU* 3.9 32.3 - - + +
307N PHE* 3.4 6.4 - - + -
309N THR* 3.7 22.7 - - + -
322N PHE* 6.2 3.4 - - + -
338N ALA 5.5 0.2 - - - +
341N GLU* 4.0 23.6 - - + +
342N TRP* 3.9 18.8 - - + +
345N LEU* 3.2 38.8 - - + -
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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
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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