Contacts of the helix formed by residues 357 - 370 (chain A) in PDB entry 1H13
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 ASN 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE* 4.1 2.4 - - - -
307A ASN* 4.5 4.0 - - - +
355A SER* 3.1 6.6 + - - -
356A THR* 1.3 76.7 - - - +
358A ALA* 1.3 58.8 + - - +
359A GLY* 2.8 30.3 + - - -
360A GLN* 2.9 40.8 + - - +
361A ALA* 2.9 25.5 + - - +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.7 30.4 - - + +
4A ASN* 4.5 10.7 - - + +
356A THR 4.0 3.4 + - - -
357A ASN* 1.3 72.4 + - - +
359A GLY* 1.3 56.5 + - - +
361A ALA* 3.2 1.7 + - - +
362A ASN* 2.9 29.6 + - - +
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Residues in contact with GLY 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN* 2.8 10.9 + - - -
358A ALA* 1.3 76.1 - - - +
360A GLN* 1.3 61.4 + - - -
362A ASN* 3.3 6.2 + - - +
363A GLU* 3.1 22.6 + - - +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ASN* 2.9 45.6 + - - +
310A LEU* 3.8 25.2 - - + +
311A GLY* 3.4 12.3 + - - -
314A SER* 6.0 3.1 - - - -
352A LEU* 4.3 0.9 - - - -
355A SER* 3.2 21.8 + - - +
357A ASN* 2.9 30.7 + - + +
359A GLY* 1.3 72.1 - - - +
361A ALA* 1.3 66.4 + - - +
363A GLU* 3.3 3.3 + - - -
364A PHE* 2.8 41.2 + - + +
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.7 26.9 - - + -
24A MET* 3.1 24.2 - - + -
352A LEU* 3.7 15.5 - - + +
357A ASN 2.9 12.9 + - - +
358A ALA 3.5 8.1 - - - +
359A GLY 3.2 0.2 - - - -
360A GLN* 1.3 78.7 - - - +
362A ASN* 1.3 56.5 + - - +
365A PHE* 2.7 35.3 + - - +
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Residues in contact with ASN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 4.0 8.9 - - - +
358A ALA 2.9 16.8 + - - +
359A GLY* 3.7 7.0 - - - +
360A GLN 3.3 0.4 - - - -
361A ALA* 1.3 77.4 - - - +
363A GLU* 1.3 63.5 + - - +
365A PHE* 5.0 0.2 - - - -
366A ASN* 3.0 42.0 + - - +
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A GLY 3.1 11.3 + - - +
360A GLN* 3.7 7.9 - - - +
362A ASN* 1.3 79.8 - - - +
364A PHE* 1.3 72.3 + - + +
366A ASN* 4.0 1.9 - - - +
367A GLU* 3.1 24.3 + - - +
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Residues in contact with PHE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU* 3.7 54.7 - - + -
313A LEU* 4.2 8.7 - - + -
314A SER* 4.3 13.7 - - - -
325A TYR* 3.6 34.5 - + - -
345A LYS* 4.8 3.2 - - - +
348A ASN* 3.9 25.6 - - + +
349A ALA* 4.4 2.9 - - - +
352A LEU* 4.1 16.4 - - + -
360A GLN* 2.8 38.1 + - + +
363A GLU* 1.3 82.7 - - + +
365A PHE* 1.3 62.4 + - - +
367A GLU* 3.5 6.5 + - + +
368A PHE* 3.2 21.0 + - - +
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.8 24.9 - - + -
21A ALA* 3.6 17.3 - - + -
24A MET* 3.7 27.6 - - + -
26A LYS* 3.8 25.4 - - + -
349A ALA* 4.4 7.4 - - + -
352A LEU* 3.7 11.3 - - + +
361A ALA 2.7 24.8 + - - +
362A ASN 4.4 0.4 - - - +
364A PHE* 1.3 73.1 - - - +
366A ASN* 1.3 61.0 + - - +
368A PHE* 3.1 9.9 + + - +
369A TRP* 2.8 61.6 + + + -
393A VAL* 3.8 27.1 - - + -
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Residues in contact with ASN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 5.3 2.1 - - - +
26A LYS* 2.9 34.2 + - - +
362A ASN* 3.0 34.4 + - - +
363A GLU* 4.2 1.6 - - - +
365A PHE* 1.3 81.1 - - - +
367A GLU* 1.3 61.5 + - - +
369A TRP* 4.4 3.8 - - - +
370A SER* 3.0 28.4 + - - -
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Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LYS* 6.4 0.7 - - - +
325A TYR* 6.1 0.4 - - - +
345A LYS* 4.3 22.5 + - + +
363A GLU 3.1 17.8 + - - +
364A PHE* 3.9 7.4 - - + +
365A PHE 3.2 0.2 - - - -
366A ASN* 1.3 76.9 - - - +
368A PHE* 1.3 60.8 + - - +
370A SER* 3.3 10.9 + - - -
371A LEU* 3.3 21.7 - - - +
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 6.2 0.2 - - - -
345A LYS* 4.0 7.5 - - - +
346A ALA* 3.5 32.3 - - + -
349A ALA* 3.8 21.3 - - + -
364A PHE 3.2 12.0 + - - +
365A PHE* 3.1 13.8 + + - +
367A GLU* 1.3 76.7 - - - +
369A TRP* 1.3 75.4 - + - +
371A LEU* 3.1 33.0 + - + +
386A TYR* 3.6 28.2 + + - -
389A ALA* 3.9 15.9 - - + -
390A MET* 3.7 35.2 - - + -
393A VAL* 4.0 17.5 - - + -
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Residues in contact with TRP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.0 19.7 - - + -
26A LYS* 3.5 46.3 - - + +
27A THR 4.4 7.3 + - - -
29A ILE* 4.2 24.2 - - + -
32A LYS* 2.7 59.1 + - + +
365A PHE* 2.8 43.7 + + + +
366A ASN* 4.1 3.4 - - - +
368A PHE* 1.3 86.3 - + - +
370A SER* 1.3 61.2 + - - +
371A LEU 3.4 0.7 + - - +
390A MET* 3.7 27.4 - - + -
393A VAL* 4.2 6.1 - - + -
394A SER* 6.1 0.2 - - - -
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Residues in contact with SER 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ASN 3.0 18.4 + - - -
367A GLU* 3.3 12.8 + - - -
369A TRP* 1.3 78.0 - - - +
371A LEU* 1.3 64.3 + - - +
372A SER* 3.7 1.2 + - - -
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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