Contacts of the helix formed by residues 338 - 348 (chain H) in PDB entry 2HAK
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 ALA 338 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271E PHE 4.8 2.7 + - - +
275E THR* 5.9 6.3 - - + -
333H VAL* 5.1 0.4 - - - -
336H GLY 4.0 0.6 + - - +
337H PHE* 1.3 75.5 - - - +
339H ARG* 1.3 67.6 + - - +
340H ASP* 2.9 13.0 + - - +
341H GLU* 2.9 40.4 + - + +
342H ILE* 3.1 13.5 + - - +
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Residues in contact with ARG 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329H ILE* 3.7 20.9 - - + +
330H ASP* 3.4 23.6 + - - -
333H VAL* 3.9 34.3 - - + +
338H ALA* 1.3 68.8 - - - +
340H ASP* 1.3 68.5 + - - +
341H GLU 3.2 0.2 + - - -
342H ILE* 3.2 12.7 + - - +
343H ASN* 2.9 22.5 + - - +
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Residues in contact with ASP 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E THR* 5.4 7.6 - - - +
338H ALA* 2.9 11.6 + - - +
339H ARG* 1.3 83.4 + - - +
341H GLU* 1.3 66.8 + - - +
343H ASN* 3.5 7.1 + - - +
344H ASP* 2.9 40.4 + - - +
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Residues in contact with GLU 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E PHE* 5.0 13.1 - - - +
273E MET 5.2 5.2 - - - +
275E THR* 5.5 7.1 - - - +
278E GLU* 5.7 1.2 - - - +
337H PHE* 6.0 1.0 - - + -
338H ALA* 2.9 27.2 + - + +
340H ASP* 1.3 83.4 - - - +
342H ILE* 1.3 56.2 + - + +
343H ASN 3.1 1.3 - - - -
344H ASP* 3.6 7.7 - - - +
345H ALA* 2.6 38.5 + - - +
354H VAL* 4.2 19.2 - - + +
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Residues in contact with ILE 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H PHE 5.5 0.2 - - - +
329H ILE* 4.3 26.9 - - + +
332H MET* 3.6 40.8 - - + -
333H VAL* 4.8 2.2 - - + +
337H PHE* 4.0 10.3 - - + -
338H ALA 3.3 18.6 - - - +
339H ARG* 3.4 10.3 - - - +
341H GLU* 1.3 76.9 - - - +
343H ASN* 1.3 65.9 + - - +
345H ALA* 3.7 0.7 - - - +
346H LEU* 3.1 42.3 + - + +
354H VAL* 3.7 16.5 - - + +
358H TYR* 4.0 17.3 - - + -
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Residues in contact with ASN 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H PHE* 4.6 17.9 + - - +
324H ASN* 4.9 10.1 + - - +
339H ARG 2.9 16.0 + - - +
340H ASP* 3.7 7.9 - - - +
342H ILE* 1.3 79.9 - - - +
344H ASP* 1.3 63.5 + - - +
346H LEU* 3.6 2.5 + - - +
347H ILE* 3.1 50.4 + - - +
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Residues in contact with ASP 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H ASP* 2.9 31.8 + - - +
341H GLU* 3.1 7.6 + - - +
343H ASN* 1.3 77.3 - - - +
345H ALA* 1.3 62.9 + - - +
347H ILE* 4.3 11.3 - - - +
348H ASN* 2.9 39.3 + - - +
350H LYS* 3.7 19.0 + - - +
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Residues in contact with ALA 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341H GLU 2.6 22.1 + - - +
342H ILE 3.7 1.3 - - - +
344H ASP* 1.3 73.2 - - - +
346H LEU* 1.3 57.1 + - - +
349H GLN* 3.0 6.8 + - - -
350H LYS* 2.9 39.8 + - + +
352H ASP* 3.8 17.9 - - - +
354H VAL* 3.7 29.8 - - + -
355H MET* 3.8 8.8 - - - +
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Residues in contact with LEU 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H PHE* 3.6 56.0 - - + +
342H ILE* 3.1 35.0 + - + +
343H ASN* 4.1 2.9 - - - +
345H ALA* 1.3 74.1 - - - +
347H ILE* 1.3 59.7 + - - +
349H GLN* 2.5 37.5 + - - +
355H MET* 4.0 29.8 - - + +
358H TYR* 3.7 32.5 - - + -
359H ILE* 5.1 4.0 - - + -
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Residues in contact with ILE 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H PHE* 3.8 26.2 - - + -
343H ASN* 3.1 46.4 + - - +
344H ASP* 4.3 10.5 - - - +
346H LEU* 1.3 75.2 - - - +
348H ASN* 1.3 76.8 + - - +
349H GLN* 3.4 5.7 + - - +
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Residues in contact with ASN 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344H ASP* 2.9 38.1 + - - +
347H ILE* 1.3 90.3 - - - +
349H GLN* 1.3 74.2 + - - +
350H LYS* 3.2 23.5 + - + +
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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