Contacts of the helix formed by residues 325 - 336 (chain A) 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 ASP 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ASP* 3.5 13.4 + - - +
324A ASN* 1.3 71.7 - - - +
326A THR* 1.3 64.6 + - - +
327A LYS* 3.1 22.3 + - - +
328A ARG* 2.4 49.3 + - - +
329A ILE* 2.8 30.0 + - - +
358A TYR* 2.9 17.1 + - - +
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Residues in contact with THR 326 (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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324A ASN 2.8 10.4 + - - +
325A ASP* 1.3 75.9 + - - +
327A LYS* 1.3 57.9 + - + +
329A ILE* 3.8 7.4 - - - +
330A ASP* 2.7 49.9 + - - -
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Residues in contact with LYS 327 (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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325A ASP* 3.1 13.2 + - - +
326A THR* 1.3 84.6 + - - +
328A ARG* 1.3 64.2 + - + +
330A ASP* 3.8 5.0 - - - +
331A ILE* 3.1 34.0 + - + +
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Residues in contact with ARG 328 (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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322A ASP* 4.1 10.3 + - - +
325A ASP* 2.4 46.9 + - - +
327A LYS* 1.3 81.2 - - + +
329A ILE* 1.3 64.9 + - - +
331A ILE* 3.2 7.9 + - + +
332A MET* 3.0 27.7 + - - +
358A TYR* 2.8 65.6 + - + -
359A ILE* 4.4 3.6 - - - +
361A LEU* 3.5 39.0 - - + +
362A GLY* 3.7 15.5 - - - +
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Residues in contact with ILE 329 (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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323A PHE 3.7 5.8 - - - +
324A ASN* 3.4 38.1 - - + +
325A ASP 2.8 25.3 + - - +
326A THR* 3.8 6.1 - - - +
328A ARG* 1.3 76.2 - - - +
330A ASP* 1.3 52.6 + - - +
332A MET* 2.8 10.0 + - - +
333A VAL* 2.7 39.6 + - + +
339A ARG* 4.1 32.1 - - + +
342A ILE* 4.4 22.0 - - + -
358A TYR* 4.1 11.9 - - + -
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Residues in contact with ASP 330 (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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326A THR* 2.7 35.0 + - - +
327A LYS* 3.8 5.9 - - - +
329A ILE* 1.3 69.5 - - - +
331A ILE* 1.3 52.5 - - + +
333A VAL* 3.4 5.3 + - - +
334A THR* 2.7 37.6 + - - +
339A ARG* 3.3 22.5 + - - -
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Residues in contact with ILE 331 (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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327A LYS* 3.1 23.0 + - + +
328A ARG* 3.6 11.9 - - + +
330A ASP* 1.3 76.8 - - + +
332A MET* 1.3 53.3 + - - +
334A THR* 3.3 8.8 + - - -
335A MET* 2.7 62.8 + - + +
361A LEU* 3.9 22.2 - - + -
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Residues in contact with MET 332 (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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328A ARG 3.0 13.9 + - - +
329A ILE 2.8 7.4 + - - +
331A ILE* 1.3 76.0 - - - +
333A VAL* 1.3 65.8 + - - +
335A MET* 3.0 13.2 + - - +
336A GLY 3.1 0.7 + - - -
337A PHE* 2.9 51.2 + - + +
342A ILE* 3.7 28.9 - - + -
354A VAL* 3.3 30.5 - - + +
357A THR* 3.9 10.3 - - + -
358A TYR* 3.6 38.4 - - + +
361A LEU* 3.7 15.7 - - + -
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Residues in contact with VAL 333 (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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329A ILE* 2.7 25.6 + - + +
330A ASP* 3.9 6.1 - - - +
332A MET* 1.3 72.1 - - - +
334A THR* 1.3 66.6 + - - +
335A MET 2.9 1.2 + - - -
336A GLY* 2.9 13.2 + - - -
337A PHE 3.4 17.1 - - - +
339A ARG* 3.8 48.9 - - + +
342A ILE* 4.7 2.2 - - + -
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Residues in contact with THR 334 (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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330A ASP* 2.7 23.3 + - - +
331A ILE* 3.5 9.8 - - - -
332A MET 3.2 0.2 - - - -
333A VAL* 1.3 78.5 - - - +
335A MET* 1.4 60.3 + - - +
336A GLY 3.4 0.3 + - - -
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Residues in contact with MET 335 (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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74A LEU* 3.2 40.4 - - + +
75A THR* 4.3 11.7 - - + -
331A ILE* 2.7 50.7 + - + +
332A MET* 3.6 11.0 - - - +
333A VAL 2.9 1.0 + - - -
334A THR* 1.4 77.8 - - - +
336A GLY* 1.3 57.9 + - - +
337A PHE* 3.8 15.2 - - + -
357A THR* 4.1 18.4 - - - -
361A LEU* 4.3 4.5 - - + -
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Residues in contact with GLY 336 (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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333A VAL 2.9 9.1 + - - -
334A THR 3.3 1.4 + - - -
335A MET* 1.3 81.9 - - - +
337A PHE* 1.3 68.1 + - - +
338A ALA* 3.8 0.7 + - - +
341A GLU* 4.6 1.6 - - - +
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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