Contacts of the helix formed by residues 328 - 340 (chain A) in PDB entry 1AMZ
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 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASP 6.1 0.2 - - - +
62A GLU 3.7 20.9 - - - +
63A GLY* 3.7 21.5 - - - +
64A ILE* 4.3 12.3 - - + +
71A ILE* 5.1 14.3 - - + +
72A PRO* 5.7 4.5 - - + -
323A LEU* 4.4 3.6 - - + -
326A THR 3.2 8.7 - - - +
327A ASP* 1.3 90.7 - - - +
329A ARG* 1.3 56.1 + - - +
331A THR* 3.2 11.6 + - - +
332A CYS* 2.9 30.8 + - - +
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Residues in contact with ARG 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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64A ILE* 4.8 4.9 - - + -
66A PHE* 6.0 0.2 - - - -
71A ILE* 3.8 23.1 - - + -
234A ILE* 3.4 30.8 + - + +
235A HIS* 5.1 2.0 - - - +
237A ASP 5.0 0.4 + - - -
238A HIS* 3.1 34.3 + - - -
320A HIS* 4.2 2.4 + - - -
327A ASP* 2.9 31.0 + - - +
328A PRO* 1.3 77.7 - - - +
330A TYR* 1.3 60.8 + - - +
332A CYS* 3.5 7.5 + - - +
333A GLN* 3.2 29.2 + - - +
373A ASN* 5.3 0.2 - - - +
374A VAL* 3.5 36.4 - - + +
397A PHE* 4.9 2.0 - - - -
401A ARG* 3.8 8.5 - - - +
702A MLT 2.7 45.3 + - - -
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Residues in contact with TYR 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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318A TYR* 4.4 2.7 + - - -
326A THR* 4.0 10.1 - - + -
327A ASP* 2.8 15.5 + - + +
329A ARG* 1.3 78.2 - - - +
331A THR* 1.3 69.1 + - - +
333A GLN* 3.0 12.8 + - - +
334A ARG* 3.0 29.1 + - - +
350A VAL* 3.8 17.5 + - + +
351A ALA* 5.0 1.2 - - - -
354A TYR* 3.4 40.2 - + - +
372A PRO* 3.6 41.2 - - + +
373A ASN 3.6 21.1 - - - +
374A VAL* 4.4 1.3 - - - +
376A ALA* 3.9 12.3 - - + -
377A HIS* 3.5 38.4 + + + -
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Residues in contact with THR 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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326A THR* 3.8 15.6 + - - +
327A ASP 3.2 6.8 + - - -
328A PRO* 3.2 14.7 + - - +
330A TYR* 1.3 80.1 - - - +
332A CYS* 1.3 64.7 + - - +
334A ARG* 3.3 13.4 + - + +
335A GLU* 3.0 35.1 + - + +
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Residues in contact with CYS 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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71A ILE* 4.3 17.9 - - + -
75A GLN* 4.1 19.3 - - - -
230A LEU* 3.9 32.9 - - - +
234A ILE* 4.5 8.5 - - + -
328A PRO 2.9 16.5 + - - +
329A ARG* 3.8 8.3 - - - +
331A THR* 1.3 78.8 - - - +
333A GLN* 1.3 60.6 + - - +
335A GLU* 3.4 16.5 + - - +
336A PHE* 3.2 19.6 + - - +
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Residues in contact with GLN 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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230A LEU* 5.4 4.3 - - + -
231A TYR* 4.7 4.0 - - - -
234A ILE* 4.0 19.0 - - + +
235A HIS* 4.1 5.5 - - - -
329A ARG 3.2 18.2 + - - +
330A TYR* 3.0 6.9 + - - +
332A CYS* 1.3 77.9 - - - +
334A ARG* 1.3 61.6 + - - +
336A PHE* 3.0 8.7 + - - +
337A ALA* 2.9 21.1 + - - +
374A VAL* 3.2 36.0 + - - +
377A HIS* 3.7 18.4 - - + +
378A SER* 3.0 32.4 - - - -
381A LEU* 3.8 23.6 - - + +
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Residues in contact with ARG 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 TYR* 3.0 25.2 + - + +
331A THR* 3.3 15.7 - - - +
333A GLN* 1.3 77.1 - - - +
335A GLU* 1.3 56.6 + - + +
337A ALA* 3.0 3.5 + - - +
338A LEU* 2.8 53.8 + - + +
347A PHE* 4.7 7.7 - - + -
351A ALA* 4.0 28.9 + - - +
354A TYR* 4.4 23.4 - - - +
377A HIS* 3.4 24.2 + - + +
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Residues in contact with GLU 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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75A GLN* 4.2 17.7 + - - +
331A THR* 3.0 23.8 + - + +
332A CYS* 3.8 17.3 - - - +
333A GLN 3.2 0.2 - - - -
334A ARG* 1.3 80.2 - - + +
336A PHE* 1.3 61.1 + - - +
338A LEU* 3.3 5.7 + - + -
339A LYS* 3.0 46.4 + - + +
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Residues in contact with PHE 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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86A GLU* 3.8 22.9 - - - -
223A GLN* 4.1 15.0 - - - -
226A GLU 4.5 1.8 - - - -
227A LEU* 3.8 44.9 - - + -
230A LEU* 3.9 19.3 - - + -
332A CYS 3.2 11.7 + - - +
333A GLN* 3.0 12.0 + - - +
335A GLU* 1.3 76.3 - - - +
337A ALA* 1.3 66.4 + - - +
339A LYS* 3.2 2.3 + - - -
340A HIS* 2.9 61.2 + + + +
341A LEU* 4.2 8.7 - - + -
381A LEU* 4.5 7.2 - - + -
385A TYR* 3.7 22.7 - + - -
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Residues in contact with ALA 337 (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 GLN 2.9 12.0 + - - +
334A ARG 3.0 7.8 + - - +
336A PHE* 1.3 79.9 - - - +
338A LEU* 1.3 60.3 + - - +
341A LEU* 2.7 41.0 + - + -
342A PRO 3.2 7.3 - - - -
347A PHE* 3.6 35.2 - - + -
377A HIS* 4.1 1.8 - - + -
381A LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 338 (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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334A ARG* 2.8 50.8 + - + +
335A GLU* 4.6 3.6 - - + -
337A ALA* 1.3 74.1 - - - +
339A LYS* 1.3 85.3 + - - +
342A PRO* 3.3 26.3 - - + +
347A PHE* 3.7 25.6 - - + -
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Residues in contact with LYS 339 (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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85A GLU* 6.0 2.2 - - - +
335A GLU* 3.0 40.4 + - + +
336A PHE* 4.7 1.1 - - - -
337A ALA 3.1 0.6 - - - -
338A LEU* 1.3 102.2 - - - +
340A HIS* 1.3 80.4 + - + +
342A PRO* 4.4 4.4 - - - +
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Residues in contact with HIS 340 (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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85A GLU* 4.8 13.5 + - - -
86A GLU* 5.0 2.6 + - - -
223A GLN* 3.4 33.4 + - + +
336A PHE* 2.9 57.4 + + + +
339A LYS* 1.3 94.0 + - + +
341A LEU* 1.3 62.2 + - + +
342A PRO* 3.3 7.2 - - - +
384A TYR* 3.9 12.0 + - - -
385A TYR* 3.7 18.8 + - - +
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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