Contacts of the helix formed by residues 322 - 330 (chain A) in PDB entry 4P3N
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 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A HIS* 1.3 63.9 + - - +
324A ARG* 3.1 18.9 - - - +
325A LYS* 3.2 14.0 + - + +
326A ILE* 2.7 50.2 + - + +
606A GLU* 2.8 50.3 + - - +
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Residues in contact with HIS 323 (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* 1.3 87.2 + - - +
324A ARG* 1.3 87.2 + - + +
326A ILE* 4.9 0.2 - - - -
327A GLY 2.9 17.0 + - - -
333A TYR* 2.4 55.0 + + - +
450A THR* 5.0 0.6 + - - +
451A GLY* 4.1 1.6 - - - -
452A LEU* 3.5 40.6 + - + -
453A THR* 4.3 11.5 + - + +
602A ALA* 3.6 36.3 - - + +
605A THR* 3.5 16.1 - - + +
606A GLU* 4.2 15.9 - - - +
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Residues in contact with ARG 324 (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 3.1 13.4 - - - +
323A HIS* 1.3 108.0 + - + +
325A LYS* 1.3 59.8 + - - +
327A GLY* 3.1 2.4 + - - -
328A ARG* 2.9 30.2 + - - +
333A TYR* 4.4 5.5 - - - +
335A PHE* 4.6 12.8 - - + -
450A THR* 4.1 24.2 - - - +
451A GLY* 4.3 19.9 - - - +
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Residues in contact with LYS 325 (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* 3.2 16.8 + - - +
324A ARG* 1.3 78.5 - - - +
326A ILE* 1.3 60.6 + - + +
328A ARG* 3.5 4.3 + - - +
329A ASP* 2.9 47.2 + - - +
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Residues in contact with ILE 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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322A ASP* 2.7 36.9 + - + +
325A LYS* 1.3 73.6 - - + +
327A GLY* 1.3 60.6 + - - +
329A ASP* 4.1 4.9 - - - +
330A GLN* 2.8 53.2 + - + +
332A LEU* 4.8 0.4 - - + -
605A THR* 3.6 40.2 - - + +
609A GLY* 3.8 22.4 - - - +
610A GLY* 4.1 10.8 - - - -
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Residues in contact with GLY 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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323A HIS 2.9 16.8 + - - -
324A ARG 3.1 3.8 + - - -
326A ILE* 1.3 76.1 - - - +
328A ARG* 1.3 55.1 + - - +
331A GLU* 3.1 4.7 + - - -
332A LEU* 2.6 47.9 + - - -
333A TYR* 3.5 23.8 + - - +
605A THR* 4.5 0.2 - - - +
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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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324A ARG 2.9 15.4 + - - +
325A LYS* 3.9 5.4 - - - +
327A GLY* 1.3 74.2 - - - +
329A ASP* 1.3 64.4 + - - +
331A GLU* 3.0 23.7 + - - +
333A TYR 4.2 7.5 + - - +
334A PHE* 6.4 1.1 - - + -
422B HIS* 6.1 3.8 - - - +
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Residues in contact with ASP 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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325A LYS* 2.9 39.9 + - - +
326A ILE* 4.1 4.5 - - - +
328A ARG* 1.3 77.0 - - - +
330A GLN* 1.3 59.9 + - + +
331A GLU* 3.3 2.0 - - - +
619A ARG* 4.7 1.7 + - - -
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Residues in contact with GLN 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 ILE* 2.8 27.4 + - + +
329A ASP* 1.3 78.0 - - + +
331A GLU* 1.3 67.9 + - - +
332A LEU* 3.4 19.9 - - + +
348A LYS* 3.6 3.5 - - - +
610A GLY* 2.7 35.1 + - - -
612A TRP* 3.0 25.6 + - - +
619A ARG* 2.5 51.9 + - - +
668A ALA* 4.5 3.3 + - - +
669A GLN* 4.1 14.8 - - - +
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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