Contacts of the helix formed by residues 324 - 337 (chain A) in PDB entry 4NZP
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 SER 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LEU* 4.7 0.2 - - - +
321A TYR* 2.6 36.1 + - - +
322A TRP 3.1 2.4 + - - -
323A PHE* 1.3 76.6 - - - +
325A PRO* 1.3 71.1 - - - +
326A GLU* 3.2 25.3 + - - +
327A ARG* 3.4 12.8 + - - +
328A MET* 3.2 27.1 + - - +
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Residues in contact with PRO 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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323A PHE 4.8 0.7 - - - +
324A SER* 1.3 81.1 - - - +
326A GLU* 1.3 76.1 + - - +
328A MET* 3.2 8.7 + - + +
329A MET* 2.9 33.6 + - + +
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Residues in contact with GLU 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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316A LEU* 3.8 32.6 - - + +
321A TYR* 4.3 9.4 - - - -
324A SER* 3.2 27.6 + - - +
325A PRO* 1.3 85.3 - - - +
327A ARG* 1.3 58.1 + - - +
329A MET* 3.0 14.4 + - - +
330A LEU* 2.9 31.5 + - + +
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Residues in contact with ARG 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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79A PRO* 5.6 0.2 - - - +
313A TYR* 3.6 28.5 - - + -
316A LEU* 4.3 18.4 - - + -
317A ILE* 4.9 2.0 - - + -
321A TYR 3.5 10.5 - - - +
322A TRP* 2.7 78.6 + - + +
323A PHE* 4.6 5.7 - - - -
324A SER* 3.3 17.9 + - - +
325A PRO 3.3 0.8 - - - -
326A GLU* 1.3 80.3 - - - +
328A MET* 1.3 78.2 + - - +
330A LEU* 3.7 3.2 - - - +
331A GLN* 2.8 61.0 + - - +
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Residues in contact with MET 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 TRP 5.0 0.2 - - - +
323A PHE* 5.8 3.8 - - - -
324A SER 3.2 18.9 + - - +
325A PRO* 3.6 10.3 - - + +
326A GLU 3.2 0.2 - - - -
327A ARG* 1.3 103.8 - - - +
329A MET* 1.3 65.1 + - - +
331A GLN* 3.7 6.8 - - + +
332A ALA* 3.0 23.7 + - - +
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Residues in contact with MET 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 PRO* 2.9 23.8 + - + +
326A GLU* 3.0 12.3 + - - +
328A MET* 1.3 77.2 - - + +
330A LEU* 1.3 65.3 + - + +
332A ALA* 3.3 15.1 + - - +
333A LEU* 3.3 12.6 + - - +
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Residues in contact with LEU 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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309A LEU* 4.2 38.1 - - + +
312A LYS* 4.2 16.6 - - + -
313A TYR* 4.0 32.1 - - + +
316A LEU* 3.6 31.6 - - + -
326A GLU* 2.9 15.6 + - + +
327A ARG* 3.8 4.3 - - - +
329A MET* 1.3 78.8 - - + +
331A GLN* 1.3 57.7 + - - +
333A LEU* 3.3 9.6 + - + +
334A ILE* 2.9 35.1 + - + +
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Residues in contact with GLN 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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79A PRO* 3.2 36.8 + - + +
82A ARG* 5.2 0.2 - - - +
313A TYR* 2.5 28.1 + - - -
322A TRP* 3.8 1.4 - - - -
327A ARG* 2.8 47.5 + - - +
328A MET* 3.7 9.4 - - + +
329A MET 3.3 0.2 - - - -
330A LEU* 1.3 75.1 - - - +
332A ALA* 1.3 52.6 + - - +
334A ILE* 3.5 12.2 - - - +
335A ASP* 2.7 70.3 + - - +
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Residues in contact with ALA 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 MET 3.0 17.2 + - - +
329A MET* 3.6 8.3 - - - +
330A LEU 3.3 0.4 - - - -
331A GLN* 1.3 75.2 - - - +
333A LEU* 1.3 62.0 + - - +
335A ASP* 4.1 5.0 - - - +
336A GLU* 3.2 24.3 + - - +
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Residues in contact with LEU 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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305A LEU* 4.2 22.2 - - + -
306A LYS* 4.6 17.9 - - + -
309A LEU* 3.7 35.4 - - + -
329A MET 3.3 8.5 + - - +
330A LEU* 3.3 16.5 + - + +
332A ALA* 1.3 77.5 - - - +
334A ILE* 1.3 77.1 + - + +
336A GLU* 3.4 7.2 + - - +
337A SER* 3.3 20.1 + - - -
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Residues in contact with ILE 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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82A ARG* 3.6 35.9 - - + -
83A ALA* 3.6 22.0 - - + +
306A LYS* 4.1 16.6 - - + -
313A TYR* 3.5 39.7 - - + +
330A LEU* 2.9 21.6 + - + +
331A GLN* 3.2 16.1 + - - +
333A LEU* 1.3 85.1 - - + +
335A ASP* 1.3 63.5 + - - +
337A SER* 2.5 27.8 + - - -
338A GLN* 3.3 4.5 - - - +
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Residues in contact with ASP 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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82A ARG* 3.0 34.4 + - - -
331A GLN* 2.7 47.2 + - - +
332A ALA* 4.1 5.2 - - - +
334A ILE* 1.3 70.0 - - - +
336A GLU* 1.3 61.2 + - - +
338A GLN* 2.9 27.2 + - - +
339A ILE* 3.6 9.2 + - - +
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Residues in contact with GLU 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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332A ALA 3.2 16.5 + - - +
333A LEU* 3.7 7.4 - - - +
335A ASP* 1.3 79.1 - - - +
337A SER* 1.3 61.7 + - - +
338A GLN 3.0 1.3 + - - -
339A ILE* 3.4 30.9 + - - +
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Residues in contact with SER 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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298A LEU* 3.4 31.4 - - - +
302A ALA* 4.7 19.0 - - - +
306A LYS* 3.4 19.2 - - - +
333A LEU* 3.3 10.0 + - - -
334A ILE 2.5 20.6 + - - -
336A GLU* 1.3 81.1 - - - +
338A GLN* 1.3 72.9 + - - +
339A ILE 3.5 0.6 + - - -
340A HIS 4.9 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