Contacts of the helix formed by residues 317 - 330 (chain A) in PDB entry 4N20
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 ASN 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A CYS* 4.3 6.2 - - + +
314A MET* 3.0 23.1 + - + +
315A LYS 3.3 0.6 - - - -
316A ASP* 1.3 75.8 + - - +
318A TYR* 1.3 61.2 + - - +
319A LEU* 4.2 2.8 + - - +
320A PHE* 3.3 22.3 + - + +
321A LEU* 3.2 27.1 + - - +
633A ASP 4.2 4.2 - - - +
634A ASP 3.4 15.1 + - - +
636A SER 5.5 0.2 + - - -
637A ALA* 3.6 22.5 + - - +
638A TYR* 4.0 13.9 + - - -
647A CYS* 3.4 29.7 - - - -
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Residues in contact with TYR 318 (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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315A LYS 3.6 19.2 - - - -
316A ASP* 2.9 38.0 + - + +
317A ASN* 1.3 72.0 + - - +
319A LEU* 1.3 62.5 + - - +
321A LEU* 3.3 9.0 + - + +
322A LYS* 2.9 31.5 + - - +
637A ALA* 5.1 1.2 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASN* 3.5 3.5 + - - +
318A TYR* 1.3 76.0 - - - +
320A PHE* 1.3 64.9 + - - +
322A LYS* 3.9 23.5 - - - +
323A GLU* 2.9 49.4 + - - +
633A ASP* 3.5 36.1 - - + +
636A SER* 4.1 14.1 - - - +
637A ALA 6.3 0.4 - - - +
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Residues in contact with PHE 320 (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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311A VAL* 4.0 21.1 - - + -
312A CYS 4.3 0.4 - - - -
313A CYS* 3.7 35.7 - - + -
317A ASN* 3.3 26.2 + - - +
318A TYR 3.3 0.2 - - - -
319A LEU* 1.3 79.2 - - - +
321A LEU* 1.3 59.9 + - + +
323A GLU* 3.8 1.1 - - - +
324A VAL* 2.8 56.3 + - + +
592A ILE* 5.7 0.4 - - + -
632A ILE* 3.6 23.3 - - + -
633A ASP 3.5 11.3 + - - +
634A ASP* 3.7 18.8 - - + -
647A CYS* 3.8 21.3 - - + -
648A GLY 4.4 0.7 - - - -
649A THR* 4.0 23.6 - - + -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 4.5 8.1 - - + -
313A CYS* 3.7 28.0 - - - -
315A LYS 3.8 20.9 - - - +
317A ASN 3.2 17.8 + - - +
318A TYR* 3.8 9.2 - - + +
319A LEU 3.3 0.2 - - - -
320A PHE* 1.3 82.2 - - + +
322A LYS* 1.3 58.0 + - - +
324A VAL* 3.9 3.5 - - + +
325A LYS* 2.9 50.6 + - + +
335A LEU* 5.1 0.6 - - + +
337A VAL* 3.7 33.4 - - + -
339A PHE* 4.3 11.2 - - + -
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TYR 2.9 17.5 + - - +
319A LEU* 3.9 24.4 - - - +
321A LEU* 1.3 76.2 - - - +
323A GLU* 1.3 72.6 + - - +
325A LYS* 3.3 9.3 + - - +
326A ASN* 3.0 52.1 + - - +
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Residues in contact with GLU 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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319A LEU* 2.9 37.2 + - + +
320A PHE 4.0 1.8 - - - +
322A LYS* 1.3 90.4 + - - +
324A VAL* 1.3 63.9 + - - +
326A ASN* 3.4 7.5 + - - +
327A LEU* 3.0 23.4 + - - +
602A LYS* 5.6 1.3 - - - +
630A THR* 4.8 4.5 - - + +
631A PHE 3.5 12.8 - - - +
632A ILE* 3.6 19.1 - - + +
633A ASP* 2.8 38.0 + - - +
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Residues in contact with VAL 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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309A VAL* 4.8 3.4 - - + -
311A VAL* 3.9 24.5 - - + -
320A PHE* 2.8 52.7 + - + +
321A LEU* 4.0 4.7 - - - +
323A GLU* 1.3 75.9 - - - +
325A LYS* 1.3 63.3 + - - +
327A LEU* 3.2 4.8 + - + +
328A VAL* 3.0 28.9 + - + +
335A LEU* 3.9 17.7 - - + -
592A ILE* 4.4 14.6 - - + -
632A ILE* 3.8 16.2 - - + -
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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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321A LEU* 2.9 41.1 + - - +
322A LYS* 3.6 8.3 - - - +
323A GLU 3.3 0.2 - - - -
324A VAL* 1.3 75.5 - - - +
326A ASN* 1.3 58.5 + - - +
328A VAL* 3.3 3.7 + - - +
329A GLU* 2.8 44.8 + - + +
335A LEU* 3.4 28.3 - - + -
337A VAL* 4.8 10.5 - - - -
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Residues in contact with ASN 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 LYS* 3.0 44.8 + - - +
323A GLU* 3.8 8.0 - - - +
324A VAL 3.3 0.2 - - - -
325A LYS* 1.3 76.9 - - - +
327A LEU* 1.3 62.4 + - - +
329A GLU* 3.3 28.5 + - - +
330A LYS* 3.3 19.3 + - - +
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Residues in contact with LEU 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 GLU 3.0 14.0 + - - +
324A VAL* 3.4 10.1 - - + +
326A ASN* 1.3 76.8 - - - +
328A VAL* 1.3 65.6 + - + +
330A LYS* 3.0 27.7 + - - +
331A THR* 3.7 6.1 - - - +
592A ILE* 4.1 20.0 - - + -
594A LEU* 3.9 20.2 - - + -
597A ASP* 4.1 23.1 - - + -
598A LEU 4.2 1.1 - - - +
599A GLY* 3.7 33.2 - - - +
630A THR* 4.0 28.4 - - + +
632A ILE* 4.5 8.5 - - + -
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Residues in contact with VAL 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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309A VAL* 3.9 28.3 - - + -
324A VAL* 3.0 30.4 + - + +
325A LYS* 3.9 3.4 - - - +
327A LEU* 1.3 79.4 - - + +
329A GLU* 1.3 58.2 + - + +
331A THR* 2.7 38.1 + - - +
333A CYS* 3.4 32.3 - - + +
334A GLU 4.1 0.2 - - - -
335A LEU* 4.0 24.5 - - + +
594A LEU* 4.4 7.6 - - + -
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Residues in contact with GLU 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* 2.8 29.6 + - + +
326A ASN* 3.3 26.5 - - - +
327A LEU 3.1 0.4 - - - -
328A VAL* 1.3 76.4 - - + +
330A LYS* 1.3 58.4 + - - +
331A THR 3.1 7.5 + - - +
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Residues in contact with LYS 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 ASN 3.3 17.3 - - - +
327A LEU* 3.0 16.0 + - - +
329A GLU* 1.3 76.0 - - + +
331A THR* 1.3 59.0 + - - +
596A LYS* 5.0 5.7 + - - +
597A ASP* 2.8 37.9 + - - +
628A GLU* 2.8 25.1 + - - +
629A CYS 5.8 0.4 + - - -
630A THR* 4.0 21.3 + - - -
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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