Contacts of the helix formed by residues 396 - 403 (chain A) in PDB entry 4NTY
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 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ALA* 3.7 3.0 - - - +
395A LYS* 1.3 79.9 - - - +
397A GLU* 1.3 62.6 + - - +
398A GLN* 3.7 8.6 + - - +
399A TYR* 3.2 22.8 + - - +
400A ILE* 3.4 23.2 + - - +
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Residues in contact with GLU 397 (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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381A PRO* 5.1 1.0 - - - +
383A LYS 5.2 1.7 - - - +
386A ALA* 3.8 33.4 - - + +
387A LYS* 3.4 37.8 - - + +
390A ALA* 4.1 6.5 - - + +
396A SER* 1.3 73.2 - - - +
398A GLN* 1.3 65.1 + - - +
400A ILE* 3.5 5.6 + - - +
401A GLY* 3.4 17.3 + - - -
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Residues in contact with GLN 398 (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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396A SER* 3.3 8.1 + - - +
397A GLU* 1.3 77.1 - - - +
399A TYR* 1.3 63.4 + - - +
401A GLY* 3.4 9.3 + - - -
402A GLU* 2.7 42.4 + - + +
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Residues in contact with TYR 399 (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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224A ASP* 2.6 40.1 + - - -
226A GLN* 4.0 4.2 - - - +
228A ASP* 3.8 33.4 + - + -
395A LYS* 3.5 51.1 + - + -
396A SER* 3.2 21.8 + - - +
398A GLN* 1.3 77.3 - - - +
400A ILE* 1.3 69.9 + - + +
402A GLU* 3.0 11.6 + - - -
403A ASN* 2.5 50.3 + - + +
404A ILE* 4.7 5.4 - - + -
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Residues in contact with ILE 400 (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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380A ILE* 5.0 1.0 - - + +
381A PRO* 3.5 34.5 - - + +
386A ALA* 4.8 4.0 - - - +
389A LEU* 3.9 31.4 - - + +
390A ALA* 3.8 14.8 - - - +
393A TYR* 5.0 4.0 - - + -
395A LYS* 3.6 32.8 - - + -
396A SER 3.4 9.9 + - - +
397A GLU* 3.9 8.1 - - - +
398A GLN 3.4 1.0 - - - -
399A TYR* 1.3 81.5 - - + +
401A GLY* 1.3 59.7 + - - +
402A GLU 3.1 5.0 + - - -
404A ILE* 3.2 49.5 + - + +
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Residues in contact with GLY 401 (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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268A PRO 4.9 0.5 - - - -
269A GLY* 3.9 17.8 - - - -
380A ILE 4.6 1.3 - - - +
381A PRO* 3.7 21.1 - - - -
397A GLU 3.4 6.4 + - - -
398A GLN* 3.4 8.8 + - - -
399A TYR 3.1 1.2 - - - -
400A ILE* 1.3 78.7 - - - +
402A GLU* 1.3 59.6 + - - +
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Residues in contact with GLU 402 (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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225A ILE* 4.1 0.3 - - - +
227A GLN* 3.0 33.2 + - - +
268A PRO* 3.3 19.6 - - - +
398A GLN* 2.7 46.8 + - + +
399A TYR* 3.0 7.2 + - - +
401A GLY* 1.3 82.2 - - - +
403A ASN* 1.3 72.1 + - - +
404A ILE 3.9 0.2 - - - -
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Residues in contact with ASN 403 (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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223A LEU 3.4 3.3 - - - +
224A ASP* 3.1 18.6 - - - +
225A ILE* 2.9 38.6 + - + +
226A GLN 3.8 0.2 + - - -
227A GLN* 2.8 41.3 + - - +
268A PRO* 4.3 2.6 - - - +
399A TYR* 2.5 61.2 + - + +
402A GLU* 1.3 92.0 + - - +
404A ILE* 1.3 64.5 + - - +
405A LEU 3.8 0.3 + - - -
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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