Contacts of the helix formed by residues 216 - 225 (chain C) in PDB entry 5NSS
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 THR 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ASN* 5.4 6.1 - - - +
215C TYR* 1.3 76.5 - - - +
217C THR* 1.3 61.9 + - - +
218C GLU* 3.9 9.3 + - - +
219C GLN* 2.9 25.6 + - - +
220C ILE* 2.9 23.1 + - - +
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Residues in contact with THR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C TYR 3.9 0.2 + - - -
216C THR* 1.3 73.5 - - - +
218C GLU* 1.3 59.2 + - - +
220C ILE* 3.4 13.0 - - + +
221C LEU* 2.9 40.0 + - - +
313C ALA* 4.5 16.7 + - - +
314C ASN* 5.8 2.2 - - + -
351C LEU* 3.9 27.8 - - + -
357C ASN* 4.0 20.6 - - - +
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Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 3.1 9.5 + - - +
217C THR* 1.3 82.1 + - - +
219C GLN* 1.3 63.0 + - + +
221C LEU* 4.5 1.9 - - - +
222C ASP* 2.9 34.7 + - - +
298C ALA 5.8 0.2 - - - -
299C LYS* 5.7 6.1 - - + +
300C ASP* 5.1 17.7 - - + +
313C ALA* 5.4 5.4 - - - -
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Residues in contact with GLN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C TYR* 4.5 19.7 - - + -
216C THR* 2.9 26.4 + - - +
218C GLU* 1.3 80.3 + - - +
220C ILE* 1.3 56.4 + - - +
222C ASP* 4.5 7.4 - - - +
223C LEU* 2.5 49.6 + - + +
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C THR* 5.4 7.6 - - - +
210C LEU* 3.5 32.8 - - + -
211C ARG* 5.6 1.8 - - + +
215C TYR* 3.7 13.9 - - + +
216C THR 2.9 12.7 + - - +
217C THR* 3.0 25.1 + - + +
219C GLN* 1.3 78.1 - - - +
221C LEU* 1.3 65.9 + - + +
223C LEU* 4.7 1.1 - - - -
224C PHE* 2.9 33.3 + - + +
225C PHE* 5.0 1.0 - - + -
347C ILE* 3.8 34.1 - - + -
351C LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C THR* 2.9 21.6 + - - +
218C GLU* 4.5 1.6 - - - +
220C ILE* 1.3 81.9 - - + +
222C ASP* 1.3 52.7 + - - +
225C PHE* 2.7 63.7 + - + +
226C GLU 4.9 1.0 - - - -
227C LYS* 5.7 0.4 - - - -
298C ALA* 3.2 30.5 - - + +
299C LYS* 5.9 0.2 - - - -
313C ALA* 4.8 1.1 - - + -
314C ASN* 4.0 21.1 - - + +
336C LEU* 3.7 31.8 - - + +
347C ILE* 5.7 0.2 - - + -
351C LEU* 3.6 31.6 - - + -
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Residues in contact with ASP 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C GLU 2.9 22.3 + - - +
219C GLN* 4.5 9.0 - - - +
221C LEU* 1.3 78.8 - - - +
223C LEU* 1.3 57.4 + - - +
225C PHE 3.0 13.2 - - - +
226C GLU* 5.1 3.5 - - - +
227C LYS* 5.3 13.9 - - + +
299C LYS* 6.3 3.6 - - + -
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C TYR* 4.7 22.9 - - + -
219C GLN* 2.5 34.0 + - - +
220C ILE* 4.1 1.1 - - - +
222C ASP* 1.3 78.0 - - - +
224C PHE* 1.3 71.8 + - + +
225C PHE 3.2 3.3 + - - +
226C GLU* 4.7 6.1 - - - +
426C ILE* 4.6 21.5 - - + -
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Residues in contact with PHE 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ILE* 2.9 18.6 + - + +
223C LEU* 1.3 84.4 - - + +
225C PHE* 1.3 70.7 + - + +
226C GLU* 5.9 0.2 - - - -
347C ILE* 4.0 26.7 - - + -
430C LYS* 6.1 8.3 - - + +
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ILE* 5.1 1.1 - - + -
221C LEU* 2.7 42.4 + - + +
222C ASP* 3.0 18.5 - - - +
223C LEU 3.7 1.7 - - - +
224C PHE* 1.3 94.3 - - + +
226C GLU* 1.3 66.6 + - - +
336C LEU* 3.8 35.7 - - + -
344C GLY 4.9 7.2 - - - -
345C PRO* 5.2 2.0 - - + -
346C TYR* 3.3 36.8 - - + -
347C ILE* 4.6 14.6 - - + -
348C SER* 6.2 1.3 - - - -
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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