Contacts of the helix formed by residues 210 - 220 (chain F) 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 210 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208F GLY 3.7 3.4 + - - -
209F PHE* 1.3 77.2 - - - +
211F GLU* 1.3 62.0 + - - +
212F ARG 3.4 2.7 - - - -
213F ALA* 3.8 8.1 - - - +
214F ARG* 3.0 26.0 + - - +
246F PRO* 4.5 13.5 - - - -
247F LEU 3.3 22.9 + - - -
248F ASP* 4.3 9.2 - - - -
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Residues in contact with GLU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F THR* 1.3 75.5 - - - +
212F ARG* 1.3 59.2 + - - +
214F ARG* 4.3 2.4 - - - +
215F GLU* 2.9 34.5 + - - +
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Residues in contact with ARG 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F THR* 3.4 1.8 - - - -
211F GLU* 1.3 78.3 - - - +
213F ALA* 1.3 52.7 + - - +
215F GLU* 4.7 2.5 - - - -
216F THR* 2.7 40.5 + - - +
248F ASP* 3.2 25.2 - - + +
249F ASP* 4.6 4.2 - - + +
250F ILE 4.9 0.2 + - - -
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ALA* 5.5 4.3 - - + +
209F PHE* 4.5 7.9 - - + -
210F THR 3.6 12.4 + - - +
211F GLU 3.3 0.8 - - - -
212F ARG* 1.3 75.9 - - - +
214F ARG* 1.3 60.3 + - - +
216F THR* 4.3 0.2 - - - -
217F LEU* 2.9 33.4 + - - +
247F LEU* 3.5 19.3 - - + +
248F ASP 2.9 17.0 + - - +
250F ILE* 4.2 21.0 - - + +
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Residues in contact with ARG 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F MET* 4.0 29.9 + - + +
190F ALA* 6.1 0.7 - - - -
209F PHE* 4.6 9.6 - - + +
210F THR 3.0 17.9 + - - +
211F GLU* 4.3 2.0 - - - +
213F ALA* 1.3 74.1 - - - +
215F GLU* 1.3 62.8 + - - +
217F LEU* 4.3 2.6 - - - +
218F LEU* 2.9 32.6 + - - +
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F GLU 2.9 20.2 + - - +
212F ARG* 4.6 2.9 - - - +
214F ARG* 1.3 76.3 - - - +
216F THR* 1.3 58.3 + - - +
218F LEU* 4.1 3.3 - - - +
219F ASN* 2.9 33.1 + - - +
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Residues in contact with THR 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F ARG* 2.7 23.8 + - - +
213F ALA* 4.3 1.8 - - - -
215F GLU* 1.3 78.7 - - - +
217F LEU* 1.3 60.1 + - - +
219F ASN* 4.0 3.5 - - - +
220F TYR* 3.3 22.9 + - - +
249F ASP* 5.8 1.8 - - - -
250F ILE* 4.9 15.3 - - - -
252F ILE* 5.2 3.8 - - - +
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Residues in contact with LEU 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F ILE* 3.7 25.7 - - + +
190F ALA* 4.9 8.7 - - + -
213F ALA 2.9 21.5 + - - +
214F ARG* 4.3 2.7 - - - +
216F THR* 1.3 77.6 - - - +
218F LEU* 1.3 60.9 + - - +
220F TYR* 3.7 15.7 + - - +
222F TRP* 5.6 3.6 - - - +
232F VAL* 6.4 2.2 - - + -
250F ILE* 4.9 10.9 - - + +
252F ILE* 5.5 6.5 - - + -
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 3.3 47.1 - - + +
186F ILE* 3.8 6.0 - - + +
187F MET* 5.5 2.5 - - + +
214F ARG 2.9 21.6 + - - +
215F GLU* 4.1 4.0 - - - +
217F LEU* 1.3 77.8 - - - +
219F ASN* 1.3 60.7 + - - +
220F TYR 3.5 4.5 + - - +
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Residues in contact with ASN 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F GLU 2.9 20.2 + - - +
216F THR* 3.6 4.9 + - - +
218F LEU* 1.3 75.1 - - - +
220F TYR* 1.3 64.2 + - - +
221F ARG 3.9 0.5 + - - -
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Residues in contact with TYR 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F LEU 5.6 0.7 - - - +
183F GLU* 5.5 1.7 - - - +
216F THR 3.3 16.8 + - - +
217F LEU* 3.9 10.6 - - - +
218F LEU 3.3 8.5 - - - +
219F ASN* 1.3 82.5 - - - +
221F ARG* 1.3 66.1 + - - +
222F TRP* 3.4 11.9 - - + +
252F ILE* 4.4 17.0 - - + -
254F PRO* 4.3 11.9 - - + -
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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