Contacts of the helix formed by residues 216 - 225 (chain I) in PDB entry 6PSS
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211I ARG* 3.4 9.9 - - - +
214I ASN 5.6 2.0 - - - -
215I TYR* 1.3 77.8 - - - +
217I THR* 1.3 60.6 + - - +
218I GLU* 3.3 23.9 + - - +
219I GLN* 3.0 25.0 + - - +
220I ILE* 2.9 28.3 + - - +
358I ASP* 5.0 11.9 - - - +
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Residues in contact with THR 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I ARG* 2.4 37.5 + - - +
216I THR* 1.3 72.9 - - - +
218I GLU* 1.3 60.7 + - - +
220I ILE* 3.3 5.5 + - - +
221I LEU* 3.0 38.1 + - + +
313I ALA* 4.9 6.1 - - + +
314I ASN* 3.8 24.7 - - + +
351I LEU* 3.8 24.0 - - + -
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Residues in contact with GLU 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I THR* 3.3 17.9 + - - +
217I THR* 1.3 79.0 - - - +
219I GLN* 1.3 73.7 + - - +
221I LEU* 3.8 2.2 - - - +
222I ASP* 2.8 29.1 + - - +
227I LYS* 5.7 0.2 - - - -
298I ALA 4.1 19.7 - - - +
299I LYS* 4.4 22.3 - - + +
300I ASP* 5.1 5.4 - - + +
313I ALA* 4.9 5.9 - - + +
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Residues in contact with GLN 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I ASN 4.3 3.6 + - - +
215I TYR* 3.8 23.0 - - + -
216I THR* 3.0 40.6 + - - +
217I THR 3.2 0.4 - - - -
218I GLU* 1.3 95.2 + - - +
220I ILE* 1.3 60.4 + - - +
222I ASP* 3.2 13.0 - - - +
223I LEU* 3.0 32.8 + - - +
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Residues in contact with ILE 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I THR* 4.0 18.4 - - + +
210I LEU* 3.7 37.9 - - + -
211I ARG* 4.5 3.8 - - + +
215I TYR* 3.9 22.7 - - + +
216I THR 2.9 22.6 + - - +
217I THR* 3.3 4.7 + - - +
219I GLN* 1.3 75.7 - - - +
221I LEU* 1.3 57.3 + - - +
223I LEU* 3.1 8.4 + - + -
224I PHE* 3.0 39.7 + - + +
347I ILE* 3.7 23.1 - - + -
351I LEU* 3.8 21.8 - - + -
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Residues in contact with LEU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217I THR* 3.0 25.4 + - + +
218I GLU 4.0 3.4 - - - +
220I ILE* 1.3 72.8 - - - +
222I ASP* 1.3 65.2 + - - +
225I PHE* 3.4 39.9 + - + +
227I LYS* 3.9 8.4 - - - -
297I VAL 4.1 16.4 - - - +
298I ALA 4.1 13.9 - - - +
313I ALA* 4.1 10.1 - - + -
314I ASN* 4.2 10.3 - - + +
336I LEU* 3.7 39.7 - - + -
347I ILE* 4.0 6.7 - - + -
348I SER* 4.3 4.9 - - - -
351I LEU* 3.7 21.5 - - + -
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Residues in contact with ASP 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I GLU* 2.8 20.8 + - - +
219I GLN* 3.2 15.2 - - - +
221I LEU* 1.3 77.4 - - - +
223I LEU* 1.3 65.0 + - - +
225I PHE 4.3 4.9 - - - +
227I LYS* 3.5 28.1 + - - +
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Residues in contact with LEU 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I LEU* 6.3 0.2 - - + -
215I TYR* 4.3 25.8 - - + -
219I GLN 3.0 17.0 + - - +
220I ILE* 3.1 10.5 + - + +
222I ASP* 1.3 84.3 - - - +
224I PHE* 1.3 77.9 + - + +
225I PHE 3.3 5.4 + - - +
426I ILE* 3.8 36.6 - - + -
430I LYS* 3.3 37.8 + - + +
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Residues in contact with PHE 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I LEU* 3.7 24.9 - - + -
220I ILE* 3.0 25.7 + - + +
221I LEU 3.7 0.2 + - - -
222I ASP 3.6 0.2 - - - -
223I LEU* 1.3 90.1 - - + +
225I PHE* 1.3 71.9 + - - +
347I ILE* 3.5 35.2 - - + +
426I ILE* 4.2 20.2 - - + -
429I MET* 3.8 32.8 - - + -
430I LYS* 3.6 37.0 - - + +
433I ILE* 3.8 21.3 - - + +
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Residues in contact with PHE 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221I LEU* 3.4 33.7 + - + +
222I ASP 4.3 7.1 - - - +
223I LEU 3.3 4.9 + - - +
224I PHE* 1.3 90.2 - - - +
226I GLU* 1.3 59.3 + - - +
227I LYS* 4.3 7.1 + - - +
336I LEU* 3.7 24.9 - - + -
337I PHE 3.9 17.7 - - - -
338I THR* 3.6 21.3 - - + -
343I HIS* 4.7 3.6 - - + -
344I GLY 4.2 11.2 - - - -
345I PRO* 3.9 12.1 - - + -
346I TYR 4.2 2.7 - - - -
347I ILE* 3.7 14.4 - - + -
348I SER* 3.4 43.1 - - - -
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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