Contacts of the helix formed by residues 208 - 218 (chain I) in PDB entry 4PHZ
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 ILE 208 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203I PHE* 3.5 34.9 + - + -
207I GLY* 1.3 71.3 - - - -
209I ILE* 1.3 55.5 - - - +
211I SER* 3.1 5.0 + - - -
212I TYR* 2.7 32.3 + - - +
27J ASP* 3.1 26.4 + - - +
30J LEU* 3.8 26.7 - - + -
31J LEU* 3.7 26.7 - - + +
34J LEU* 6.0 1.1 - - + -
84J TRP* 4.0 21.5 - - + -
88J PHE* 3.5 30.2 - - + -
90J LEU* 4.2 6.7 - - + -
92J PHE* 5.5 0.2 - - + -
239K LEU* 4.7 0.7 - - + -
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Residues in contact with ILE 209 (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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208I ILE* 1.3 75.0 - - - +
210I THR* 1.3 68.0 + - - +
212I TYR* 3.3 8.1 + - + +
213I ILE* 2.9 43.7 + - + +
23J VAL* 4.1 36.8 - - + +
26J VAL* 3.7 31.2 - - + -
27J ASP* 3.1 18.9 + - - +
30J LEU* 4.7 2.2 - - + -
239K LEU* 3.8 23.3 - - + -
242K ILE* 4.7 19.5 - - + -
255K THR* 5.6 2.7 - - + -
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Residues in contact with THR 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I LYS* 5.9 0.4 - - - -
207I GLY* 4.0 20.1 - - - +
208I ILE 3.5 1.4 - - - +
209I ILE* 1.3 80.3 - - - +
211I SER* 1.3 53.4 + - - +
213I ILE* 3.4 7.0 + - - +
214I ARG* 2.8 67.3 + - + +
23J VAL* 5.1 6.6 - - - +
27J ASP* 5.0 0.9 + - - -
255K THR* 3.6 34.0 + - - +
256K GLU 5.2 0.6 - - - +
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Residues in contact with SER 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I LYS* 3.3 22.9 - - - +
207I GLY 2.9 25.5 + - - -
208I ILE 3.1 3.6 + - - -
210I THR* 1.3 78.3 - - - +
212I TYR* 1.3 66.5 + - - +
214I ARG* 3.3 2.1 + - - +
215I VAL* 2.9 29.3 + - - +
223I VAL* 3.5 15.8 - - - +
88J PHE* 3.3 26.2 - - - -
90J LEU* 4.1 1.8 - - - +
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Residues in contact with TYR 212 (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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208I ILE 2.7 19.8 + - - +
209I ILE* 3.5 5.8 - - + +
211I SER* 1.3 72.1 - - - +
213I ILE* 1.3 62.3 + - + +
215I VAL* 3.3 2.9 + - - +
216I ALA* 2.8 47.8 + - + +
87J ASN* 3.7 21.3 - - + -
88J PHE* 3.8 14.2 - + + -
236K LEU* 4.0 23.8 + - + +
239K LEU* 3.1 50.9 - - + -
240K MET* 3.1 32.4 + - - +
242K ILE* 6.4 0.4 - - + -
243K HIS* 4.2 15.6 + - + +
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Residues in contact with ILE 213 (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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209I ILE* 2.9 35.6 + - + +
210I THR* 3.5 5.4 - - - +
212I TYR* 1.3 84.7 - - + +
214I ARG* 1.3 69.3 + - - +
216I ALA* 3.1 6.2 + - - +
217I GLU* 2.7 39.7 + - + +
242K ILE* 5.5 3.6 - - + -
243K HIS* 3.9 29.4 - - + +
246K VAL* 5.6 6.1 - - + -
251K VAL* 3.9 24.0 - - + -
255K THR* 4.2 18.2 - - + +
256K GLU 4.7 11.2 - - - +
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Residues in contact with ARG 214 (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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206I LYS* 5.3 10.4 - - - +
210I THR* 2.8 48.4 + - + +
211I SER* 3.3 4.7 + - - +
213I ILE* 1.3 76.1 - - - +
215I VAL* 1.3 63.7 + - - +
217I GLU* 3.2 12.4 + - - +
218I GLY 3.2 0.5 + - - -
219I LYS 2.7 32.5 + - - +
222I ASP* 2.9 44.1 + - + +
223I VAL* 3.8 16.3 - - + +
255K THR 4.2 4.9 + - - -
256K GLU* 3.4 40.1 + - - +
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Residues in contact with VAL 215 (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 SER 2.9 20.6 + - - +
212I TYR 3.5 3.4 - - - +
214I ARG* 1.3 74.7 - - - +
216I ALA* 1.3 63.7 + - - +
218I GLY* 3.2 16.1 + - - +
220I ALA* 3.8 14.9 - - + +
223I VAL* 3.9 8.5 - - + -
86J VAL 3.6 17.3 - - - +
87J ASN* 3.5 15.3 - - - +
88J PHE 3.7 23.6 - - - -
89J ARG* 3.8 24.5 - - + +
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Residues in contact with ALA 216 (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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212I TYR* 2.8 37.7 + - + +
213I ILE* 3.6 4.3 - - - +
215I VAL* 1.3 75.7 - - - +
217I GLU* 1.3 61.5 + - - +
218I GLY* 3.5 0.5 + - - -
243K HIS* 4.1 20.9 - - + +
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Residues in contact with GLU 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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213I ILE* 2.7 37.3 + - + +
214I ARG* 3.2 7.8 + - - +
216I ALA* 1.3 72.6 - - - +
218I GLY* 1.3 57.5 + - - +
219I LYS 4.8 1.6 - - - +
243K HIS* 3.1 29.5 + - - +
251K VAL* 3.1 20.2 - - + +
252K LYS* 3.1 29.3 - - + +
256K GLU 6.0 0.7 - - - +
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Residues in contact with GLY 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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214I ARG 3.2 1.8 + - - -
215I VAL 3.2 9.6 + - - +
216I ALA 3.3 0.6 - - - -
217I GLU* 1.3 80.4 - - - +
219I LYS* 1.3 81.1 + - - +
220I ALA* 3.1 10.0 - - - +
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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