Contacts of the helix formed by residues 205 - 209 (chain H) in PDB entry 4PIW
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 205 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU 3.4 20.0 - - - +
202H ARG* 3.8 16.8 + - + +
204H GLU* 1.3 74.1 - - + +
206H ILE* 1.3 62.0 + - + +
207H ARG 3.0 8.5 + - - -
208H GLU 3.1 9.4 + - - -
209H LYS 2.9 37.1 - - - +
210H GLY* 3.3 11.3 + - - -
211H THR* 4.0 21.0 + - + +
227H ARG* 4.1 18.8 - - + -
228H ASP* 3.9 22.9 - - + +
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Residues in contact with ILE 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H MSE 3.7 47.6 - - + +
64H LEU* 3.8 25.6 - - + +
65H LEU* 4.1 11.9 - - + +
202H ARG* 3.7 30.9 + - + +
203H ALA 4.9 0.2 - - - +
205H ILE* 1.3 75.3 - - + +
207H ARG* 1.3 61.1 + - - +
208H GLU 3.3 0.6 + - - -
209H LYS 3.9 0.9 - - - -
228H ASP* 4.9 2.9 - - - +
229H ILE* 3.2 22.0 - - + +
230H GLY* 3.7 15.0 - - - -
231H SER 2.8 30.1 + - - +
233H TYR* 3.6 5.0 - - + -
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Residues in contact with ARG 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ASP* 3.9 15.6 + - - -
33H THR* 4.4 11.7 - - - +
37H GLN* 3.2 22.0 + - - -
50H LEU* 3.7 37.5 - - + +
51H LEU* 3.2 21.2 + - - +
52H THR* 5.7 0.2 - - - +
61H MSE 4.7 6.1 - - + -
203H ALA 3.7 10.5 + - - +
204H GLU* 3.4 9.5 + - - +
205H ILE 3.0 0.4 - - - -
206H ILE* 1.3 83.6 - - - +
208H GLU* 1.3 87.0 + - - +
231H SER 2.9 13.8 - - - +
233H TYR* 3.2 27.8 + - + +
234H LEU* 3.5 31.7 - - - +
235H MSE 5.7 0.2 - - - +
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Residues in contact with GLU 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G VAL* 5.4 0.7 - - - +
29H ASP* 4.2 6.6 - - + +
204H GLU* 2.8 26.7 - - - +
205H ILE 3.1 2.7 + - - -
207H ARG* 1.3 112.6 + - - +
209H LYS* 1.3 54.4 + - - +
210H GLY* 2.4 27.5 + - - +
212H ASN* 3.5 47.2 + - + +
231H SER 4.3 1.3 - - - -
232H SER* 5.6 0.7 - - - +
234H LEU* 4.2 16.8 - - + +
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Residues in contact with LYS 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G VAL* 3.5 57.7 + - + +
83G SER* 5.6 2.0 - - - +
85G ALA* 5.4 2.0 - - - +
86G ASN* 3.1 41.4 - - + +
324G LEU* 4.9 7.9 - - - +
329G ALA* 4.5 7.8 - - - +
205H ILE* 2.9 20.9 + - - +
206H ILE 3.8 4.4 + - - -
207H ARG 3.7 1.6 - - - -
208H GLU* 1.3 70.5 - - - +
210H GLY* 1.3 64.6 + - - +
227H ARG 4.1 15.7 - - - +
228H ASP 3.0 26.4 - - - +
229H ILE 3.8 3.8 - - - +
230H GLY* 4.0 14.4 - - - -
231H SER* 4.1 6.2 + - - -
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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