Contacts of the helix formed by residues 193 - 203 (chain H) in PDB entry 1P8J
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 ARG 193 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189H MET 4.9 8.3 + - - -
190H ASN* 3.3 22.2 - - + +
191H ASP 3.4 2.8 - - - +
192H ASN* 1.3 75.7 - - - +
194H HIS* 1.3 68.7 + - - +
195H GLY 3.4 1.3 - - - -
196H THR* 3.3 5.6 + - - -
197H ARG* 3.1 60.9 + - - +
355H ASP* 3.5 16.1 + - - +
356H LEU* 3.5 20.9 - - + +
4043H SO4 2.8 39.7 + - - +
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Residues in contact with HIS 194 (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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153H ASP* 2.5 30.0 + - - +
154H ASP* 3.1 15.8 + - - +
191H ASP 4.6 1.3 + - - +
193H ARG* 1.3 82.4 - - - +
195H GLY* 1.3 62.8 + - - +
197H ARG* 3.3 5.2 + - - +
198H CYS* 3.2 28.5 + - - -
253H SER* 3.2 20.9 - - - -
364H HIS* 5.0 0.6 + - - -
368H SER* 2.9 16.9 - - - -
4043H SO4 3.2 26.7 - - - +
804R LYS* 3.6 20.5 - - + +
805R AR7 3.2 2.2 + - - -
806R 0QE 1.5 44.4 - - + +
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Residues in contact with GLY 195 (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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151H ILE* 3.9 9.3 - - - +
153H ASP* 3.5 19.9 + - - -
154H ASP* 2.7 17.5 + - - -
155H GLY 3.2 18.8 - - - -
156H ILE* 4.9 1.6 - - - -
194H HIS* 1.3 73.4 - - - +
196H THR* 1.3 57.0 + - - +
198H CYS* 3.2 4.2 + - - +
199H ALA* 2.9 28.3 + - - +
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Residues in contact with THR 196 (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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155H GLY 3.5 4.1 + - - -
156H ILE* 3.8 4.0 - - - +
157H GLU* 3.1 35.2 + - + +
160H HIS* 4.4 1.3 - - + -
163H LEU* 4.0 12.8 - - + -
184H PRO* 4.5 1.6 - - - +
192H ASN 4.9 1.2 + - - -
193H ARG 3.3 9.7 + - - -
195H GLY* 1.3 74.6 - - - +
197H ARG* 1.3 64.1 + - - +
199H ALA* 3.2 7.2 + - - +
200H GLY 3.1 10.6 + - - -
354H THR* 3.0 43.4 + - - +
355H ASP 4.0 12.3 - - - +
356H LEU* 4.0 14.1 - - - +
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Residues in contact with ARG 197 (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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193H ARG* 3.1 65.6 + - - +
194H HIS* 3.7 6.1 - - - +
196H THR* 1.3 75.4 - - - +
198H CYS* 1.3 61.9 + - - +
201H GLU* 3.5 8.6 + - - +
353H THR* 2.7 32.2 + - + +
354H THR 3.2 17.7 - - - +
355H ASP* 2.8 37.3 + - - +
361H THR* 3.9 16.4 + - - +
363H SER* 4.0 19.2 + - - -
364H HIS* 3.7 34.0 - - + +
4043H SO4 3.4 13.0 + - - -
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Residues in contact with CYS 198 (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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151H ILE* 3.8 20.2 - - + -
153H ASP* 4.2 7.6 - - - -
194H HIS* 3.2 20.4 + - - -
195H GLY 3.6 6.7 - - - +
197H ARG* 1.3 77.4 - - - +
199H ALA* 1.3 66.3 + - - +
201H GLU* 3.2 16.8 + - - -
202H VAL* 3.4 9.4 + - - +
251H SER* 5.6 0.7 - - - +
253H SER* 3.8 19.7 - - - -
364H HIS* 4.2 7.4 - - - -
368H SER 3.5 24.2 - - - -
372H PRO* 3.4 17.6 - - + +
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Residues in contact with ALA 199 (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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151H ILE* 3.8 15.2 - - + +
156H ILE* 3.7 29.6 - - + -
163H LEU* 4.0 11.2 - - + -
195H GLY 2.9 13.8 + - - +
196H THR 3.4 8.5 - - - +
198H CYS* 1.3 76.6 - - - +
200H GLY* 1.3 64.7 + - - +
202H VAL* 3.0 5.9 + - - +
203H ALA* 3.0 21.0 + - - -
221H ILE* 4.0 12.2 - - + +
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Residues in contact with GLY 200 (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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163H LEU* 3.7 10.7 - - - +
196H THR 3.1 8.3 + - - -
197H ARG 3.6 0.2 + - - -
198H CYS 3.3 0.4 - - - -
199H ALA* 1.3 80.6 - - - +
201H GLU* 1.3 58.4 + - - +
204H ALA* 3.0 34.6 + - - +
213H VAL 4.3 1.2 - - - +
214H GLY* 3.4 4.7 - - - -
352H VAL 5.7 0.4 - - - -
353H THR* 3.3 16.4 - - - -
354H THR* 3.3 12.9 + - - -
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Residues in contact with GLU 201 (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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121H GLN* 6.2 0.4 - - - +
123H TYR* 5.4 0.7 - - + +
197H ARG 3.5 9.9 - - - +
198H CYS* 3.2 5.7 + - - +
199H ALA 3.2 0.8 - - - -
200H GLY* 1.3 76.3 - - - +
202H VAL* 1.3 58.4 + - - +
213H VAL 5.4 1.1 - - - -
214H GLY* 3.4 2.1 - - - -
215H VAL* 3.0 31.4 + - - +
351H ILE* 2.9 34.2 - - + +
352H VAL 4.5 3.1 - - - +
353H THR* 3.3 10.7 + - - +
364H HIS* 2.5 37.7 + - - +
369H ALA* 3.5 10.2 - - - +
372H PRO* 3.0 31.9 - - + +
373H LEU* 4.0 17.7 - - + +
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Residues in contact with VAL 202 (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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149H VAL* 3.8 35.2 - - + -
151H ILE* 3.9 13.9 - - + -
198H CYS 3.5 5.6 - - - +
199H ALA 3.0 6.6 + - - +
201H GLU* 1.3 79.1 - - - +
203H ALA* 1.3 62.4 + - + +
214H GLY* 3.9 0.9 - - - -
215H VAL* 3.3 1.6 + - - +
216H ALA* 2.9 33.0 + - + +
219H ALA* 5.5 0.2 - - + -
221H ILE* 4.0 7.9 - - + -
372H PRO* 3.2 39.9 - - + +
375H ALA* 4.2 6.3 - - + -
376H GLY* 4.2 13.9 - - - +
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Residues in contact with ALA 203 (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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162H ASP 4.2 1.7 - - - +
163H LEU* 4.4 6.0 - - - +
166H ASN* 2.9 23.0 + - - +
199H ALA 3.0 11.3 + - - -
202H VAL* 1.3 83.8 - - + +
204H ALA* 1.3 62.4 + - - +
205H VAL 3.4 0.3 + - - -
214H GLY* 4.2 1.6 - - - -
216H ALA 3.3 19.5 - - - +
217H TYR* 4.5 0.2 - - - -
219H ALA* 3.8 20.9 - - + +
221H ILE* 4.0 20.3 - - + +
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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