Contacts of the strand formed by residues 220 - 226 (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 220 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ASN* 4.7 12.3 + - - +
358D GLN* 5.9 0.2 + - - -
146H GLY* 4.8 14.9 + - - +
147H ILE 2.9 11.3 + - - +
148H VAL* 3.6 28.7 - - + +
149H VAL* 3.0 29.1 + - - +
166H ASN* 3.3 14.8 - - - +
167H TYR 5.3 1.3 - - - +
168H ASP* 3.9 26.6 + - + +
218H ASN 5.4 2.2 - - - +
219H ALA* 1.3 76.5 - - - +
221H ILE* 1.3 59.7 + - - +
246H HIS* 3.9 5.5 - - - -
248H HIS* 5.8 0.2 - - - -
4042H SO4 2.9 46.2 + - - -
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Residues in contact with ILE 221 (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* 3.3 34.1 - - + +
151H ILE* 3.9 19.5 - - + -
156H ILE* 4.4 9.2 - - + -
163H LEU* 4.5 16.6 - - + +
166H ASN* 2.8 31.4 + - + +
167H TYR* 3.3 9.4 - - - +
168H ASP* 2.9 22.5 + - - -
199H ALA* 4.0 21.8 - - + +
202H VAL* 4.0 15.9 - - + -
203H ALA* 4.0 12.8 - - + -
219H ALA 3.9 0.4 + - - -
220H ARG* 1.3 75.8 - - - +
222H GLY* 1.3 63.5 + - - +
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Residues in contact with GLY 222 (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 2.9 10.3 + - - +
150H SER* 3.5 0.8 - - - -
151H ILE* 3.0 28.6 + - - +
156H ILE* 4.1 8.7 - - - +
167H TYR* 4.6 0.2 - - - -
168H ASP 3.8 1.6 - - - -
171H ALA* 3.4 21.4 - - - +
172H SER* 3.1 13.9 - - - -
221H ILE* 1.3 75.7 - - - +
223H GLY* 1.3 59.5 + - - -
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Residues in contact with GLY 223 (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* 3.4 10.1 - - - -
155H GLY 5.3 1.3 - - - -
156H ILE* 3.7 24.0 - - - +
171H ALA 3.4 1.2 + - - -
172H SER* 2.8 16.1 + - - -
173H PHE 3.0 21.7 + - - -
182H PRO* 3.2 10.6 - - - +
222H GLY* 1.3 75.5 - - - -
224H VAL* 1.3 64.2 + - - -
225H ARG 4.0 0.2 - - - -
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Residues in contact with VAL 224 (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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150H SER* 3.4 10.8 - - - +
151H ILE 2.8 9.3 + - - +
152H LEU* 3.4 28.0 - - + -
153H ASP 3.0 27.0 + - - +
155H GLY* 4.1 2.4 + - - -
171H ALA 4.2 0.2 - - - +
173H PHE 3.1 10.8 - - - +
175H VAL* 3.8 15.3 - - + -
223H GLY* 1.3 74.2 - - - +
225H ARG* 1.3 59.8 + - - +
226H MET* 3.2 8.2 + - + +
239H SER* 3.7 27.8 - - - +
242H LEU* 3.4 32.1 - - + -
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Residues in contact with ARG 225 (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 3.6 3.8 - - - -
154H ASP 3.7 18.3 + - - +
155H GLY* 3.7 12.3 - - - +
173H PHE 2.9 8.6 + - - +
174H ASP* 2.9 43.6 + - + +
175H VAL 3.0 25.6 + - - -
176H ASN* 3.2 18.6 + - - +
177H ASP* 3.5 22.3 + - - -
182H PRO* 4.2 6.5 - - + +
183H GLN 3.4 24.5 + - - -
185H ARG* 3.8 23.2 - - - +
223H GLY 4.0 1.2 - - - -
224H VAL* 1.3 69.8 - - - +
226H MET* 1.3 59.3 + - - +
228H ASP* 3.1 38.8 + - + +
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Residues in contact with MET 226 (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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152H LEU* 4.1 3.8 - - + -
153H ASP 2.8 12.8 + - - +
175H VAL* 4.2 3.8 - - + -
176H ASN* 3.2 23.3 + - - +
224H VAL* 3.6 17.0 - - + +
225H ARG* 1.3 74.2 - - - +
227H LEU* 1.3 77.4 + - + +
231H VAL* 3.6 24.3 - - + +
235H VAL* 3.6 17.0 - - + +
236H GLU* 4.2 13.7 - - - -
239H SER* 3.1 38.8 - - - +
254H TRP* 3.4 40.2 - - + -
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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