Contacts of the strand formed by residues 220 - 227 (chain H) in PDB entry 4OZF
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 HIS 220 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173H TRP 3.7 1.8 + - - +
174H VAL* 3.4 4.5 - - - +
175H ASN* 2.8 43.8 + - - +
176H GLY* 4.8 11.5 + - - -
219H ASN* 1.3 71.4 - - - +
221H PHE* 1.3 64.0 + - - +
222H ARG* 4.1 23.0 - - + +
251H GLU* 3.2 42.0 + - + +
252H ALA 3.7 5.2 - - - -
253H TRP* 3.6 46.8 - + + -
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Residues in contact with PHE 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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140H VAL* 5.0 0.7 - - - +
156H LEU* 3.7 22.0 - - + -
172H TRP* 4.4 8.4 - - + -
173H TRP 3.7 4.0 - - - -
174H VAL* 3.7 22.4 - - + +
207H LEU* 4.0 9.4 - - + -
209H VAL* 4.2 13.9 - - + -
213H PHE* 3.5 44.9 - + - -
214H TRP* 3.7 35.4 - + - -
219H ASN* 3.8 26.9 - - + -
220H HIS* 1.3 73.6 - - - +
222H ARG* 1.3 60.0 + - - +
250H ALA 4.0 1.4 - - - +
251H GLU* 3.5 0.9 - - - -
252H ALA* 2.8 47.4 + - - +
254H GLY* 4.1 4.0 - - - -
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Residues in contact with ARG 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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172H TRP* 3.5 8.7 - - - -
173H TRP* 2.9 73.5 + - + +
176H GLY* 4.7 10.7 + - - -
220H HIS* 4.1 25.2 - - + +
221H PHE* 1.3 74.0 - - - +
223H CYS* 1.4 60.9 + - - +
224H GLN* 2.9 42.6 + - - +
247H ILE* 5.5 0.2 - - - +
249H SER* 3.7 27.8 + - - -
250H ALA 3.5 5.8 - - - +
251H GLU* 4.1 10.1 - - + +
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Residues in contact with CYS 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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138H VAL* 3.8 7.8 - - + +
140H VAL* 4.8 1.1 - - + -
158H CYS* 2.0 52.5 - - + -
170H LEU* 3.7 26.0 - - - -
171H SER 3.8 2.9 - - - -
172H TRP* 4.0 14.3 - - + -
222H ARG* 1.4 72.0 - - - +
224H GLN* 1.3 59.0 + - - +
225H VAL* 4.5 1.1 - - - -
248H VAL 3.8 1.4 - - - +
249H SER* 3.1 7.0 - - - -
250H ALA* 2.8 37.0 + - + +
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Residues in contact with GLN 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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169H GLU 3.6 1.5 + - - +
170H LEU* 3.6 1.0 - - - +
171H SER* 2.8 54.3 + - - +
173H TRP* 3.4 31.2 + - - +
222H ARG* 2.9 30.8 + - - +
223H CYS* 1.3 71.7 - - - +
225H VAL* 1.3 64.7 + - - +
226H GLN* 4.2 7.4 - - - +
247H ILE* 3.4 43.4 - - + +
249H SER* 4.0 4.7 - - - +
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Residues in contact with VAL 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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136H PRO* 3.7 25.4 - - + -
138H VAL* 3.7 27.1 - - + -
160H ALA* 4.0 14.8 - - + -
168H VAL* 4.0 24.7 - - + -
169H GLU 3.5 4.7 - - - +
170H LEU* 3.9 21.3 - - + -
203H LEU* 6.1 0.2 - - + -
223H CYS* 4.5 0.9 - - - -
224H GLN* 1.3 79.6 - - - +
226H GLN* 1.3 62.3 + - - +
227H PHE* 3.4 1.6 + - - +
246H GLN 3.6 0.3 - - - +
247H ILE* 3.3 5.8 - - - -
248H VAL* 3.0 39.3 + - - +
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Residues in contact with GLN 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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167H HIS 3.7 0.5 - - - +
168H VAL* 3.2 9.3 - - - -
169H GLU* 2.9 52.2 + - + +
224H GLN* 4.2 7.0 - - - +
225H VAL* 1.3 69.4 - - - +
227H PHE* 1.3 84.1 + - - +
228H TYR* 3.7 27.2 - - + +
245H THR* 4.1 8.3 - - - +
246H GLN* 3.8 6.8 + - - +
247H ILE* 3.4 35.2 - - + +
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Residues in contact with PHE 227 (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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133H VAL* 4.2 3.8 - - + -
134H PHE 3.3 26.5 - - - -
135H PRO* 3.9 17.0 - - + -
136H PRO* 3.6 31.4 - - + -
163H PHE* 4.4 1.8 - - + -
164H TYR 3.7 17.3 - - - -
165H PRO* 4.1 13.2 - - + -
167H HIS 3.8 2.7 - - - -
168H VAL* 4.1 13.7 - - + -
225H VAL 3.4 1.4 + - - +
226H GLN* 1.3 82.9 - - - +
228H TYR* 1.3 75.1 + - - +
229H GLY* 3.7 15.7 - - - -
243H PRO 4.1 7.0 - - - -
244H VAL 3.3 26.7 - - - -
245H THR* 3.4 3.1 - - - +
246H GLN* 2.7 42.6 + - + +
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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