Contacts of the strand formed by residues 179 - 185 (chain F) in PDB entry 4U8T
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 179 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F HIS 4.0 7.4 - - - +
178F SER* 1.3 78.2 - - - +
180F PHE* 1.3 68.5 + - - +
181F PHE* 4.0 12.7 - - + -
213F ALA* 3.3 35.4 + - - +
216F SER* 4.6 9.4 - - - -
217F LEU* 4.3 15.2 - - + +
222F LYS 3.1 7.1 + - - +
223F ILE* 3.2 15.0 - - + -
224F TYR* 2.9 24.9 + - - -
300F GLU* 2.9 43.1 + - - +
301F ILE 5.6 0.2 - - - -
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Residues in contact with PHE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F VAL* 3.7 25.4 - - + -
178F SER* 3.5 22.4 - - - -
179F ARG* 1.3 78.0 - - - +
181F PHE* 1.3 62.8 + - - +
224F TYR* 3.5 40.4 - + + +
226F LEU* 5.3 6.1 - - + -
300F GLU* 3.3 10.2 + - - +
301F ILE* 2.9 42.1 + - + +
303F ALA* 3.6 28.3 - - + -
306F SER* 3.3 38.4 - - - +
307F LYS* 4.9 4.7 - - + -
310F LEU* 4.4 13.7 - - + -
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Residues in contact with PHE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F ARG* 4.0 20.0 - - + -
180F PHE* 1.3 75.6 - - - +
182F VAL* 1.3 61.4 + - - +
183F ILE* 5.2 0.7 - - + -
209F ARG* 4.7 15.5 - - + -
210F LEU* 4.0 17.5 - - + -
213F ALA* 4.0 19.1 - - + -
223F ILE* 3.6 34.5 - - + -
224F TYR 2.9 9.4 + - - +
225F LEU* 3.4 13.2 - - + -
226F LEU* 2.8 32.8 + - - +
298F THR* 3.6 23.6 - - - -
299F GLN 3.4 2.7 - - - +
300F GLU* 3.5 38.8 - - + -
301F ILE* 4.1 4.2 - - - +
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Residues in contact with VAL 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F PHE* 1.3 70.3 - - - +
183F ILE* 1.3 68.6 + - - +
184F LYS* 4.2 11.2 - - + -
226F LEU 3.6 4.0 - - - +
235F PHE* 4.0 25.6 - - + -
292F VAL* 4.1 8.5 - - + -
295F SER* 3.8 31.2 - - - +
296F ARG 4.0 12.6 - - - +
298F THR* 2.7 34.8 + - - -
299F GLN 2.9 15.9 + - - +
301F ILE* 3.4 24.9 - - + +
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Residues in contact with ILE 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F PHE* 3.6 0.4 + - + -
182F VAL* 1.3 78.8 - - - +
184F LYS* 1.3 65.8 + - - +
200F TRP* 3.4 36.8 - - + +
202F SER* 5.2 1.3 - - - -
210F LEU* 4.1 26.7 - - + -
225F LEU* 3.6 36.3 - - + -
226F LEU 2.8 13.8 + - - +
227F PHE* 3.7 24.9 - - + -
228F SER* 2.8 27.5 + - - +
297F ASP* 3.4 14.1 - - - +
298F THR* 4.4 4.0 - - + -
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Residues in contact with LYS 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F VAL* 4.2 7.6 - - + -
183F ILE* 1.3 80.5 - - - +
185F SER* 1.3 61.7 + - - +
228F SER* 2.4 45.1 + - - +
229F VAL 3.6 8.9 + - - -
230F ASN* 3.5 8.1 - - - +
235F PHE* 5.1 3.6 - - - -
276F ASN* 6.1 0.8 - - - +
293F THR 5.1 3.0 + - - -
295F SER 3.8 13.2 - - - +
296F ARG 4.1 0.9 - - - -
297F ASP* 3.1 25.1 + - + +
0R 6MZ 3.2 41.6 + - - +
1R C 3.4 35.7 - - - +
2R A 3.2 22.6 + - - -
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Residues in contact with SER 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F LYS* 1.3 75.3 - - - +
186F SER* 1.3 60.1 + - - +
187F SER 2.8 28.0 + - - -
190F HIS* 4.0 0.7 - - - +
191F VAL* 3.7 26.0 - - - +
200F TRP* 3.9 14.4 - - - -
227F PHE* 5.4 1.8 - - - -
228F SER 3.0 9.9 + - - +
229F VAL* 3.2 5.9 - - - +
230F ASN 2.7 25.9 + - - -
0R 6MZ 3.4 21.0 + - - -
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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