Contacts of the strand formed by residues 164 - 170 (chain F) in PDB entry 4BEI
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 LEU 164 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160F GLU* 3.3 3.0 - - - -
161F LEU* 2.8 55.6 + - + +
162F ASN 3.3 1.8 + - - -
163F GLY* 1.3 73.4 - - - +
165F THR* 1.3 59.2 + - - +
166F ILE* 3.4 13.7 - - + +
190F LEU* 4.4 7.9 - - + -
191F ASN 3.4 21.8 - - - +
192F ASN* 3.5 26.9 - - + +
194F ARG* 4.0 13.4 - - - +
198F ALA* 4.3 7.9 - - + -
200F VAL* 3.3 36.8 - - + -
224F ILE* 4.4 10.3 - - + -
253F VAL* 4.7 2.0 - - + -
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Residues in contact with THR 165 (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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158F LEU* 3.2 42.6 + - + +
159F PRO 3.7 4.8 + - - -
160F GLU* 4.0 7.9 + - - +
163F GLY 3.3 4.4 + - - +
164F LEU* 1.3 75.4 - - - +
166F ILE* 1.3 60.6 + - - +
167F ASP* 5.5 1.1 - - + +
189F ASP 3.8 1.5 - - - +
190F LEU* 3.4 4.3 - - - +
191F ASN* 2.8 65.3 + - + +
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Residues in contact with ILE 166 (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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158F LEU* 3.7 7.2 - - - +
159F PRO* 2.9 40.1 + - + +
161F LEU* 4.5 4.0 - - + +
164F LEU* 3.4 25.8 - - + +
165F THR* 1.3 81.3 + - - +
167F ASP* 1.3 62.9 + - - +
168F ILE* 3.4 28.5 - - + -
189F ASP 3.7 2.2 - - - -
190F LEU* 4.2 9.4 - - + -
253F VAL* 3.6 31.9 - - + -
262F VAL* 3.9 23.8 - - + -
263F GLU 5.7 0.2 - - - -
264F GLN* 3.6 14.0 - - + +
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Residues in contact with ASP 167 (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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158F LEU* 3.6 32.1 - - + +
165F THR* 5.7 1.8 - - + -
166F ILE* 1.3 74.1 - - - +
168F ILE* 1.3 62.6 + - - +
169F LYS* 3.2 39.2 + - - +
187F THR* 3.5 5.5 + - - +
189F ASP* 2.7 55.9 + - + +
264F GLN* 4.2 1.0 - - - +
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Residues in contact with ILE 168 (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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166F ILE* 3.4 31.9 - - + -
167F ASP* 1.3 77.1 + - - +
169F LYS* 1.3 71.3 + - - +
186F PHE* 4.7 4.3 - - + -
187F THR 3.3 9.6 - - - +
188F VAL* 4.1 23.8 - - + -
190F LEU* 4.7 1.8 - - + -
202F PHE* 4.5 7.9 - - + -
204F MET* 4.3 15.7 - - + -
251F ALA* 3.5 27.1 - - + -
253F VAL* 5.3 0.7 - - + -
264F GLN* 3.4 29.3 + - + +
266F MET* 3.7 34.9 - - + +
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Residues in contact with LYS 169 (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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167F ASP* 3.2 35.9 + - - +
168F ILE* 1.3 81.0 - - - +
170F ASN* 1.3 64.1 + - - +
171F GLN* 3.0 5.1 + - - -
186F PHE* 3.3 9.6 - - - -
187F THR* 3.0 46.5 + - - +
189F ASP* 5.6 2.6 + - - -
266F MET* 4.2 2.5 - - - -
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Residues in contact with ASN 170 (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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169F LYS* 1.3 71.6 - - - +
171F GLN* 1.3 66.7 + - - +
172F PHE* 3.1 3.3 + - - -
173F GLY* 3.1 14.7 + - - +
174F ILE* 2.7 50.0 + - - +
175F ASN* 4.4 7.8 - - - +
184F VAL* 3.7 20.9 - - - +
185F PRO 4.3 0.3 - - - +
186F PHE* 3.5 23.1 - - + -
266F MET* 4.0 14.6 - - + +
267F THR 5.1 1.0 + - - -
268F VAL* 4.2 6.3 - - - +
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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