Contacts of the strand formed by residues 164 - 170 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160G GLU* 3.3 2.2 - - - -
161G LEU* 2.8 56.9 + - + +
162G ASN 3.3 1.4 + - - -
163G GLY* 1.3 72.2 - - - +
165G THR* 1.3 59.1 + - - +
166G ILE* 3.4 13.4 - - + +
190G LEU* 4.4 7.6 - - + -
191G ASN 3.4 23.3 - - - +
192G ASN* 3.5 26.7 - - + +
194G ARG* 4.0 13.0 - - - +
198G ALA* 4.3 8.1 - - + -
200G VAL* 3.3 36.8 - - + -
224G ILE* 4.4 11.2 - - + -
253G VAL* 4.7 2.5 - - + -
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Residues in contact with THR 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LEU* 3.2 42.2 + - + +
159G PRO 3.7 5.2 + - - -
160G GLU* 4.0 9.1 + - - +
163G GLY 3.3 5.5 + - - +
164G LEU* 1.3 74.5 - - - +
166G ILE* 1.3 60.1 + - - +
167G ASP* 5.7 0.9 - - + -
189G ASP 3.8 1.5 - - - +
190G LEU* 3.4 4.0 - - - +
191G ASN* 2.8 66.3 + - + +
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Residues in contact with ILE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LEU* 3.7 8.2 - - - +
159G PRO* 2.9 30.7 + - + +
161G LEU* 4.5 3.6 - - + +
164G LEU* 3.4 26.2 - - + +
165G THR* 1.3 80.1 + - - +
167G ASP* 1.3 61.9 + - - +
168G ILE* 3.4 29.2 - - + -
189G ASP 3.7 2.2 - - - -
190G LEU* 4.2 10.1 - - + -
251G ALA 6.1 0.2 - - - +
253G VAL* 3.6 32.1 - - + -
262G VAL* 3.9 23.8 - - + -
263G GLU 5.7 0.2 - - - -
264G GLN* 3.3 24.8 + - + +
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Residues in contact with ASP 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LEU* 3.5 33.3 - - + +
165G THR* 4.2 1.5 - - + -
166G ILE* 1.3 74.7 - - - +
168G ILE* 1.3 64.0 + - - +
169G LYS* 3.2 40.8 + - - +
187G THR* 3.5 5.2 + - - +
189G ASP* 2.7 55.7 + - + +
264G GLN* 4.3 0.7 + - - +
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Residues in contact with ILE 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G ILE* 3.4 31.2 - - + -
167G ASP* 1.3 77.1 + - - +
169G LYS* 1.3 71.0 + - - +
186G PHE* 4.7 4.3 - - + -
187G THR 3.3 10.1 - - - +
188G VAL* 4.1 18.6 - - + -
190G LEU* 4.7 1.6 - - + -
202G PHE* 4.5 12.3 - - + -
204G MET* 4.3 15.5 - - + -
251G ALA* 3.5 27.4 - - + -
253G VAL* 5.3 1.1 - - + -
264G GLN* 3.6 32.8 - - + +
266G MET* 3.7 33.7 - - + +
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Residues in contact with LYS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ASP* 3.2 35.4 + - - +
168G ILE* 1.3 81.4 - - - +
170G ASN* 1.3 64.4 + - - +
171G GLN* 3.0 4.8 + - - -
186G PHE* 3.3 9.6 - - - -
187G THR* 2.9 46.7 + - - +
189G ASP* 5.6 2.4 + - - -
264G GLN* 5.7 0.2 - - - +
266G MET* 4.2 2.7 - - - -
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Residues in contact with ASN 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G LYS* 1.3 70.0 - - - +
171G GLN* 1.3 65.8 + - - +
172G PHE 3.1 2.8 + - - -
173G GLY* 3.1 14.6 + - - +
174G ILE* 2.7 49.7 + - - +
175G ASN* 4.4 7.4 - - - +
184G VAL* 3.7 19.5 - - - +
185G PRO 4.3 0.3 - - - +
186G PHE* 3.5 24.4 - - + -
266G MET* 4.0 15.3 - - + +
267G THR 5.1 1.2 + - - -
268G 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