Contacts of the strand formed by residues 251 - 256 (chain B) in PDB entry 4G83
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 THR 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B GLN* 6.4 0.2 - - - -
160B PRO* 4.8 10.5 - - + -
161B ILE 3.4 4.7 - - - +
162B GLN* 3.9 21.5 - - + +
249B PHE* 4.3 16.6 - - + +
250B THR* 1.3 80.3 - - - +
252B ILE* 1.3 65.8 + - - +
253B LEU* 4.3 12.6 - - + +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO* 3.3 1.4 - - - +
161B ILE* 2.9 49.9 + - + +
163B ILE* 5.0 10.8 - - + +
175B ILE* 4.1 28.9 - - + -
217B VAL* 5.2 4.5 - - + -
220B ASN* 6.5 0.4 - - + -
238B VAL* 5.0 20.9 - - + -
250B THR* 4.9 5.8 - - + +
251B THR* 1.3 77.2 - - - +
253B LEU* 1.3 64.2 + - - +
254B TYR* 3.4 42.4 + - + +
275B ILE* 5.3 8.5 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B THR* 3.5 22.9 - - + +
160B PRO* 3.6 27.6 - - + -
217B VAL* 3.3 10.2 - - - +
218B GLU* 2.9 33.2 + - + +
219B GLY* 3.8 25.3 - - - +
251B THR* 4.8 11.4 - - + +
252B ILE* 1.3 74.0 - - - +
254B TYR* 1.3 63.0 + - - +
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B THR* 3.2 0.5 - - - -
159B CYS* 2.9 49.3 + - - +
161B ILE* 4.6 19.5 - - + -
175B ILE* 4.9 5.9 + - - +
176B ARG 4.7 2.4 - - - -
177B ALA* 3.4 35.1 + - + +
215B ILE* 3.6 16.8 - - + -
216B ARG 3.3 13.5 - - - -
217B VAL* 3.6 23.4 - - + +
236B VAL* 4.6 4.0 + - + -
238B VAL* 5.8 1.7 - - - +
252B ILE* 3.4 46.0 + - + +
253B LEU* 1.3 71.5 - - - +
255B ASN* 1.3 74.2 + - - +
256B PHE* 4.8 6.1 - + + -
273B ILE* 6.2 2.5 - - + -
275B ILE* 4.8 11.6 - - + +
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Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 4.7 5.5 - - - +
157B LYS 4.3 2.7 - - - -
158B THR* 3.3 15.3 + - - +
214B LEU 3.8 1.4 - - - +
215B ILE* 3.9 2.8 - - - +
216B ARG* 2.9 42.7 + - + +
218B GLU* 2.9 53.1 + - - +
254B TYR* 1.3 87.4 + - - +
256B PHE* 1.3 64.7 + - - +
257B MET* 3.6 25.6 + - + +
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Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.2 17.9 - - + -
153B CYS* 3.8 23.8 - - + -
154B GLN 4.6 2.9 - - - +
155B ILE* 3.5 4.2 - - - -
156B ALA* 2.6 34.7 + - - +
157B LYS 4.5 3.2 + - - -
159B CYS* 3.2 34.3 - - - -
161B ILE* 6.4 0.4 - - + -
214B LEU* 4.0 12.3 - - + -
215B ILE* 4.8 20.9 - - + -
254B TYR* 4.8 7.6 - + + -
255B ASN* 1.3 74.3 - - - +
257B MET* 1.3 57.8 + - - +
258B CYS 3.4 3.6 - - - +
273B ILE* 4.2 31.4 - - + -
292B GLY* 6.0 2.5 - - - -
294B ILE* 3.8 37.2 - - + -
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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