Contacts of the strand formed by residues 249 - 256 (chain B) in PDB entry 3C8J
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 TYR 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B ASN 3.7 0.3 - - - +
157B LYS* 3.1 16.7 - - - +
158B THR* 2.8 32.4 + - - +
194B ASN* 3.5 38.4 + - + +
196B TRP* 3.6 30.8 - + + +
234B PHE* 3.3 48.2 - + + -
243B ILE* 4.1 17.1 - - + +
247B ILE* 3.1 25.8 + - + +
248B PRO* 1.3 83.3 - - - +
250B TYR* 1.3 68.5 + - - +
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Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE 3.2 12.1 - - - +
155B MET* 3.4 41.7 - - - -
156B ASN 3.7 4.5 - - - -
157B LYS* 3.7 33.4 - - + +
191B ILE* 5.5 4.2 - - + +
192B PRO 4.7 4.7 + - - -
193B GLY* 4.5 14.6 - - - -
194B ASN 3.0 17.3 + - - +
195B TYR* 3.7 35.7 - + + -
196B TRP* 2.8 30.7 + - - -
249B TYR* 1.3 77.0 - - - +
251B CYS* 1.3 62.6 + - - +
192C PRO* 3.4 29.5 + - + +
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Residues in contact with CYS 251 (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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152B TYR 3.8 0.2 - - - +
153B PHE* 3.7 2.1 - - - -
154B ILE* 3.0 53.8 + - + +
156B ASN 5.3 0.4 - - - +
158B THR* 5.0 4.5 - - + -
163B CYS* 2.0 58.3 - - + -
166B ASN* 5.4 0.2 - - - -
167B CYS* 3.6 17.7 - - - -
195B TYR* 4.0 3.4 - - - -
196B TRP 4.0 4.3 - - - +
250B TYR* 1.3 81.7 - - - +
252B ILE* 1.3 67.3 + - - +
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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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151B TYR* 4.2 8.7 - - + -
152B TYR 3.5 9.9 - - - +
153B PHE* 3.7 28.7 - - + -
167B CYS* 4.1 0.4 - - - -
174B ILE* 3.7 9.9 - - - +
175B LEU* 2.8 51.5 + - + +
186B LEU* 5.1 3.8 - - + -
190B VAL* 4.3 5.8 - - + -
195B TYR* 3.6 33.2 - - + -
196B TRP 3.2 12.4 + - - +
197B ILE* 4.6 2.5 - - + -
235B LEU* 4.5 15.7 - - + -
251B CYS* 1.3 79.2 - - - +
253B CYS* 1.3 70.4 + - - +
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Residues in contact with CYS 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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151B TYR* 3.1 9.0 - - - +
152B TYR* 2.9 41.0 + - + -
154B ILE* 3.8 20.6 - - - -
167B CYS* 2.0 50.5 - - - -
170B TYR* 5.8 0.9 - - - -
172B VAL* 3.1 26.9 - - + +
173B PRO 3.4 5.2 - - - -
175B LEU* 4.2 0.7 - - - -
251B CYS* 4.4 0.4 - - - -
252B ILE* 1.3 78.1 - - - +
254B GLY* 1.3 56.4 + - - +
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Residues in contact with GLY 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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149B LYS* 4.2 6.9 - - - -
150B CYS 3.6 8.1 - - - -
151B TYR* 4.2 3.1 - - - -
172B VAL* 3.5 5.1 - - - +
173B PRO* 3.0 24.3 + - - +
174B ILE 5.2 0.2 - - - +
175B LEU* 3.8 24.4 - - - +
176B LYS 5.3 1.4 + - - -
253B CYS* 1.3 74.3 - - - +
255B LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 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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260A PHE* 4.5 11.0 - - + -
261A PRO 3.5 25.5 + - - -
262A ASP* 4.1 14.6 - - - +
149B LYS* 3.3 4.8 - - - +
150B CYS* 3.0 33.6 + - - +
171B GLY 4.3 16.8 - - - +
172B VAL* 3.7 14.3 - - + +
173B PRO* 5.0 7.2 - - + -
254B GLY* 1.3 74.2 - - - +
256B LYS* 1.3 77.3 + - - +
257B LEU* 3.4 14.3 + - - +
258B ASP* 5.1 8.1 + - - -
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Residues in contact with LYS 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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148B THR 3.8 7.6 - - - +
149B LYS* 3.9 19.6 - - + +
178B GLU* 5.4 19.5 - - + +
255B LYS* 1.3 85.2 + - - +
257B LEU* 1.3 66.0 + - - +
258B ASP* 3.9 4.3 + - - +
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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