Contacts of the strand formed by residues 203 - 208 (chain D) in PDB entry 3CRK
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 PRO 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D GLN* 3.4 37.5 - - + +
135D VAL 3.7 7.2 - - - +
136D LEU* 3.9 7.2 - - + -
190D LEU* 3.5 20.8 - - + +
191D VAL* 3.4 17.4 - - - +
201D GLY 3.5 8.2 - - - +
202D THR* 1.3 85.3 - - + +
204D LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D VAL* 2.9 9.8 + - + +
136D LEU 4.3 1.3 - - - -
137D LEU* 3.8 38.6 - - + +
149D VAL* 4.1 24.2 - - + -
152D TRP* 3.6 26.3 - - + -
169D ILE* 4.8 7.4 - - + -
178D PHE* 4.2 24.9 - - + -
190D LEU* 2.8 29.3 + - - -
191D VAL* 3.3 21.1 + - + -
198D VAL* 4.4 8.7 - - + -
202D THR* 3.5 15.7 - - - +
203D PRO* 1.3 73.9 - - - +
205D CYS* 1.3 60.0 + - - +
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Residues in contact with CYS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLN* 3.8 3.9 - - - +
135D VAL* 3.0 42.3 + - - +
152D TRP* 3.6 30.3 - - + -
166D LEU* 4.0 12.8 - - - -
186D LEU* 4.7 6.7 - - + -
188D LYS 3.3 16.6 - - - +
189D ILE* 4.6 1.3 - - - -
190D LEU* 3.7 4.3 - - - -
203D PRO 3.7 0.6 - - - -
204D LEU* 1.3 78.1 - - - +
206D ILE* 1.3 64.9 + - - +
207D ILE* 3.6 23.3 - - + -
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Residues in contact with ILE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D HIS* 3.9 32.5 - - + +
133D MET 3.4 11.7 - - - +
134D GLN* 4.1 22.7 - - + +
186D LEU* 4.2 0.2 - - - -
187D ALA* 3.2 32.1 + - + +
188D LYS* 3.3 20.4 + - + +
190D LEU* 3.7 23.1 - - + +
205D CYS* 1.3 79.5 - - - +
207D ILE* 1.3 67.7 + - - +
208D VAL* 5.1 3.8 - - + -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D MET* 2.8 54.1 + - + +
135D VAL* 3.8 15.7 - - + -
160D LEU* 3.5 29.4 - - + -
166D LEU* 5.0 0.7 - - + -
182D GLU* 4.8 4.9 - - + +
183D GLU 4.5 5.4 - - - +
184D GLY* 3.8 13.9 - - - +
185D TYR 3.3 29.4 - - - +
186D LEU* 3.8 7.2 - - + -
205D CYS* 3.6 30.3 - - + -
206D ILE* 1.3 80.0 - - - +
208D VAL* 1.3 65.3 + - - +
209D GLU 4.4 0.2 + - - -
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D HIS* 3.9 27.8 - - + +
133D MET 5.0 0.7 - - - +
185D TYR* 3.0 38.4 + - + +
187D ALA* 4.5 15.0 - - + -
206D ILE* 5.1 5.2 - - + -
207D ILE* 1.3 79.9 - - - +
209D GLU* 1.3 65.3 + - - +
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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