Contacts of the strand formed by residues 204 - 210 (chain C) in PDB entry 3UAJ
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 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C LEU* 3.8 36.6 - - + -
164C TRP* 4.2 7.2 - - + -
165C ASN* 3.5 19.5 - - - -
169C LEU* 3.7 19.3 - - + -
192C VAL* 5.1 0.4 - - + -
194C VAL* 3.5 39.3 - - + +
195C PRO* 5.1 0.2 - - - +
198C SER* 3.4 29.6 + - - -
199C LEU* 4.8 8.1 - - + -
202C GLN* 3.5 38.8 - - + +
203C THR* 1.3 70.5 - - - +
205C ILE* 1.3 57.6 + - - +
220C LYS* 3.5 3.7 - - - +
221C VAL* 2.8 43.6 + - - +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TRP* 3.8 6.0 - - - -
165C ASN* 2.9 44.1 + - - +
203C THR* 4.2 20.4 - - - +
204C TYR* 1.3 79.2 - - - +
206C CYS* 1.3 58.4 + - - +
207C ASN* 3.5 7.5 - - - +
218C ASP* 4.1 17.0 - - + -
219C LYS 3.4 29.6 - - - +
220C LYS* 3.8 16.8 - - + +
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Residues in contact with CYS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 3.9 16.2 - - - -
150C CYS* 2.0 51.4 - - + -
162C VAL* 4.6 7.2 - - + -
163C SER 3.5 6.3 - - - +
164C TRP* 3.8 22.9 - - + -
205C ILE* 1.3 71.9 - - - +
207C ASN* 1.3 60.1 + - - +
208C VAL* 4.2 4.5 - - - -
217C VAL 3.6 2.8 - - - +
218C ASP* 3.4 6.2 - - - -
219C LYS* 3.0 30.4 + - - -
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Residues in contact with ASN 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C THR 3.1 8.1 - - - +
163C SER* 2.7 47.1 + - - +
165C ASN* 4.1 0.2 - - - -
166C SER* 2.9 47.8 + - - +
205C ILE* 3.5 12.0 - - - +
206C CYS* 1.3 69.4 - - - +
208C VAL* 1.3 60.8 + - - +
209C ASP* 3.9 0.3 + - - +
216C LYS* 3.9 22.2 - - - +
218C ASP* 2.8 28.2 + - - +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PRO* 4.2 9.9 - - + +
131C VAL* 3.8 32.1 - - + -
152C VAL* 3.9 30.5 - - + -
160C VAL* 3.8 23.8 - - + -
161C THR 3.4 2.9 - - - -
162C VAL* 3.9 17.3 - - + -
206C CYS* 4.2 8.3 - - - -
207C ASN* 1.3 72.8 - - - +
209C ASP* 1.3 59.3 + - - +
215C THR 4.0 1.0 - - - +
216C LYS* 3.4 6.1 - - - +
217C VAL* 2.9 43.0 + - + +
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Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 3.4 4.7 - - - +
161C THR* 2.7 56.7 + - + +
207C ASN 5.1 0.2 - - - +
208C VAL* 1.3 73.2 - - - +
210C HIS* 1.3 62.0 + - - +
211C LYS* 3.6 36.5 + - - +
215C THR 3.8 6.9 - - - +
216C LYS* 3.5 29.0 - - + +
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Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS 3.7 19.8 + - - -
129C PRO* 3.7 28.2 - - + +
155C TYR* 3.6 17.8 - + + -
156C PHE 3.8 12.3 - - - -
157C PRO 2.8 24.4 + - - -
159C PRO 3.2 24.7 - - - -
160C VAL* 4.1 3.8 - - + -
208C VAL 4.3 0.4 - - - -
209C ASP* 1.3 73.8 - - - +
211C LYS* 1.3 58.9 + - - +
212C PRO* 3.7 17.2 - - + +
213C SER* 2.7 30.0 + - - +
214C ASN 3.1 20.8 + - - -
215C THR* 3.0 19.6 + - - +
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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