Contacts of the helix formed by residues 205 - 212 (chain B) in PDB entry 3U1K
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ARG* 3.9 16.2 - - - +
162B VAL* 3.2 34.5 - - + +
163B ASN* 5.0 5.4 - - - +
203B ASN 3.4 0.6 + - - +
204B PRO* 1.3 75.6 - - - +
206B ARG* 1.3 59.9 + - - +
207B LYS* 3.6 7.8 + - - +
208B GLU* 2.9 36.9 + - - +
209B MET* 2.8 29.0 + - - +
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Residues in contact with ARG 206 (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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108B ALA* 4.2 20.7 + - - +
109B ALA* 3.2 32.6 - - - +
111B ARG* 4.1 15.2 - - - +
161B GLY 3.5 21.5 - - - +
162B VAL* 2.9 14.8 + - + +
164B GLU* 5.4 11.7 + - + +
205B THR* 1.3 73.7 - - - +
207B LYS* 1.3 62.0 + - - +
209B MET* 3.4 13.0 + - + +
210B SER* 3.2 26.7 + - - +
634D GLU 4.3 15.6 + - - -
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Residues in contact with LYS 207 (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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162B VAL* 6.0 0.2 - - - +
205B THR* 3.2 7.0 + - - +
206B ARG* 1.3 76.4 - - - +
208B GLU* 1.3 66.7 + - + +
210B SER* 3.2 20.0 + - - -
211B SER* 3.5 9.7 + - - -
659D GLU* 5.8 4.5 - - - -
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Residues in contact with GLU 208 (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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54B ARG* 3.0 18.9 + - - -
196B ILE* 3.8 26.4 - - + +
201B VAL* 3.7 19.3 - - - +
204B PRO* 3.2 13.0 - - + +
205B THR* 2.9 37.4 + - - +
207B LYS* 1.3 80.0 - - + +
209B MET* 1.3 57.4 + - - +
211B SER* 2.8 22.3 + - - -
212B SER* 2.8 16.1 + - - -
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Residues in contact with MET 209 (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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164B GLU* 3.9 28.0 - - + +
166B ASP* 5.6 0.2 - - - +
192B ARG* 3.6 28.5 - - - +
204B PRO* 3.8 26.4 - - + +
205B THR 2.8 19.6 + - - +
206B ARG* 3.5 10.8 - - - +
208B GLU* 1.3 71.8 - - - +
210B SER* 1.3 61.9 + - - +
211B SER 3.1 0.9 + - - -
212B SER* 3.3 22.6 + - - +
215B ASN* 3.6 28.7 - - + +
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Residues in contact with SER 210 (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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206B ARG* 3.2 18.5 + - - +
207B LYS* 3.4 14.1 - - - -
208B GLU 3.1 0.4 - - - -
209B MET* 1.3 74.5 - - - +
211B SER* 1.3 60.6 + - - +
212B SER 5.2 0.6 - - - +
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Residues in contact with SER 211 (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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195B ILE 4.5 1.4 - - - +
196B ILE* 5.1 8.1 - - - +
207B LYS 3.5 7.8 + - - -
208B GLU* 2.8 10.0 + - - -
210B SER* 1.3 80.8 + - - +
212B SER* 1.3 64.0 - - - +
213B THR* 3.7 5.7 + - - +
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Residues in contact with SER 212 (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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194B GLY* 3.4 2.1 - - - -
195B ILE 2.8 32.7 + - - -
196B ILE* 4.0 6.7 - - - -
204B PRO* 5.7 0.4 - - - -
208B GLU 2.8 13.1 + - - -
209B MET* 3.3 19.1 + - - +
210B SER 5.2 0.7 - - - +
211B SER* 1.3 79.7 - - - +
213B THR* 1.3 59.8 + - - +
214B LEU 2.7 30.4 + - - -
234B GLU* 4.5 6.6 - - - +
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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