Contacts of the helix formed by residues 206 - 210 (chain A) in PDB entry 1UU1
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 LEU 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.5 35.4 - - + -
200A PHE* 3.4 26.4 + - + +
201A SER* 3.5 11.5 + - - -
204A PHE* 3.2 13.9 - - + +
205A SER* 1.3 83.9 - - - +
207A ALA* 1.3 65.4 + - - +
208A ALA 3.2 3.4 - - - -
209A GLN* 3.1 32.0 + - + +
210A ARG* 3.7 6.8 + - - -
211A VAL* 5.0 5.0 + - + +
240A PHE* 3.9 38.6 - - + +
241A ALA* 4.4 2.7 - - + +
244A ALA* 4.1 4.3 - - + -
50B LEU* 3.4 8.7 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 5.1 0.4 - - + -
201A SER* 3.5 25.5 + - - +
206A LEU* 1.3 78.6 - - - +
208A ALA* 1.3 56.6 + - - +
210A ARG* 3.0 32.6 + - - -
50B LEU 3.2 3.0 + - - -
51B ARG 3.6 16.6 - - - +
52B ILE 3.5 16.8 - - - +
53B TYR* 3.8 28.1 - - + -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA* 1.3 77.0 - - - +
209A GLN* 1.3 59.7 + - - +
210A ARG* 3.5 4.7 + - - +
49B ALA 3.3 15.0 - - - +
50B LEU* 3.0 17.7 + - - +
52B ILE 3.0 19.4 + - - +
54B TYR* 4.0 11.3 - - + +
234B SER* 3.2 7.1 - - - -
235B TYR* 3.0 43.2 + - + -
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.1 22.1 + - + +
208A ALA* 1.3 82.2 + - - +
210A ARG* 1.3 73.1 + - - +
211A VAL* 3.6 4.4 - - + +
234A SER* 4.8 0.3 + - - -
236A VAL* 4.8 0.3 - - - +
237A SER* 2.6 50.6 + - - +
240A PHE* 3.8 24.8 - - + -
50B LEU* 3.8 17.7 - - + +
209B GLN* 5.5 0.2 - - - +
234B SER* 3.5 9.9 + - - -
235B TYR* 3.6 1.8 - - - +
236B VAL* 3.1 50.7 - - - +
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLY 3.9 0.3 - - - +
83A ASN* 3.0 31.0 + - - +
84A GLY* 3.4 22.1 + - - +
86A ASP* 3.7 17.6 + - - +
201A SER* 3.6 5.5 + - - -
206A LEU 3.7 3.2 + - - -
207A ALA 3.0 26.3 + - - -
208A ALA* 3.8 11.7 - - - +
209A GLN* 1.3 82.4 - - - +
211A VAL* 1.3 61.4 + - - +
233A VAL* 4.3 5.9 - - - +
237A SER* 4.7 0.2 - - - -
1335A PMP 2.8 45.2 + - - -
53B TYR* 3.7 6.5 - - - -
54B TYR 6.2 0.7 - - - +
231B PHE* 3.0 41.0 + - - +
233B VAL 4.7 1.3 - - - -
234B SER* 4.2 15.9 - - - +
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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