Contacts of the strand formed by residues 206 - 212 (chain B) in PDB entry 1U2X
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 GLY 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PRO* 5.2 7.0 - - - -
186B GLU* 3.5 2.3 - - - +
187B PHE* 2.9 46.7 + - - +
205B SER* 1.3 75.9 - - - +
207B ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 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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41B ILE* 6.3 0.2 - - - +
91B PRO* 3.4 14.0 - - + +
92B ALA 3.3 22.5 + - - +
115B ARG* 5.1 6.3 - - - +
184B ILE* 3.8 37.4 - - + +
185B PHE 3.3 6.1 - - - +
186B GLU* 4.5 16.7 + - + -
187B PHE* 3.3 6.2 - - - -
206B GLY* 1.3 80.8 - - - +
208B PHE* 1.3 61.3 + - - +
209B ILE* 4.0 26.5 - - + +
451B VAL* 4.8 19.0 - - - +
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Residues in contact with PHE 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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72B ILE* 4.6 2.0 - - + -
78B PHE* 3.8 22.4 - + - -
81B ARG* 3.8 30.3 - - + -
82B LEU* 3.7 31.0 - - + -
85B THR* 3.6 30.5 - - + -
92B ALA* 3.4 11.9 - - + -
94B VAL* 3.8 34.1 - - + -
185B PHE* 2.7 48.7 + + + +
187B PHE* 3.7 1.3 - - + -
207B ARG* 1.3 74.0 - - - +
209B ILE* 1.3 60.6 + - - +
210B VAL* 3.5 26.2 - - + -
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Residues in contact with ILE 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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92B ALA 2.9 14.8 + - - +
93B ALA* 3.2 12.5 - - + +
94B VAL* 2.9 27.2 + - - +
182B ASN* 5.3 4.0 - - + -
183B ARG 3.3 10.1 - - - +
184B ILE* 4.3 26.0 - - + -
207B ARG* 4.2 33.0 - - + +
208B PHE* 1.3 78.1 - - - +
210B VAL* 1.3 67.6 + - - +
211B SER* 3.7 21.4 + - - +
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Residues in contact with VAL 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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72B ILE* 3.6 21.5 - - + -
78B PHE* 4.0 12.3 - - + -
94B VAL 3.3 9.0 - - - +
96B LEU* 3.7 29.2 - - + -
105B PHE* 4.1 14.6 - - + -
181B ILE 4.3 1.9 - - - +
182B ASN* 3.5 2.3 - - - -
183B ARG* 2.9 44.0 + - + +
185B PHE* 4.3 4.0 - - + -
208B PHE* 3.5 32.3 - - + -
209B ILE* 1.3 73.4 - - - +
211B SER* 1.3 58.2 + - - +
212B ALA 4.0 0.2 + - - -
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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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93B ALA* 5.1 5.7 - - - +
94B VAL 3.4 6.2 + - - -
95B PRO* 3.5 8.0 - - - +
96B LEU* 2.9 26.6 + - - -
181B ILE 4.7 0.2 - - - -
182B ASN* 3.3 17.0 + - - +
209B ILE* 3.7 17.6 + - - +
210B VAL* 1.3 71.7 - - - +
212B ALA* 1.3 65.9 + - - +
213B ARG* 3.2 9.7 + - - +
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Residues in contact with ALA 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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96B LEU* 4.4 4.0 - - - -
180B LYS* 3.6 35.2 - - + -
181B ILE 3.5 23.5 + - - +
182B ASN* 2.7 11.9 + - - +
211B SER* 1.3 69.3 - - - +
213B ARG* 1.3 67.4 + - - +
214B PHE* 3.9 23.6 - - + -
217B ILE* 3.6 11.7 - - + +
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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