Contacts of the strand formed by residues 197 - 202 (chain B) in PDB entry 1UB5
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 4.2 1.6 - - - +
137B VAL* 4.8 20.0 - - + -
153B TRP* 4.9 6.5 - + + -
154B LYS 3.7 2.5 - - - -
155B ILE* 3.7 35.6 - - + +
184B LEU* 5.2 1.8 - - + -
186B LEU* 4.4 8.6 - - + +
190B GLU 4.0 0.9 + - - -
191B TYR* 2.7 58.7 + + - -
194B HIS* 3.3 15.5 - - + +
195B ASN* 3.9 20.9 - - - -
196B GLY* 1.3 79.9 - - - -
198B THR* 1.3 61.6 + - - +
212B LYS 4.1 0.3 - - - +
213B SER* 3.0 25.1 - - - -
214B PHE* 3.1 41.7 + + + -
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Residues in contact with THR 198 (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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152B LYS 3.5 0.2 - - - +
153B TRP* 3.2 17.4 - - - -
154B LYS* 2.7 60.5 + - + +
157B GLY 5.7 1.4 + - - -
196B GLY 4.8 2.4 + - - -
197B TYR* 1.3 73.5 - - - +
199B CYS* 1.3 69.5 + - - +
200B GLU* 4.2 12.1 - - + +
211B VAL* 4.6 11.0 - - + -
212B LYS 4.2 0.9 - - - +
213B SER* 2.6 23.2 + - - +
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Residues in contact with CYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 4.4 7.2 - - - +
122B ILE* 3.7 14.7 - - + +
139B CYS* 2.0 50.5 - - + -
141B LEU* 4.2 11.0 - - - -
151B VAL* 4.1 14.6 - - - -
152B LYS 3.9 1.8 - - - -
153B TRP* 4.3 5.8 - - + -
198B THR* 1.3 72.3 - - - +
200B GLU* 1.3 60.5 + - - +
201B ALA* 4.0 0.7 + - - -
210B ILE 4.2 1.0 - - - +
211B VAL* 3.6 1.2 - - - -
212B LYS* 2.8 38.8 + - + +
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Residues in contact with GLU 200 (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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150B ASN 3.8 0.5 - - - +
151B VAL* 3.0 9.1 - - - +
152B LYS* 2.6 84.6 + - + +
154B LYS* 3.1 17.5 - - - +
198B THR* 3.8 7.6 - - + +
199B CYS* 1.3 73.6 - - - +
201B ALA* 1.3 62.5 + - - +
202B THR* 3.8 20.0 + - - +
209B PRO* 4.3 8.0 - - + +
211B VAL* 3.4 25.7 - - + +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 4.9 4.1 - - + +
120B VAL* 4.3 11.2 - - + -
141B LEU* 3.3 36.8 - - + -
149B ILE* 4.8 6.3 - - + -
150B ASN 3.6 4.3 - - - +
199B CYS 4.0 0.4 + - - -
200B GLU* 1.3 73.1 - - - +
202B THR* 1.3 63.2 + - - +
203B HIS* 3.8 3.3 + - - +
209B PRO* 3.6 2.3 - - - +
210B ILE* 3.1 41.2 + - + +
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 4.4 2.0 - - - -
150B ASN* 2.7 59.1 + - - +
200B GLU* 3.8 14.6 + - - +
201B ALA* 1.3 69.3 - - - +
203B HIS* 1.3 70.3 + - - +
204B LYS* 4.1 2.8 + - + +
206B SER 6.0 0.2 - - - +
209B PRO* 3.5 32.3 - - + +
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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