Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 1LNU
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 3.8 17.5 - - + -
158B TRP* 4.4 6.3 - - + -
159B PHE 3.2 13.0 - - - +
160B ARG* 2.6 38.4 + - + -
188B LEU* 3.8 20.9 - - + -
190B MET* 4.0 20.4 - - + -
191B THR 2.5 30.6 + - - -
192B PRO* 4.5 2.9 - - + -
196B GLU* 2.6 31.4 + - + -
197B VAL* 1.3 75.0 - - - +
199B THR* 1.3 63.7 + - - +
214B GLU* 3.4 0.2 - - - -
215B TRP* 2.6 67.0 + + + +
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 6.0 0.2 - - - -
157B ARG 4.0 0.2 - - - +
158B TRP* 3.2 10.6 - - - -
159B PHE* 3.1 50.9 + - - +
197B VAL* 4.2 10.8 - - + +
198B TYR* 1.3 82.9 - - - +
200B CYS* 1.3 63.7 + - - +
201B HIS 4.1 0.2 + - - -
212B THR* 5.2 7.3 - - - -
213B VAL 2.9 11.4 - - - -
214B GLU* 3.3 28.5 - - + -
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Residues in contact with CYS 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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126B VAL* 6.2 0.6 - - + +
128B ILE* 4.3 6.1 - - + -
144B CYS* 2.0 53.6 - - + -
156B VAL* 3.9 19.5 - - - -
157B ARG 3.6 5.4 - - - -
158B TRP* 3.9 14.8 - - + -
199B THR* 1.3 74.5 - - - +
201B HIS* 1.3 60.4 - - - +
202B VAL* 4.0 6.3 + - - +
211B ILE* 3.9 0.7 - - - +
212B THR* 3.3 7.4 - - - -
213B VAL* 2.8 35.9 + - + +
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Residues in contact with HIS 201 (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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155B LYS 3.6 1.6 - - - +
156B VAL* 3.3 4.3 - - - -
157B ARG* 2.8 78.3 + - + +
159B PHE* 3.7 25.7 - + + -
199B THR 4.1 0.8 + - - -
200B CYS* 1.3 70.8 - - - +
202B VAL* 1.3 60.5 + - - +
203B GLU* 3.8 10.4 + - + -
210B PRO* 3.3 34.2 - - + +
211B ILE 3.7 1.9 + - - -
212B THR* 3.5 24.2 - - + +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 4.0 14.4 - - + -
126B VAL* 3.8 15.0 - - + -
146B VAL* 3.8 30.3 - - + -
154B ILE* 3.6 29.4 - - + -
155B LYS 3.4 3.8 - - - -
156B VAL* 4.0 9.2 - - + -
200B CYS* 4.5 11.9 - - - +
201B HIS* 1.3 79.0 - - - +
203B GLU* 1.3 70.0 + - - +
207B LEU* 5.4 0.7 - - + -
210B PRO* 3.5 2.4 - - - +
211B ILE* 3.1 44.0 + - + +
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Residues in contact with GLU 203 (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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153B LYS* 5.9 1.0 + - - -
154B ILE* 3.8 0.2 - - - +
155B LYS* 3.0 55.4 + - + +
157B ARG* 3.1 26.4 + - - +
201B HIS* 3.8 13.7 + - + +
202B VAL* 1.3 83.5 - - - +
204B HIS* 1.3 70.6 + - - +
205B PRO* 3.4 8.3 - - - +
207B LEU* 4.6 4.0 - - - -
210B PRO* 3.8 26.8 - - + +
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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