Contacts of the helix formed by residues 208 - 214 (chain B) in PDB entry 1L0V
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 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 3.1 13.8 - - - -
207B VAL* 1.3 77.4 - - - +
209B TYR* 1.3 63.9 + - - +
210B CYS 3.2 4.1 + - - -
211B SER* 3.4 13.8 + - - -
212B GLU* 3.5 7.4 + - - +
221B ALA* 4.5 4.0 - - - -
245B F3S 3.1 21.7 - - - -
21C PHE* 3.9 9.2 - - - -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN 4.8 2.2 + - - -
72B VAL* 3.9 22.9 - - - +
73B PRO* 4.4 8.7 - - + +
157B ALA* 3.2 42.8 - - + +
207B VAL* 3.3 5.7 + - + -
208B GLY* 1.3 78.1 - - - +
210B CYS* 1.3 64.0 + - - +
212B GLU* 3.0 28.5 + - + +
213B VAL* 3.2 23.1 + - + +
245B F3S 3.4 5.4 - - - -
19C LEU* 3.2 33.0 - - + +
21C PHE* 3.5 35.4 - + + -
22C TYR* 3.3 23.6 - + + -
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B CYS* 3.5 32.8 - - + +
157B ALA* 4.1 4.2 - - - +
170B PRO* 4.2 4.5 - - + -
208B GLY 3.2 1.5 - - - -
209B TYR* 1.3 76.8 - - - +
211B SER* 1.3 70.8 + - - +
213B VAL* 3.0 24.7 + - - +
214B CYS* 3.1 7.8 + - - +
220B PRO* 3.6 20.6 - - + -
221B ALA* 3.7 14.4 - - - -
245B F3S 2.3 47.8 - - - -
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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
----------------------------------------------------------
208B GLY 3.4 4.7 + - - -
209B TYR 3.4 0.4 - - - -
210B CYS* 1.3 80.6 - - - +
212B GLU* 1.3 63.4 + - - +
213B VAL 3.2 0.5 + - - -
214B CYS* 3.5 12.5 + - - +
217B HIS* 5.7 4.0 - - - -
219B ASP* 2.7 37.2 + - - +
220B PRO* 3.9 9.0 - - - -
221B ALA* 2.8 32.0 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLY 3.5 3.9 + - - +
209B TYR* 3.0 30.6 + - + +
211B SER* 1.3 79.6 - - - +
213B VAL* 1.3 58.8 + - + +
214B CYS 5.0 0.9 - - - +
21C PHE* 3.4 34.6 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 5.0 5.4 - - + -
73B PRO* 4.0 31.4 - - + +
153B LEU* 3.6 37.1 - - + +
154B CYS* 4.2 0.4 - - - -
157B ALA* 3.8 5.2 - - + -
209B TYR* 3.6 33.0 - - + +
210B CYS* 3.0 16.8 - - - +
212B GLU* 1.3 83.2 - - + +
214B CYS* 1.3 68.7 + - - +
215B PRO* 2.8 12.5 - - - +
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Residues in contact with CYS 214 (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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210B CYS 3.1 11.8 + - - +
211B SER 3.5 12.0 + - - +
212B GLU 5.0 1.0 - - - +
213B VAL* 1.3 71.4 - - - +
215B PRO* 1.3 65.4 - - - +
216B LYS 2.9 8.1 + - - -
217B HIS* 3.3 22.4 + - - +
218B VAL* 3.1 49.6 - - - +
219B ASP 4.4 0.7 - - - +
220B PRO* 4.3 7.0 - - + -
246B SF4 2.3 38.8 - - - -
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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
------------------------------------------------------------
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