Contacts of the helix formed by residues 200 - 204 (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 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PHE* 3.2 17.0 - - - -
168B ILE* 4.0 8.7 - - - -
173B ILE* 3.9 5.8 - - - -
194B GLN 3.5 21.1 - - - -
195B LEU 3.7 0.9 - - - -
197B SER* 3.0 13.0 + - - -
198B GLN 3.0 0.6 - - - -
199B ASN* 1.3 77.6 - - - +
201B VAL* 1.3 67.4 + - - -
202B TRP 3.1 2.5 - - - -
203B SER 3.1 9.4 + - - -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.7 23.9 - - + +
195B LEU* 3.1 42.6 + - + +
200B GLY* 1.3 72.8 - - - -
202B TRP* 1.3 85.1 + - + +
203B SER 3.1 0.2 - - - -
204B CYS* 3.0 25.8 + - - +
224B ILE* 4.2 5.4 - - + +
227B GLY* 4.2 17.0 - - - -
228B LYS* 3.4 34.0 - - + +
231B SER* 4.2 4.5 - - - -
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Residues in contact with TRP 202 (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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196B ASN* 3.5 24.3 + - - +
197B SER 3.8 9.2 - - - +
198B GLN* 3.9 15.5 + - - +
200B GLY 3.1 0.8 - - - -
201B VAL* 1.3 81.6 - - + +
203B SER* 1.3 58.7 + - - +
204B CYS 3.1 10.2 + - - +
228B LYS* 3.7 30.3 - - + +
231B SER* 3.0 31.8 + - - -
232B SER* 3.6 23.8 - - - -
701B MQ7 4.7 9.8 - + - -
8D SER* 4.1 9.4 + - - +
10D GLU* 3.5 33.0 - - + +
11D PRO* 3.5 23.8 - - + +
14D TRP* 3.5 39.3 - + + -
84D HIS* 5.0 6.6 + - - -
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Residues in contact with SER 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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160B GLN* 3.3 29.1 + - - +
164B ASN* 3.1 28.6 + - - +
167B PHE* 3.3 32.3 - - - +
198B GLN* 3.2 22.3 + - - +
199B ASN* 4.1 0.8 - - - -
200B GLY 3.1 1.9 + - - -
201B VAL 3.1 1.2 - - - -
202B TRP* 1.3 78.4 - - - +
204B CYS* 1.3 58.5 + - - +
205B THR* 3.8 3.1 + - - +
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Residues in contact with CYS 204 (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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160B GLN* 4.3 0.7 - - - -
167B PHE* 4.1 15.9 - - + -
200B GLY 4.3 0.2 + - - -
201B VAL 3.0 14.3 + - - +
202B TRP 3.1 0.4 - - - +
203B SER* 1.3 78.7 - - - +
205B THR* 1.3 55.3 + - - +
206B PHE* 3.4 11.4 - - - -
224B ILE* 3.7 24.5 - - + -
225B GLN* 4.7 2.2 - - - -
228B LYS* 2.5 33.5 + - - -
245B F3S 2.2 43.1 - - - -
701B MQ7 3.5 7.9 - - - -
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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