Contacts of the helix formed by residues 198 - 202 (chain A) in PDB entry 3LM0
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 THR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASP* 5.9 0.6 + - - -
160A LYS* 4.0 25.7 + - - +
197A GLY* 1.3 69.4 - - - -
199A PRO* 1.3 75.4 - - + +
200A GLU* 3.1 14.4 + - - +
201A TYR* 3.2 38.6 + - + +
202A LEU* 3.7 9.4 + - - +
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Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY 3.3 8.7 - - - +
198A THR* 1.3 89.9 - - + -
200A GLU* 1.3 58.3 + - - +
202A LEU* 3.2 23.7 + - + +
240A ASN* 3.8 29.2 - - - +
243A THR* 3.9 13.5 - - + -
244A TYR* 3.8 30.7 - - + +
247A ILE* 3.0 22.0 - - - +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 4.4 10.1 - - + +
199A PRO* 1.3 79.2 - - - +
201A TYR* 1.3 98.1 + - + +
202A LEU 3.8 0.3 + - - +
219A TRP* 5.3 0.2 + - - -
223A ILE* 4.0 12.5 - - - +
227A MET* 5.6 0.3 - - - +
233A SER* 3.7 20.5 + - - +
234A PRO* 6.0 0.2 - - - +
235A PHE* 4.0 14.1 - - - +
236A VAL* 3.5 37.6 - - + +
243A THR* 3.6 19.1 - - + -
247A ILE* 4.1 4.9 - - - +
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Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 4.2 2.8 - - - -
158A ASP* 6.2 0.2 - - - +
160A LYS* 3.9 24.5 - - + +
161A PRO* 3.6 22.5 - - + +
162A GLN* 3.8 26.2 + - - -
198A THR* 3.2 29.5 + - + +
199A PRO 3.1 0.8 - - - -
200A GLU* 1.3 110.6 + - + +
202A LEU* 1.3 63.1 + - + +
203A ALA 3.6 0.3 + - - -
206A ILE* 5.8 0.2 - - - +
220A ASN* 2.8 35.6 + - - +
223A ILE* 4.0 22.5 - - + +
227A MET* 3.6 33.0 - - - +
233A SER* 6.1 0.2 - - - -
234A PRO* 6.2 0.2 - - + -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU 6.0 1.6 - - - +
196A MET* 4.2 12.3 - - - +
197A GLY* 3.9 30.7 - - - +
198A THR 3.7 10.3 - - - +
199A PRO* 3.2 24.4 + - + +
200A GLU 3.5 0.4 - - - -
201A TYR* 1.3 78.4 - - + +
203A ALA* 1.3 67.6 + - - +
206A ILE* 4.3 23.6 - - + -
207A LEU* 4.0 25.0 - - + +
219A TRP* 3.9 4.1 + - - -
244A TYR* 4.4 7.6 - - + +
247A ILE* 3.2 24.4 - - - +
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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