Contacts of the helix formed by residues 194 - 202 (chain F) in PDB entry 4LQL
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 ASP 194 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 2.8 37.8 + - - +
192C GLU* 5.2 1.9 - - - +
193C GLY* 2.4 34.0 + - - +
194C ASP* 4.2 12.7 + - + +
395C TYR* 4.9 5.8 - - + +
193F GLY* 1.3 70.6 - - - -
195F LYS* 1.3 74.7 + - - +
196F VAL* 3.5 6.7 + - - -
197F ALA* 3.1 18.2 + - + -
198F ALA* 3.4 9.2 + - - +
395F TYR* 3.9 8.8 - - + -
400F TYR* 2.9 22.2 + - - -
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Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLU* 4.7 19.7 - - + +
193C GLY 4.5 0.6 + - - -
193F GLY 3.5 4.8 + - - -
194F ASP* 1.3 79.6 + - - +
196F VAL* 1.3 64.4 + - - +
197F ALA 2.9 2.4 + - - -
198F ALA* 3.0 13.3 + - - +
199F GLN* 3.4 15.5 + - - +
204F TRP 5.5 0.2 - - - +
206F VAL* 5.8 4.3 - - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 6.5 0.4 - - - -
90A ILE* 4.1 8.6 - - - +
139A ARG* 3.7 10.1 - - - +
189C ALA* 5.7 8.7 - - - +
194F ASP* 3.5 12.5 + - - -
195F LYS* 1.3 77.6 - - - +
197F ALA* 1.3 56.6 + - - +
199F GLN* 3.6 11.0 + - - +
200F ILE* 3.1 28.5 - - - +
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Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 3.3 20.2 - - - +
194F ASP* 3.1 20.6 + - + -
195F LYS 2.9 4.0 + - - -
196F VAL* 1.3 69.4 - - - +
198F ALA* 1.3 63.2 + - - +
199F GLN 3.0 2.9 + - - -
200F ILE* 3.6 4.8 + - - +
201F LYS* 3.0 32.5 + - + +
395F TYR* 6.1 1.1 - - + -
399F GLY* 6.0 4.0 - - - -
400F TYR* 4.0 17.0 - - + +
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Residues in contact with ALA 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ASP 3.4 6.5 + - - +
195F LYS* 3.0 10.1 + - - +
197F ALA* 1.3 79.3 - - - +
199F GLN* 1.3 57.4 + - - +
200F ILE 3.5 0.2 - - - -
201F LYS* 4.5 1.8 - - - -
202F LEU* 2.9 36.0 + - + +
203F GLY 3.2 1.9 + - - -
204F TRP* 3.7 20.8 + - + +
393F LEU* 6.0 2.2 - - + -
400F TYR* 3.6 25.4 - - + +
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Residues in contact with GLN 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LYS* 3.5 38.2 + - - +
90A ILE* 3.9 23.1 - - + +
91A ARG* 5.3 5.0 + - - +
94A GLU* 5.3 0.7 - - - +
195F LYS* 3.4 15.1 + - - +
196F VAL* 3.9 7.7 + - - +
197F ALA 3.0 0.6 - - - -
198F ALA* 1.3 80.0 - - - +
200F ILE* 1.3 60.0 + - - +
201F LYS 3.3 0.2 - - - -
203F GLY* 3.1 25.9 + - - +
204F TRP 4.0 9.6 - - - +
205F THR* 3.5 35.5 + - - -
206F VAL 5.2 2.0 + - - +
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Residues in contact with ILE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 3.4 28.3 - - + -
94A GLU* 3.5 28.9 - - + +
136A ILE* 5.4 2.0 - - + -
139A ARG* 4.0 33.9 - - + +
140A LEU* 4.4 20.9 - - + +
196F VAL 3.1 21.3 - - - +
197F ALA* 3.6 4.0 + - - +
199F GLN* 1.3 77.7 - - - +
201F LYS* 1.3 68.9 + - + +
203F GLY* 4.3 1.2 + - - -
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Residues in contact with LYS 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F PHE* 6.0 0.7 - - - -
197F ALA* 3.0 19.7 + - + +
198F ALA* 4.2 2.0 - - - +
200F ILE* 1.3 90.1 - - + +
202F LEU* 1.3 67.2 + - + +
203F GLY 3.5 0.4 - - - -
400F TYR* 5.2 10.5 - - + -
466F PHE* 3.5 35.7 + - + +
467F LYS* 2.5 37.1 + - - -
468F VAL* 4.1 11.4 - - + +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F SER* 3.5 24.1 - - - -
174F PHE* 4.7 4.5 - - - -
198F ALA* 2.9 18.4 + - + +
201F LYS* 1.3 84.5 - - + +
203F GLY* 1.3 53.6 + - - +
204F TRP* 2.6 28.6 + - + +
317F LEU* 5.6 5.3 - - + +
393F LEU* 4.7 22.9 - - + -
400F TYR* 5.4 4.5 - - + -
466F PHE* 4.4 19.1 - - + -
468F VAL* 5.9 5.8 - - + -
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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