Contacts of the helix formed by residues 194 - 203 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C GLY* 1.3 74.9 - - - +
195C LYS* 1.3 63.7 + - - +
196C VAL* 3.3 14.5 + - - -
197C ALA* 3.1 16.1 + - - +
198C ALA 3.3 6.2 + - - -
395C TYR* 4.3 9.4 - - + -
400C TYR* 2.8 18.6 + - + +
139D ARG* 3.8 15.7 + - - -
192F GLU* 5.3 0.9 - - - +
193F GLY* 4.2 14.3 + - - -
194F ASP* 4.2 22.6 + - + +
395F TYR* 3.9 15.2 - - - -
397F ASP* 5.6 1.4 + - - -
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP* 1.3 70.3 + - - +
196C VAL* 1.3 56.1 + - - +
198C ALA* 2.8 31.0 + - - +
199C GLN* 3.1 14.4 + - - +
204C TRP 5.4 0.2 - - - +
206C VAL* 5.1 15.5 - - - +
309C PHE* 6.0 7.8 - - + -
400C TYR* 4.3 0.2 + - - -
192F GLU* 5.4 11.6 - - + +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP* 3.1 10.1 + - - -
195C LYS* 1.3 75.4 - - - +
197C ALA* 1.3 56.8 + - - +
199C GLN* 4.3 6.6 + - - +
200C ILE* 3.0 24.8 + - - +
87D LYS* 6.4 1.6 - - - -
90D ILE* 4.8 4.0 - - - +
136D ILE* 5.1 4.0 - - - +
139D ARG* 4.0 12.4 + - - +
189F ALA* 6.0 6.5 - - - +
192F GLU* 5.1 9.7 - - - +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP* 3.1 12.3 + - - +
196C VAL* 1.3 74.8 - - - +
198C ALA* 1.3 63.6 + - - +
199C GLN 3.0 2.5 - - - -
200C ILE* 3.6 11.4 - - + -
201C LYS* 3.0 33.2 + - + +
400C TYR* 4.7 13.5 - - + -
139D ARG* 3.2 24.7 - - - +
397F ASP* 5.5 4.0 - - + -
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP 3.3 5.0 + - - +
195C LYS* 2.8 25.7 + - - +
197C ALA* 1.3 79.8 - - - +
199C GLN* 1.3 55.5 + - - +
201C LYS* 4.9 1.6 - - - -
202C LEU* 3.1 33.8 + - + +
203C GLY 3.6 1.4 + - - -
204C TRP* 4.0 14.7 + - + +
309C PHE* 5.9 5.8 - - + -
400C TYR* 4.3 16.4 - - + +
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LYS 3.1 11.3 + - - +
196C VAL* 4.4 5.8 - - - +
197C ALA 3.0 0.2 - - - -
198C ALA* 1.3 77.4 - - - +
200C ILE* 1.3 62.4 + - - +
201C LYS 3.1 2.2 - - - -
203C GLY* 3.2 23.2 + - - +
204C TRP 3.2 27.4 - - - +
205C THR* 4.1 17.0 + - - -
206C VAL 5.4 0.9 - - - +
57D ALA* 6.0 1.8 - - - +
87D LYS* 2.7 44.1 + - - +
88D ASN* 5.0 0.2 - - - +
90D ILE* 3.0 42.6 - - + +
91D ARG* 4.1 13.2 - - - +
94D GLU* 5.2 1.0 - - - +
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Residues in contact with ILE 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL 3.0 24.9 - - - +
197C ALA* 3.3 10.9 + - + +
199C GLN* 1.3 77.5 - - - +
201C LYS* 1.3 67.0 + - + +
90D ILE* 3.7 20.4 - - + -
94D GLU* 3.5 23.3 - - + +
136D ILE* 5.0 4.0 - - + -
139D ARG* 3.5 41.1 - - + +
140D LEU* 3.7 29.6 - - + -
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Residues in contact with LYS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ALA* 3.0 20.8 + - + +
198C ALA* 4.9 0.4 - - - -
200C ILE* 1.3 89.7 + - + +
202C LEU* 1.3 67.7 + - + +
203C GLY 3.7 0.9 - - - -
400C TYR* 5.5 12.3 - - + -
466C PHE* 2.9 40.7 + - - +
467C LYS* 4.2 14.6 + - - +
468C VAL* 4.5 15.9 - - + -
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER* 3.4 20.1 - - - +
198C ALA* 3.1 17.9 + - + +
201C LYS* 1.3 90.1 - - + +
203C GLY* 1.3 58.6 + - - +
204C TRP* 3.0 20.8 + - + +
393C LEU* 5.3 12.6 - - + -
400C TYR* 6.2 5.6 - - + -
466C PHE* 4.8 15.5 - - + -
468C VAL* 5.1 9.0 - - + -
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Residues in contact with GLY 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER 3.4 4.3 - - - -
174C PHE* 2.7 49.0 - - - +
198C ALA 3.6 0.4 + - - -
199C GLN* 3.2 22.6 + - - +
200C ILE 5.0 0.2 - - - -
201C LYS 3.7 1.0 - - - -
202C LEU* 1.3 75.3 - - - +
204C TRP* 1.3 58.2 + - - +
205C THR* 4.0 1.4 + - - -
91D ARG* 4.5 8.3 - - - +
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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