Contacts of the helix formed by residues 194 - 199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLY* 1.3 70.2 - - - -
195B LYS* 1.3 70.6 + - - +
196B VAL* 3.7 6.6 + - - +
197B ALA* 3.0 42.5 + - + +
198B ALA* 3.1 8.5 + - - +
395B TYR* 4.8 5.1 - - + +
400B TYR* 2.3 33.6 + - + -
192D GLU* 4.9 1.6 - - - +
193D GLY* 3.6 25.1 + - - -
194D ASP* 4.3 15.9 - - + +
395D TYR* 4.7 4.3 - - + -
139E ARG* 3.2 18.9 + - - -
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Residues in contact with LYS 195 (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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180B ARG* 3.2 36.7 - - - +
183B ASP* 5.4 0.6 + - - -
192B GLU* 5.3 9.5 - - - +
193B GLY 4.1 9.0 + - - +
194B ASP* 1.3 75.8 + - - +
196B VAL* 1.3 65.1 + - - +
198B ALA* 4.3 2.3 - - - +
199B GLN* 3.5 18.5 + - - +
204B TRP 4.9 1.9 - - - +
205B THR* 6.0 0.5 - - - -
206B VAL* 3.9 45.4 + - + +
208B TYR* 5.5 2.0 - - + -
309B PHE* 4.9 8.3 - - + -
183D ASP* 4.7 3.3 + - - +
184D THR* 6.2 3.4 - - - -
192D GLU* 4.8 21.9 - - + +
195D LYS* 4.2 18.8 - - - +
87E LYS* 5.1 11.2 - - + +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 3.3 11.2 - - - +
195B LYS* 1.3 75.6 - - - +
197B ALA* 1.3 56.9 + - - +
198B ALA 3.1 0.2 - - - -
199B GLN* 3.0 22.1 + - - +
200B ILE* 3.0 14.6 - - + +
189D ALA* 3.5 35.4 - - + +
192D GLU* 4.0 18.6 - - + -
87E LYS* 4.7 11.4 - - + -
90E ILE* 3.8 21.3 - - + -
136E ILE* 4.3 12.1 - - + -
139E ARG* 4.2 20.2 - - - +
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Residues in contact with ALA 197 (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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194B ASP* 3.0 33.7 + - + +
196B VAL* 1.3 78.2 - - - +
198B ALA* 1.3 55.5 + - - +
200B ILE* 3.3 22.1 - - + +
201B LYS* 3.9 14.6 - - - +
395B TYR* 6.4 0.4 - - + -
399B GLY* 6.4 1.1 - - - -
400B TYR* 4.2 12.9 - - + -
397D ASP* 5.9 5.8 - - + -
139E ARG* 4.1 10.3 - - - +
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Residues in contact with ALA 198 (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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194B ASP 3.1 15.1 + - - +
195B LYS* 4.4 2.9 - - - +
197B ALA* 1.3 76.7 - - - +
199B GLN* 1.3 56.4 + - - +
200B ILE 3.0 5.8 - - - -
201B LYS* 3.7 6.5 - - - +
202B LEU* 3.2 18.1 + - + +
203B GLY 2.8 23.7 + - - -
204B TRP* 3.5 10.5 + - + +
393B LEU* 6.2 0.4 - - + -
400B TYR* 3.5 24.0 - - + +
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Residues in contact with GLN 199 (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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174B PHE* 5.8 0.5 - - - -
195B LYS 3.5 7.8 + - - +
196B VAL 3.0 12.8 + - - +
198B ALA* 1.3 77.8 - - - +
200B ILE* 1.3 60.1 + - - +
203B GLY* 3.5 15.6 - - - +
204B TRP 3.4 24.7 - - - +
205B THR* 4.1 18.4 + - - -
206B VAL 5.5 0.2 + - - -
57E ALA* 5.8 4.0 - - - +
87E LYS* 3.1 54.9 + - - +
88E ASN* 5.0 1.6 - - - +
90E ILE* 3.7 23.4 - - + +
91E ARG* 5.1 14.1 - - + +
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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