Contacts of the helix formed by residues 198 - 206 (chain P) in PDB entry 5L4K
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 198 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163P ALA* 4.6 1.2 - - - +
193P CYS* 3.1 20.4 + - + +
194P LEU* 5.0 0.6 - - - +
196P VAL* 3.4 31.5 - - - +
197P LYS* 1.3 77.6 - - - +
199P TYR* 1.3 64.1 + - - +
200P ILE* 3.0 6.7 + - - -
201P ARG* 3.0 50.2 + - + +
202P THR* 3.2 15.0 + - - -
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Residues in contact with TYR 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 3.9 24.7 + - + -
197P LYS* 3.4 51.2 + - + +
198P ASP* 1.3 74.6 - - - +
200P ILE* 1.3 72.9 + - + +
202P THR* 3.2 6.8 + - - -
203P GLN* 3.1 39.5 + - - +
232P GLN* 4.9 6.9 + - + -
233P LEU* 3.9 24.6 - - + +
236P HIS* 4.1 43.9 + + + +
237P GLU* 4.5 4.9 - - - +
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Residues in contact with ILE 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P LYS 6.0 0.2 - - - +
198P ASP* 3.0 1.7 + - - -
199P TYR* 1.3 90.0 - - + +
201P ARG* 1.3 68.5 + - + +
202P THR 3.5 0.2 + - - -
203P GLN* 3.8 10.1 + - - +
204P ILE* 3.3 29.6 + - + +
273Q GLY* 6.1 5.4 - - - -
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Residues in contact with ARG 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P ALA* 4.5 10.9 + - - +
164P SER* 4.7 11.1 + - - -
167P GLN* 3.2 42.5 + - - +
193P CYS* 4.4 9.0 - - - +
198P ASP* 3.0 43.9 + - + +
200P ILE* 1.3 83.8 - - + +
202P THR* 1.3 59.1 + - - +
204P ILE* 3.6 13.9 + - + +
205P ILE* 3.0 32.7 + - + +
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Residues in contact with THR 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MET* 3.7 33.0 - - + +
193P CYS* 3.6 15.9 + - - -
194P LEU* 3.9 21.0 - - + +
198P ASP 3.2 14.5 + - - -
199P TYR* 3.2 8.7 + - - -
201P ARG* 1.3 75.1 - - - +
203P GLN* 1.3 59.0 + - - +
204P ILE 2.9 9.2 + - - -
205P ILE* 4.1 4.9 - - + +
206P SER* 2.9 31.5 + - - +
233P LEU* 3.6 21.3 - - + -
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Residues in contact with GLN 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P TYR* 3.1 25.8 + - - +
200P ILE* 4.2 8.7 - - - +
201P ARG 3.6 0.2 - - - -
202P THR* 1.3 73.6 - - - +
204P ILE* 1.3 59.1 + - + +
206P SER* 4.5 2.2 - - - -
207P LYS* 3.3 29.7 + - - +
233P LEU* 3.8 28.9 - - + +
237P GLU* 3.8 29.9 + - - +
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Residues in contact with ILE 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P ILE* 3.3 27.1 - - + +
201P ARG* 3.6 15.9 + - + +
202P THR 2.9 0.6 - - - -
203P GLN* 1.3 78.8 - - + +
205P ILE* 1.3 68.4 + - + +
206P SER 3.2 2.0 - - - -
207P LYS* 3.1 22.4 + - + +
208P LYS* 4.3 7.2 + - - +
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Residues in contact with ILE 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P GLN* 3.8 25.8 - - + +
186P ILE* 3.9 26.2 - - + +
189P GLN* 3.8 26.2 - - + +
190P MET* 4.5 18.8 - - + +
193P CYS* 4.1 20.9 - - - -
201P ARG 3.0 21.6 + - - +
202P THR* 3.1 5.8 + - + +
204P ILE* 1.3 78.0 - - + +
206P SER* 1.3 65.3 + - - +
208P LYS* 3.0 34.3 + - + +
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Residues in contact with SER 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MET* 3.5 27.9 - - - +
202P THR* 2.9 19.1 + - - +
203P GLN* 4.5 1.0 - - - -
204P ILE 3.2 0.4 - - - -
205P ILE* 1.3 79.0 - - - +
207P LYS* 1.3 72.2 + - - +
208P LYS 2.9 7.1 + - - -
209P ILE* 3.0 25.0 + - - +
226P TYR* 4.8 6.6 + - - -
230P MET* 3.9 20.1 - - - -
233P LEU* 4.5 4.5 - - - +
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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