Contacts of the helix formed by residues 193 - 200 (chain C) in PDB entry 5D4D
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 LEU 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C LEU* 4.1 24.0 - - + -
182C VAL* 3.0 33.9 + - + +
183C SER 5.0 0.4 - - - -
184C MET* 3.7 37.2 - - + +
191C PHE* 3.3 5.7 + - - -
192C PRO* 1.3 71.8 - - - +
194C VAL* 1.3 63.2 + - - +
195C LEU 3.1 0.9 + - - -
196C LEU* 3.1 16.0 + - + -
197C LEU* 2.9 32.8 + - + +
303C PHE* 4.2 11.7 - - + +
307C LEU* 3.7 32.8 - - + -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C VAL* 4.9 8.7 - - + -
182C VAL* 5.0 1.1 - - + +
192C PRO* 4.1 16.8 - - + -
193C LEU* 1.3 79.4 - - - +
195C LEU* 1.3 56.2 + - - +
197C LEU* 3.2 12.1 + - - +
198C ARG* 2.9 28.4 + - - +
207C LEU* 5.2 1.8 - - + -
220C GLY 5.2 0.4 - - - +
221C LEU* 3.3 42.8 - - + +
223C ASP* 4.4 11.2 - - + -
226C VAL* 3.6 26.4 - - + +
227C PHE* 4.1 21.6 - - + -
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PHE* 4.7 3.1 - - + -
192C PRO* 3.2 20.0 + - + +
193C LEU 3.1 0.6 - - - -
194C VAL* 1.3 76.8 - - - +
196C LEU* 1.3 60.3 + - - +
198C ARG* 3.1 5.9 + - - +
199C VAL* 3.0 29.8 + - - +
226C VAL* 4.2 14.3 - - + +
229C MET* 4.1 13.7 - - + -
234C ALA* 3.7 34.8 - - + +
237C ARG* 3.7 19.5 - - + +
238C LEU* 3.6 32.3 - - + -
241C LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 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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184C MET* 3.5 18.4 - - + -
191C PHE* 4.3 10.9 - - + -
192C PRO 4.2 0.6 + - - -
193C LEU* 3.1 12.8 + - + +
195C LEU* 1.3 78.8 - - - +
197C LEU* 1.3 63.8 + - - +
199C VAL* 3.1 13.7 + - + +
200C LEU* 2.9 40.6 + - + +
238C LEU* 4.1 22.1 - - + +
257C VAL* 5.1 11.2 - - + -
261C ILE* 5.2 7.9 - - + -
303C PHE* 3.5 48.0 - - + -
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Residues in contact with LEU 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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193C LEU* 2.9 26.2 + - + +
194C VAL* 3.3 10.3 - - - +
196C LEU* 1.3 77.4 - - + +
198C ARG* 1.3 61.1 + - - +
200C LEU* 3.2 21.0 + - + +
202C TYR* 3.2 53.4 + - + +
207C LEU* 3.9 22.9 - - + -
221C LEU* 3.9 19.7 - - + -
227C PHE* 6.3 0.4 - - + -
303C PHE* 4.6 13.2 - - + -
304C LEU* 5.1 4.3 - - + +
307C LEU* 3.9 28.0 - - + -
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Residues in contact with ARG 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 VAL 2.9 13.3 + - - +
195C LEU 3.1 8.9 + - - +
197C LEU* 1.3 73.8 - - - +
199C VAL* 1.3 66.6 + - - +
201C GLY* 3.0 16.4 + - - -
202C TYR 2.7 38.8 + - - +
203C ASP* 4.0 20.8 + - - +
226C VAL* 3.5 28.9 + - + +
227C PHE* 3.8 29.0 + - + -
228C ALA 5.4 0.2 + - - -
229C MET 3.0 21.6 + - - +
230C ARG* 4.2 3.2 - - - +
231C PRO* 3.7 37.0 - - + +
234C ALA* 3.8 15.7 - - + -
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Residues in contact with VAL 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 LEU 3.0 16.9 + - - +
196C LEU* 3.1 18.4 + - + +
198C ARG* 1.3 76.8 - - - +
200C LEU* 1.3 60.6 + - + +
201C GLY* 3.2 1.7 + - - -
231C PRO* 4.2 15.9 - - - +
234C ALA 3.6 6.3 - - - +
235C LEU* 3.5 57.2 - - + +
238C LEU* 4.2 9.0 - - + -
257C VAL* 5.1 5.2 - - + -
297C GLU* 5.9 0.5 - - - +
298C PHE* 3.9 29.0 + - + +
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Residues in contact with LEU 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 LEU* 2.9 38.4 + - + +
197C LEU* 3.5 23.8 - - + +
198C ARG 3.1 0.8 - - - -
199C VAL* 1.3 76.4 - - + +
201C GLY* 1.3 59.1 + - - +
202C TYR* 4.6 8.5 - - + -
261C ILE* 5.3 2.9 - - + -
291C ALA* 3.9 26.5 - - + -
298C PHE* 3.0 34.9 - - + +
299C LYS* 4.3 6.4 - - - +
300C ASP* 3.3 42.7 + - + +
303C PHE* 4.3 8.5 - - + -
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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