Contacts of the helix formed by residues 181 - 185 (chain C) in PDB entry 5FL6
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 ILE 181 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 2.9 41.2 + - + +
55C LEU* 4.0 13.2 - - + -
61C LEU* 4.5 0.4 - - + -
72C LEU* 3.8 18.6 - - + -
74C LEU* 3.6 31.9 - - + -
78C LEU* 4.0 6.7 - - + -
93C LEU* 3.8 22.2 - - + -
120C VAL* 5.1 5.8 - - + -
179C LEU* 3.8 24.7 - - + +
180C ASP* 1.3 73.1 - - - +
182C SER* 1.3 62.7 + - - +
184C LEU* 3.1 24.4 + - + +
185C LEU* 4.3 6.2 - - + +
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 3.0 44.8 + - - +
28A PHE* 5.0 1.4 - - - -
50C LEU* 5.2 5.4 - - - -
53C PHE* 3.8 24.3 - - - +
54C GLN* 4.4 6.9 - - - +
180C ASP* 2.5 23.2 + - - -
181C ILE* 1.3 78.5 - - - +
183C ALA* 1.3 58.1 + - - +
185C LEU* 3.1 17.1 + - - +
189C PHE* 4.9 9.2 - - - -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.1 28.0 - - - +
26A GLY 3.9 1.1 - - - +
27A ARG* 3.7 27.1 - - - +
250A ASN* 5.5 3.1 + - - +
154C ASN* 5.2 2.8 + - - +
156C ALA* 3.7 17.1 - - + +
157C TYR* 5.0 1.0 - - - -
180C ASP* 3.1 14.0 + - - +
182C SER* 1.3 80.2 + - - +
184C LEU* 1.3 57.4 + - - +
185C LEU 3.2 7.0 + - - +
217C VAL* 5.6 1.2 - - - +
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Residues in contact with LEU 184 (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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93C LEU* 3.8 27.6 - - + -
118C ILE* 4.2 12.2 - - + +
156C ALA* 3.7 26.2 - - + +
157C TYR* 2.7 66.8 + - + +
160C LEU* 4.3 11.4 - - + -
179C LEU* 4.1 19.1 - - + -
180C ASP 4.5 2.9 - - - +
181C ILE* 3.1 19.9 + - + +
183C ALA* 1.3 75.9 - - - +
185C LEU* 1.3 64.1 + - + +
217C VAL* 3.7 8.8 - - - +
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Residues in contact with LEU 185 (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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27A ARG* 3.0 14.4 + - - +
250A ASN* 4.7 2.6 + - - +
50C LEU* 3.5 31.9 - - + -
53C PHE* 5.1 3.8 - - + -
118C ILE* 4.6 14.1 - - + -
120C VAL* 4.3 23.6 - - + -
143C LEU* 4.6 7.9 - - + +
145C ALA* 4.6 1.6 - - + +
181C ILE* 4.3 7.2 - - + +
182C SER* 3.1 19.1 + - - +
183C ALA 4.0 4.5 - - - +
184C LEU* 1.3 88.3 - - + +
186C PRO* 1.3 76.2 - - + +
189C PHE* 4.2 9.0 - - + -
213C PHE* 4.2 23.6 - - + -
217C VAL* 3.7 6.6 - - - +
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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
------------------------------------------------------------
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