Contacts of the helix formed by residues 154 - 162 (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 ASN 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C GLU 3.4 2.2 + - - -
153C GLU* 1.3 70.4 - - - +
155C SER* 1.3 59.0 + - - +
156C ALA* 2.9 21.9 + - - +
157C TYR* 3.0 24.1 + - + -
158C GLU* 3.1 13.2 + - - +
183C ALA 5.4 2.4 + - - -
217C VAL* 3.5 23.0 - - - +
218C MET 3.0 28.1 + - - +
219C LEU* 4.3 2.5 - - + -
223C GLN* 2.8 40.2 + - - +
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 3.3 38.5 - - - +
24A CYS 3.3 19.2 + - - -
25A ALA* 3.6 9.1 - - - +
244A ARG* 5.6 1.3 - - - -
247A GLN* 5.2 5.5 + - - -
153C GLU* 3.5 7.6 + - - -
154C ASN* 1.3 72.5 + - - +
156C ALA* 1.3 69.5 + - - +
158C GLU* 3.4 12.5 + - - +
159C GLN 3.7 2.6 + - - -
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.7 6.1 - - - +
154C ASN* 2.9 8.6 + - - +
155C SER* 1.3 81.4 + - - +
157C TYR* 1.3 62.3 + - + +
159C GLN* 3.0 32.0 + - - +
160C LEU* 4.2 1.7 + - - +
179C LEU* 4.5 2.1 - - - +
180C ASP 5.2 0.7 - - - +
183C ALA* 3.7 38.4 - - + +
184C LEU* 3.7 21.3 - - + +
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 4.3 12.1 - - + -
118C ILE* 3.4 24.9 - - + +
147C LEU* 3.4 34.7 - - + +
154C ASN* 3.0 34.1 + - + +
156C ALA* 1.3 75.5 - - + +
158C GLU* 1.3 60.8 + - - +
160C LEU* 2.9 14.8 + - + +
161C LEU* 2.9 45.5 + - + +
184C LEU* 2.7 53.9 + - + -
217C VAL* 3.5 16.6 - - + -
219C LEU* 3.9 18.4 - - + -
223C GLN* 4.6 0.2 - - - +
227C LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 158 (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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16A PRO* 3.8 28.1 - - + +
18A PRO* 4.8 6.3 - - + -
153C GLU* 3.5 27.2 - - - +
154C ASN 3.1 18.5 + - - +
155C SER* 3.5 11.2 - - - +
156C ALA 3.2 0.4 - - - -
157C TYR* 1.3 76.9 - - - +
159C GLN* 1.3 59.5 + - - +
161C LEU* 4.4 6.6 - - - +
162C SER* 2.9 52.9 + - - -
223C GLN* 3.2 21.9 + - - +
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Residues in contact with GLN 159 (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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18A PRO* 3.8 21.5 + - + +
22A PRO* 3.7 24.7 + - - +
25A ALA* 3.3 29.1 - - - +
155C SER 3.7 0.6 + - - +
156C ALA* 3.0 19.6 + - - +
157C TYR 3.2 0.2 - - - -
158C GLU* 1.3 78.2 - - - +
160C LEU* 1.3 61.8 + - + +
162C SER* 3.9 3.7 + - - -
163C ARG* 3.3 23.6 + - - +
176C VAL* 5.0 4.2 - - - +
177C PRO* 6.1 0.5 - - - +
178C GLY 4.5 1.2 + - - -
179C LEU* 3.4 46.0 - - + +
180C ASP 5.0 1.3 - - - +
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Residues in contact with LEU 160 (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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63C LEU* 4.2 25.4 - - + +
70C VAL* 6.6 0.4 - - + -
72C LEU* 4.4 20.6 - - + -
93C LEU* 4.3 24.0 - - + -
95C LEU* 5.3 12.3 - - + -
118C ILE* 5.7 0.9 - - + -
156C ALA 4.8 2.7 - - - +
157C TYR* 2.9 16.6 + - + +
159C GLN* 1.3 79.5 - - - +
161C LEU* 1.3 70.1 + - + +
162C SER 3.3 1.6 - - - -
163C ARG* 3.1 18.3 + - - +
164C LEU* 3.6 16.2 + - + +
176C VAL* 4.8 4.5 - - + -
179C LEU* 4.4 20.0 - - + -
184C LEU* 4.3 21.8 - - + -
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Residues in contact with LEU 161 (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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95C LEU* 5.1 6.1 - - + -
157C TYR* 2.9 25.1 + - + +
158C GLU* 4.4 7.4 - - - +
160C LEU* 1.3 78.7 - - + +
162C SER* 1.3 61.1 + - - +
163C ARG 3.2 1.0 + - - -
164C LEU* 3.3 22.2 + - + +
165C GLU 4.9 0.9 + - - -
219C LEU* 4.0 15.3 - - + -
223C GLN* 3.5 46.4 - - + +
226C THR* 3.5 25.9 - - + +
227C LEU* 3.8 42.8 - - + -
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Residues in contact with SER 162 (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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16A PRO* 6.1 0.9 - - - -
158C GLU* 2.9 41.3 + - - +
159C GLN* 3.9 5.5 + - - -
161C LEU* 1.3 76.3 - - - +
163C ARG* 1.3 74.0 + - - +
164C LEU 3.5 0.4 + - - -
165C GLU* 4.8 7.4 + - - +
166C GLU* 4.6 2.8 + - - +
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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