Contacts of the helix formed by residues 154 - 162 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU 3.4 1.8 + - - -
153B GLU* 1.3 70.9 - - - +
155B SER* 1.3 63.3 + - - +
156B ALA* 2.9 20.9 + - - +
157B TYR* 3.0 27.5 + - + -
158B GLU* 3.1 9.3 + - - +
183B ALA 5.4 2.0 + - - -
217B VAL* 3.4 23.6 - - - +
218B MET 3.0 29.3 + - - +
219B LEU* 4.3 2.0 - - - -
223B GLN* 2.8 39.6 + - - +
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Residues in contact with SER 155 (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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153B GLU 3.6 6.4 + - - -
154B ASN* 1.3 70.6 + - - +
156B ALA* 1.3 66.9 + - - +
158B GLU* 3.4 17.9 + - - +
159B GLN* 3.7 11.9 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 2.9 8.6 + - - +
155B SER* 1.3 79.8 - - - +
157B TYR* 1.3 63.3 + - + +
159B GLN* 3.0 32.9 + - - +
160B LEU* 4.1 1.4 + - - +
179B LEU* 4.4 1.4 - - - +
180B ASP 5.1 1.1 - - - +
183B ALA* 3.6 38.4 - - + +
184B LEU* 3.7 23.9 - - + +
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Residues in contact with TYR 157 (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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95B LEU* 4.2 18.6 - - + -
118B ILE* 3.4 17.3 - - + +
147B LEU* 3.3 40.9 - - + +
154B ASN* 3.0 29.8 + - + +
156B ALA* 1.3 75.3 - - + +
158B GLU* 1.3 59.7 + - - +
160B LEU* 3.0 16.6 + - + +
161B LEU* 2.9 46.0 + - + +
183B ALA 5.0 0.2 - - - -
184B LEU* 2.6 54.2 + - + -
217B VAL* 4.0 15.9 - - + -
219B LEU* 3.9 14.4 - - + -
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Residues in contact with GLU 158 (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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153B GLU* 3.7 12.6 - - + +
154B ASN 3.1 18.1 + - - +
155B SER* 3.5 10.1 - - - +
156B ALA 3.3 0.4 - - - -
157B TYR* 1.3 75.7 - - - +
159B GLN* 1.3 55.3 + - - +
161B LEU* 4.4 5.6 - - - +
162B SER* 2.8 58.0 + - - -
223B GLN* 3.2 21.5 + - - +
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Residues in contact with GLN 159 (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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155B SER 4.0 8.5 - - - +
156B ALA* 3.0 28.7 - - - +
157B TYR 3.2 0.6 - - - -
158B GLU* 1.3 77.0 - - - +
160B LEU* 1.3 60.2 + - + +
162B SER* 3.8 3.2 + - - -
163B ARG* 3.4 24.6 + - - +
176B VAL* 5.1 5.0 - - - +
177B PRO 6.1 0.7 - - - +
178B GLY 4.5 3.8 + - - -
179B LEU* 3.3 45.4 - - + +
180B ASP 4.9 2.9 + - - +
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Residues in contact with LEU 160 (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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63B LEU* 4.2 25.5 - - + +
70B VAL* 6.5 0.9 - - + -
72B LEU* 4.4 22.4 - - + -
93B LEU* 4.3 21.5 - - + -
95B LEU* 5.0 13.7 - - + -
118B ILE* 5.7 0.4 - - + -
156B ALA 4.6 5.6 - - - +
157B TYR* 3.0 18.6 + - + +
159B GLN* 1.3 81.7 - - - +
161B LEU* 1.3 69.4 + - + +
162B SER 3.3 0.2 - - - -
163B ARG* 3.1 17.8 + - - +
164B LEU* 3.6 14.5 + - + +
176B VAL* 5.2 3.8 - - + -
179B LEU* 4.5 15.0 - - + -
184B LEU* 4.2 22.9 - - + -
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Residues in contact with LEU 161 (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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95B LEU* 5.3 5.6 - - + -
157B TYR* 2.9 35.3 + - + +
158B GLU* 4.3 7.6 - - - +
160B LEU* 1.3 77.0 - - + +
162B SER* 1.3 62.8 + - - +
163B ARG 3.1 1.2 + - - -
164B LEU* 3.1 35.1 + - + +
165B GLU 4.8 0.7 + - - -
219B LEU* 4.1 7.4 - - + -
223B GLN* 3.5 42.6 - - + +
226B THR* 3.7 20.5 - - + +
227B LEU* 3.8 38.1 - - + +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 2.8 42.6 + - - -
159B GLN* 3.8 5.9 + - - -
161B LEU* 1.3 76.3 - - - +
163B ARG* 1.3 73.4 + - - +
164B LEU 3.5 0.6 + - - -
165B GLU* 4.7 8.0 + - - +
166B GLU* 5.1 1.6 - - - +
226B THR* 5.7 0.7 - - - -
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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