Contacts of the helix formed by residues 220 - 230 (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 SER 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLU* 4.5 0.9 - - - -
150B GLY 3.5 11.4 - - - -
151B PRO 5.0 2.9 - - - -
152B GLU 3.4 19.2 + - - -
153B GLU* 2.7 32.6 + - - -
219B LEU* 1.3 74.9 - - - +
221B ALA* 1.3 64.5 + - - +
222B LYS* 3.6 2.4 + - - -
223B GLN* 3.0 25.8 + - - +
224B LEU* 3.0 21.2 + - - +
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Residues in contact with ALA 221 (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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149B GLU* 3.8 34.4 - - - +
150B GLY 4.3 1.2 + - - -
220B SER* 1.3 73.0 - - - +
222B LYS* 1.3 56.0 + - - +
224B LEU* 3.3 6.3 + - - +
225B HIS* 2.8 30.8 + - - +
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Residues in contact with LYS 222 (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* 4.2 8.7 - - - +
220B SER* 3.3 8.1 + - - +
221B ALA* 1.3 79.2 - - - +
223B GLN* 1.3 56.9 + - - +
225B HIS* 3.3 8.4 + - - +
226B THR* 2.8 33.8 + - - +
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Residues in contact with GLN 223 (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* 3.3 22.3 + - - +
154B ASN* 2.8 52.9 + - - +
157B TYR 4.3 0.4 - - - -
158B GLU* 3.2 30.9 + - - +
161B LEU* 3.5 24.6 - - + +
219B LEU* 3.6 7.2 - - + -
220B SER* 3.0 30.5 + - - +
222B LYS* 1.3 76.8 - - - +
224B LEU* 1.3 57.1 + - - +
226B THR* 3.2 8.5 + - - -
227B LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 4.0 27.4 - - + -
116B ALA* 4.4 16.6 - - + -
147B LEU* 4.8 4.9 - - + -
148B GLU 4.1 1.6 - - - +
149B GLU* 3.8 42.6 - - + +
219B LEU* 4.0 25.6 - - + +
220B SER 3.0 16.7 + - - +
221B ALA* 3.7 7.4 - - - +
223B GLN* 1.3 71.5 - - - +
225B HIS* 1.3 65.5 + - - +
227B LEU* 3.3 10.1 + - + +
228B SER* 3.2 24.2 + - - -
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Residues in contact with HIS 225 (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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100B ALA* 5.4 10.0 - - + +
221B ALA 2.8 18.6 + - - +
222B LYS* 3.5 8.7 + - - +
224B LEU* 1.3 75.0 - - - +
226B THR* 1.3 67.2 + - - +
228B SER* 3.2 5.6 + - - -
229B ASP* 2.9 67.3 + - + +
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Residues in contact with THR 226 (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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161B LEU* 3.7 33.4 - - + +
162B SER* 5.7 0.4 - - - -
164B LEU* 4.0 4.4 - - + +
222B LYS* 2.8 22.5 + - - +
223B GLN* 3.2 11.7 + - - -
225B HIS* 1.3 76.8 + - - +
227B LEU* 1.3 64.3 + - - +
229B ASP* 5.3 0.7 - - - -
230B THR* 2.6 39.7 + - + +
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Residues in contact with LEU 227 (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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70B VAL* 4.6 1.6 - - + -
95B LEU* 3.9 27.8 - - + -
97B TRP* 3.5 60.9 + - + -
116B ALA* 4.0 17.7 - - + -
147B LEU* 4.6 8.5 - - + -
161B LEU* 3.8 19.9 - - + +
164B LEU* 4.1 14.1 - - + +
219B LEU* 5.1 3.1 - - + -
223B GLN 2.9 12.9 + - - +
224B LEU* 3.6 15.3 - - + +
225B HIS 3.2 0.4 - - - -
226B THR* 1.3 78.7 - - - +
228B SER* 1.3 60.5 + - - +
230B THR 4.4 2.4 + - - -
231B LEU* 4.9 3.6 + - - +
239B LEU 4.9 0.2 - - - +
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Residues in contact with SER 228 (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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97B TRP* 3.4 25.4 - - - -
98B GLY 3.8 13.9 - - - -
99B ALA* 4.1 14.4 - - - -
100B ALA* 5.3 0.2 - - - -
224B LEU 3.2 14.3 + - - -
225B HIS* 3.4 2.8 + - - -
227B LEU* 1.3 79.8 - - - +
229B ASP* 1.3 75.1 + - - +
230B THR 3.7 0.7 - - - -
231B LEU 5.2 1.6 + - - +
238B ARG* 4.8 0.9 + - - -
239B LEU 3.9 3.5 - - - +
240B GLN* 3.0 27.9 + - - +
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Residues in contact with ASP 229 (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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100B ALA* 4.5 11.9 + - - +
225B HIS* 2.9 52.1 + - + +
226B THR* 5.3 0.2 - - - -
228B SER* 1.3 98.1 + - - +
230B THR* 1.3 59.9 + - - +
231B LEU 3.8 0.7 - - - -
232B TRP* 5.0 0.7 + - - -
238B ARG* 2.7 41.2 + - - +
240B GLN* 3.7 13.3 + - - -
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Residues in contact with THR 230 (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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164B LEU* 3.6 19.3 - - + +
165B GLU* 3.5 36.6 - - + +
168B ALA* 3.6 11.2 - - + +
226B THR* 2.6 36.5 + - + +
227B LEU 4.4 0.2 + - - -
228B SER 3.7 0.4 - - - -
229B ASP* 1.3 79.8 - - - +
231B LEU* 1.3 64.3 + - - +
232B TRP* 3.5 15.7 + - - -
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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