Contacts of the helix formed by residues 220 - 231 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D GLU* 4.3 0.7 - - - -
150D GLY 3.6 10.5 - - - -
151D PRO 4.8 3.4 - - - -
152D GLU 3.6 16.9 + - - -
153D GLU* 4.1 10.5 - - - +
219D LEU* 1.3 76.1 - - - +
221D ALA* 1.3 65.0 + - - +
222D LYS* 3.3 9.6 + - - +
223D GLN* 2.9 39.8 + - - +
224D LEU* 3.1 21.8 + - - +
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.8 36.4 - - - +
150D GLY 4.1 2.6 + - - +
220D SER* 1.3 73.6 - - - +
222D LYS* 1.3 62.4 + - - +
224D LEU* 3.4 5.1 + - - +
225D HIS* 3.0 22.1 + - - +
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Residues in contact with LYS 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D GLU* 4.7 12.3 + - - -
158D GLU* 5.5 3.8 + - - -
220D SER* 3.2 7.6 + - - +
221D ALA* 1.3 78.8 - - - +
223D GLN* 1.3 58.7 + - + +
225D HIS* 3.1 11.2 + - + +
226D THR* 2.8 40.9 + - - +
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Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D GLU* 3.4 13.1 - - + +
154D ASN* 2.7 49.9 + - - +
157D TYR 4.3 0.2 - - - -
158D GLU* 3.0 35.7 + - - +
161D LEU* 3.5 22.4 - - + +
219D LEU* 3.5 12.3 - - + -
220D SER* 2.9 33.6 + - - +
222D LYS* 1.3 78.1 - - + +
224D LEU* 1.3 56.4 + - - +
226D THR* 3.2 7.9 + - - -
227D LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TRP* 6.0 0.2 - - - +
115D PRO* 4.1 25.1 - - + -
116D ALA* 4.4 17.3 - - + -
147D LEU* 4.6 6.1 - - + -
148D GLU 4.0 2.9 - - - +
149D GLU* 3.7 45.8 - - + +
219D LEU* 3.9 21.8 - - + -
220D SER 3.1 15.8 + - - +
221D ALA* 3.8 7.0 - - - +
223D GLN* 1.3 74.4 - - - +
225D HIS* 1.3 57.8 + - - +
227D LEU* 3.6 8.9 + - + +
228D SER* 2.9 29.6 + - - -
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Residues in contact with HIS 225 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D ALA* 5.8 10.1 - - + -
221D ALA 3.0 15.4 + - - +
222D LYS* 3.4 14.8 + - + +
224D LEU* 1.3 74.8 - - - +
226D THR* 1.3 62.0 + - - +
228D SER* 3.3 7.2 + - - -
229D ASP* 2.8 72.0 + - + +
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.6 33.9 - - + +
162D SER* 5.7 0.2 - - - -
164D LEU* 4.0 4.6 - - + +
165D GLU 6.1 0.2 - - - +
222D LYS* 2.8 32.4 + - - +
223D GLN* 3.5 10.8 - - - -
225D HIS* 1.3 76.7 + - - +
227D LEU* 1.3 66.4 + - - +
229D ASP* 5.0 0.4 - - - -
230D THR* 2.6 40.3 + - + +
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D VAL* 4.6 1.6 - - + -
95D LEU* 3.6 29.2 - - + -
97D TRP* 3.6 60.2 - - + -
116D ALA* 4.0 17.0 - - + -
147D LEU* 4.6 9.6 - - + -
157D TYR* 6.4 0.2 - - + -
161D LEU* 3.9 16.5 - - + +
164D LEU* 3.9 18.4 - - + +
219D LEU* 4.9 2.9 - - + -
223D GLN 2.9 15.7 + - - +
224D LEU* 3.6 14.8 - - + +
225D HIS 3.3 0.2 - - - -
226D THR* 1.3 79.3 - - - +
228D SER* 1.3 59.4 + - - +
229D ASP 3.5 0.3 + - - -
230D THR 4.3 2.6 + - - -
231D LEU* 4.8 3.6 + - - +
239D LEU 5.0 0.2 - - - +
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TRP* 3.5 24.9 - - - -
98D GLY 3.9 12.3 - - - -
99D ALA* 4.2 16.2 - - - -
100D ALA* 4.9 1.2 + - - -
224D LEU 2.9 19.2 + - - -
225D HIS* 3.5 11.3 + - - -
227D LEU* 1.3 75.5 - - - +
229D ASP* 1.3 60.0 + - - +
230D THR 3.7 0.6 + - - -
231D LEU 5.4 1.5 - - - +
238D ARG* 5.0 0.7 + - - +
239D LEU 4.0 3.8 - - - +
240D GLN* 2.9 31.7 + - - +
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Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D HIS* 2.8 57.3 + - + +
226D THR* 5.0 0.4 - - - -
228D SER* 1.3 74.4 - - - +
230D THR* 1.3 61.9 + - - +
231D LEU 3.9 1.3 - - - -
232D TRP* 5.3 0.9 + - - -
238D ARG* 2.9 46.4 + - - +
240D GLN* 4.6 5.3 + - - +
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Residues in contact with THR 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D LEU* 3.6 20.0 - - + +
165D GLU* 3.5 37.9 - - + +
168D ALA* 3.5 17.6 - - + +
226D THR* 2.6 37.3 + - + +
227D LEU 4.3 0.2 + - - -
228D SER 3.7 0.4 - - - -
229D ASP* 1.3 79.8 - - - +
231D LEU* 1.3 64.3 + - - +
232D TRP* 3.5 10.4 + - - -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ASN* 3.8 12.1 - - - +
70D VAL* 3.8 30.1 - - + +
97D TRP* 3.8 24.5 - - + -
164D LEU* 3.6 41.1 - - + +
167D ILE* 3.4 31.6 - - + +
168D ALA* 3.9 2.0 - - - -
227D LEU 4.8 3.6 + - - +
228D SER 5.4 0.9 - - - +
229D ASP 5.1 1.4 - - - -
230D THR* 1.3 78.4 + - - +
232D TRP* 1.3 62.2 + - - +
238D ARG* 3.8 5.5 + - - +
239D LEU* 2.8 39.9 + - + +
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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