Contacts of the helix formed by residues 180 - 189 (chain B) in PDB entry 5H8Q
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 4.5 3.6 - - - -
95B THR* 3.5 8.4 - - - +
132B ARG* 4.0 4.7 - - - +
177B VAL* 2.7 26.4 + - - -
178B LYS 4.2 2.7 - - - -
179B GLN* 1.3 77.6 - - - +
181B SER* 1.3 63.7 + - - +
182B VAL* 3.4 5.0 + - - +
183B ASP* 3.1 15.4 + - - +
184B ILE* 3.1 17.3 + - - +
224B TRP* 3.5 29.9 - - - -
301B GLY 3.5 10.1 - - - -
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Residues in contact with SER 181 (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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127B THR* 3.4 31.8 + - - +
129B ASN* 4.1 8.2 + - - -
132B ARG* 3.6 10.2 - - - +
147B LEU* 5.6 1.0 - - - +
180B SER* 1.3 69.3 - - - +
182B VAL* 1.3 67.0 + - - +
184B ILE* 3.4 12.4 + - - +
185B TYR* 2.9 28.4 + - - +
225B ASP* 4.8 1.6 + - - -
301B GLY* 2.8 33.7 + - - -
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.6 31.4 - - + -
176B THR* 3.2 27.8 - - - +
180B SER* 3.2 2.6 - - - +
181B SER* 1.3 77.4 - - - +
183B ASP* 1.3 65.4 + - - +
185B TYR* 3.3 5.2 + - - +
186B PHE* 3.1 55.2 + - + -
223B ILE* 4.0 12.1 - - + +
224B TRP* 3.6 30.1 - - + -
225B ASP* 4.8 1.6 - - - +
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Residues in contact with ASP 183 (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 THR* 4.5 3.5 + - + +
176B THR* 4.2 8.3 - - + +
177B VAL 3.9 6.1 - - - +
178B LYS* 4.6 0.8 - - - -
179B GLN* 3.4 21.5 + - - +
180B SER* 3.1 22.8 + - - +
182B VAL* 1.3 79.1 - - - +
184B ILE* 1.4 54.5 + - - +
186B PHE* 3.5 3.1 + - - +
187B ARG* 3.0 55.8 + - - +
196B TYR* 3.7 18.7 + - - -
200B GLU* 5.8 0.3 - - - +
203B ASN* 3.7 20.5 + - - -
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Residues in contact with ILE 184 (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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94B GLY 3.8 12.3 - - - +
95B THR* 3.5 34.8 - - + -
96B GLN 5.4 0.9 - - - +
107B TRP* 4.5 7.6 - - + -
129B ASN* 3.6 22.7 - - - +
131B GLU* 3.4 41.5 - - + +
132B ARG* 3.9 9.4 - - + +
180B SER 3.1 9.8 + - - +
181B SER* 3.4 8.7 - - - +
182B VAL 3.3 0.2 - - - -
183B ASP* 1.4 75.5 - - - +
185B TYR* 1.4 57.0 + - - +
187B ARG* 3.4 8.0 + - - +
188B ARG* 3.0 32.9 + - - +
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Residues in contact with TYR 185 (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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267A GLY 3.8 5.4 + - - -
147B LEU* 4.0 12.1 - - + -
181B SER 2.9 19.7 + - - +
182B VAL* 3.3 8.3 + - - +
184B ILE* 1.4 74.3 - - - +
186B PHE* 1.3 72.1 + + - +
188B ARG* 3.4 33.6 - - - +
189B GLN* 3.1 38.4 + - + +
192B LEU* 3.5 26.3 - - + +
246B PHE* 4.0 23.0 + + - -
247B PHE* 3.5 50.9 - + + +
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Residues in contact with PHE 186 (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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147B LEU* 4.6 0.2 - - + -
160B ILE* 4.1 5.8 - - + -
182B VAL* 3.1 44.7 + - + +
183B ASP* 4.1 3.4 - - - +
185B TYR* 1.3 93.2 - + - +
187B ARG* 1.4 61.3 + - - +
189B GLN 3.6 14.2 - - - +
192B LEU* 3.8 31.4 - - + +
193B SER* 4.6 1.2 + - - -
195B MET* 3.8 34.3 - - + -
196B TYR* 3.5 27.9 - - + +
199B MET* 3.9 23.1 - - + -
223B ILE* 4.0 18.2 - - + -
246B PHE* 3.9 24.5 - + - -
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Residues in contact with ARG 187 (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 THR* 5.3 6.4 + - - -
96B GLN 4.3 15.8 + - - -
97B GLU* 4.8 19.4 + - - +
183B ASP* 3.0 45.3 + - - +
184B ILE* 3.8 7.4 - - - +
185B TYR 3.3 0.2 - - - -
186B PHE* 1.4 77.6 - - - +
188B ARG* 1.3 60.4 + - - +
189B GLN 4.8 1.2 - - - -
190B VAL* 5.1 1.7 + - - +
196B TYR* 3.0 44.4 + - + -
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Residues in contact with ARG 188 (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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267A GLY* 2.8 39.9 + - - -
268A ASP* 4.8 2.0 - - - +
129B ASN* 6.0 1.0 - - - +
131B GLU* 2.9 36.4 + - - +
184B ILE* 3.0 13.4 + - + +
185B TYR* 3.4 35.2 - - - +
187B ARG* 1.3 77.1 - - - +
189B GLN* 1.3 78.5 + - - +
190B VAL* 3.0 17.7 + - - +
247B PHE* 5.3 0.2 - - - -
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Residues in contact with GLN 189 (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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267A GLY 3.2 13.1 + - - +
268A ASP* 3.6 29.2 + - - +
185B TYR* 3.1 30.8 + - + +
186B PHE 3.6 5.4 - - - +
187B ARG 3.7 0.9 - - - -
188B ARG* 1.3 112.7 + - - +
190B VAL* 1.4 53.7 + - - +
191B GLU* 3.2 24.6 + - - +
192B LEU* 2.8 47.5 + - + +
193B SER* 3.6 3.5 + - - -
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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