Contacts of the helix formed by residues 176 - 186 (chain B) in PDB entry 4IX8
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 PRO 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLN* 3.4 19.7 - - - +
56B PRO* 4.4 15.0 - - + -
57B LEU* 4.5 24.0 - - + -
174B SER* 3.1 9.6 - - - +
175B PHE* 1.3 98.8 - - + +
177B HIS* 1.3 62.8 + - - +
178B TYR 3.1 0.7 - - - -
179B LYS* 3.1 13.2 + - + +
180B SER* 3.0 21.3 + - - -
191B TYR* 6.1 0.2 - - - +
225B ASN* 5.6 0.7 - - - +
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN 3.2 26.9 - - - -
320A LEU* 2.8 24.6 + - + -
322A ALA* 5.3 1.6 - - + -
55B GLN* 3.4 20.7 + - - +
151B SER* 3.6 34.2 + - - -
154B ILE* 4.0 10.8 - - + -
175B PHE* 3.0 31.8 + + + -
176B PRO* 1.3 79.6 - - - +
178B TYR* 1.3 57.2 + - - +
180B SER* 3.1 6.2 + - - -
181B VAL* 2.9 57.3 + - + +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.4 46.0 - - + +
158B LEU* 4.5 11.2 - - + +
168B ILE* 5.4 0.2 - - + -
170B VAL* 4.1 26.9 - - + -
174B SER* 5.8 0.4 - - - +
175B PHE* 3.5 22.4 - + - +
176B PRO 3.1 0.6 - - - -
177B HIS* 1.3 76.5 - - - +
179B LYS* 1.3 62.3 + - - +
181B VAL* 3.9 1.2 - - - +
182B CYS* 3.0 30.4 + - - -
189B CYS* 4.7 0.4 - - - -
219B VAL* 3.8 30.9 - - + +
221B ILE* 4.0 21.8 - - + -
251B ILE* 5.0 3.3 - - + +
253B ASP* 2.3 43.7 + - + +
281B LEU* 3.7 9.8 - - + +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 6.1 6.1 - - + -
174B SER* 5.9 1.3 - - - +
175B PHE 4.8 0.4 + - - -
176B PRO* 3.1 14.1 + - + +
178B TYR* 1.3 79.5 - - - +
180B SER* 1.3 63.2 + - - +
182B CYS* 3.2 2.9 + - - +
183B ASP* 3.0 54.3 + - - +
189B CYS* 3.9 33.0 + - + +
191B TYR* 3.8 32.7 - - + +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 6.5 0.7 - - - -
320A LEU* 4.6 5.3 - - - +
53B THR* 5.3 1.2 - - - +
54B LEU 2.8 31.1 + - - +
55B GLN* 3.4 33.7 + - - -
56B PRO* 4.0 4.0 - - - +
176B PRO 3.0 10.1 + - - -
177B HIS* 3.5 11.2 - - - -
179B LYS* 1.3 78.4 - - - +
181B VAL* 1.3 64.3 + - - +
183B ASP* 3.5 5.1 + - - +
184B SER* 3.1 24.7 + - - -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.2 8.3 - - + -
154B ILE* 4.2 5.8 - - + -
155B VAL* 4.0 26.5 - - + -
158B LEU* 3.9 25.8 - - + -
159B THR* 4.8 0.9 - - + -
177B HIS* 2.9 47.9 + - + +
178B TYR 3.9 2.9 - - - +
180B SER* 1.3 76.9 - - - +
182B CYS* 1.3 63.8 + - - +
184B SER* 3.2 5.1 + - - -
185B TYR* 3.1 43.2 + - + +
187B ILE* 5.7 0.9 - - + -
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Residues in contact with CYS 182 (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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158B LEU* 4.2 7.9 - - - -
168B ILE* 3.5 37.5 - - - -
178B TYR 3.0 23.5 + - - +
179B LYS 3.2 4.2 + - - +
181B VAL* 1.3 78.6 - - - +
183B ASP* 1.3 57.8 + - - +
185B TYR 3.3 1.6 + - - -
186B GLY 2.9 8.3 + - - -
187B ILE* 2.8 58.1 + - - +
189B CYS* 4.0 21.1 - - + +
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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
----------------------------------------------------------
52B ARG* 3.2 36.0 + - + +
54B LEU* 5.5 6.0 - - + +
179B LYS* 3.0 55.2 + - - +
180B SER* 4.0 5.3 - - - +
182B CYS* 1.3 78.3 - - - +
184B SER* 1.3 63.7 + - - +
185B TYR 3.3 0.3 + - - -
186B GLY* 3.4 5.8 + - - +
187B ILE 4.4 5.3 - - - +
188B GLU* 5.9 0.2 - - - -
189B CYS 5.3 1.9 + - - -
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 3.6 22.0 - - - +
49B HIS* 3.0 33.5 + - - -
52B ARG* 2.9 26.0 + - - +
53B THR* 2.5 30.6 + - - -
180B SER 3.1 19.7 + - - -
181B VAL 3.5 5.8 - - - -
182B CYS 3.2 0.2 - - - -
183B ASP* 1.3 75.7 - - - +
185B TYR* 1.3 59.8 + - - +
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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
----------------------------------------------------------
49A HIS* 4.9 9.2 - + - -
185A TYR* 4.6 20.6 + + - -
320A LEU* 3.9 18.0 - - + +
49B HIS* 3.9 20.5 + + - -
52B ARG* 3.5 10.9 + - - +
155B VAL* 3.8 17.3 - - + +
159B THR* 3.6 33.4 - - + -
164B GLU* 3.9 16.5 + - - +
181B VAL* 3.1 37.0 + - + +
184B SER* 1.3 86.1 - - - +
186B GLY* 1.3 62.1 + - - +
187B ILE* 3.2 20.2 + - + +
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 3.6 17.1 - - - +
164B GLU* 3.5 11.4 - - - +
165B GLY* 3.2 24.6 + - - -
182B CYS 2.9 4.3 + - - -
183B ASP* 3.4 9.6 + - - -
184B SER 3.5 0.4 - - - -
185B TYR* 1.3 77.9 - - - +
187B ILE* 1.3 62.2 + - - +
188B GLU 4.1 0.3 + - - -
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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