Contacts of the helix formed by residues 177 - 190 (chain B) in PDB entry 4IYM
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 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.8 13.6 - - + +
21B ILE* 3.7 14.8 - - + -
33B VAL* 3.8 24.0 - - + -
88B GLU* 3.6 4.5 - - - +
173B SER 3.8 9.9 - - - +
174B GLU* 3.7 16.8 - - - +
175B ARG 3.8 0.7 - - - -
176B ASP* 1.4 87.6 - - - +
178B SER* 1.3 65.5 + - - +
179B VAL 3.5 1.3 - - - -
180B PRO* 3.3 16.7 - - + +
181B ILE* 3.6 13.9 + - - +
201B ASN* 3.4 27.8 + - - +
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Residues in contact with SER 178 (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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0B TYR* 3.7 9.7 + - - -
2B LEU* 3.5 19.7 - - - +
10B ARG* 5.6 1.0 + - - -
84B MSE 3.8 26.6 - - - +
87B ARG* 5.3 2.3 + - - -
88B GLU* 2.6 34.6 + - - -
176B ASP 3.5 0.2 - - - -
177B PRO* 1.3 79.2 - - - +
179B VAL* 1.3 64.3 + - - +
181B ILE* 3.4 4.1 + - - +
182B ARG* 3.2 20.3 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.6 17.7 - - + +
84B MSE 3.5 28.7 - - + -
85B LEU* 3.7 24.7 - - + +
88B GLU* 4.5 1.2 + - - -
100B ILE* 4.3 9.2 - - + -
150B PRO* 3.4 24.9 - - + +
151B GLY* 3.8 15.3 - - - +
176B ASP 4.6 0.8 + - - +
178B SER* 1.3 75.0 - - - +
180B PRO* 1.4 62.4 - - + +
182B ARG* 3.0 5.0 + - - +
183B LEU* 2.8 39.7 + - + +
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Residues in contact with PRO 180 (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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150B PRO* 3.6 22.7 - - + +
154B PRO* 4.8 0.9 - - + -
170B LEU* 3.8 17.5 - - + +
172B PRO* 3.6 38.8 - - + -
176B ASP 3.9 6.3 - - - +
177B PRO* 3.3 18.2 - - + +
179B VAL* 1.4 94.5 - - + +
181B ILE* 1.3 62.0 + - - +
183B LEU* 3.4 9.0 + - + +
184B ALA 3.2 17.0 + - - -
197B LEU* 5.9 0.2 - - - +
199B VAL* 3.8 13.5 - - + +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.1 25.4 - - + -
3B GLY 3.8 15.3 - - - +
4B HIS 4.8 2.2 - - - +
5B PHE* 4.2 23.2 - - + +
10B ARG* 3.4 38.6 - - + +
177B PRO 3.6 8.4 + - - +
178B SER* 3.4 7.6 + - - +
179B VAL 3.3 0.8 - - - -
180B PRO* 1.3 78.0 - - - +
182B ARG* 1.3 57.4 + - - +
184B ALA* 3.1 5.6 + - - +
185B GLU* 3.0 25.6 + - - +
199B VAL* 4.3 14.4 - - + -
201B ASN* 3.6 28.5 - - - +
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Residues in contact with ARG 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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10B ARG* 4.2 10.5 - - - +
77B ASN* 3.3 22.2 + - - +
80B GLU* 3.0 26.4 + - - +
81B LEU* 3.7 19.5 - - + -
84B MSE 3.9 18.4 - - - -
178B SER 3.2 10.3 + - - +
179B VAL 3.0 8.8 + - - +
181B ILE* 1.3 78.9 - - - +
183B LEU* 1.3 56.9 + - - +
185B GLU* 2.7 50.8 + - - +
186B LEU* 2.9 52.1 + - + +
189B GLU* 4.9 6.3 + - - -
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Residues in contact with LEU 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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70B PHE* 3.5 15.2 - - + -
74B LEU* 3.8 28.5 - - + -
81B LEU* 4.2 19.1 - - + -
100B ILE* 5.2 0.4 - - + -
150B PRO 4.2 4.3 - - - +
151B GLY* 4.0 20.4 - - - +
154B PRO* 4.6 3.4 - - + -
155B MSE 4.1 22.4 - - + -
158B PHE* 4.4 13.9 - - + -
179B VAL* 2.8 33.3 + - + +
180B PRO* 3.7 10.8 - - + +
181B ILE 3.3 0.2 - - - -
182B ARG* 1.3 73.5 - - - +
184B ALA* 1.3 59.4 + - - +
186B LEU* 3.2 5.3 + - + +
187B MSE 2.9 27.4 + - - +
197B LEU* 4.7 0.9 - - + -
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.5 29.1 - - + -
180B PRO 3.2 2.0 + - - -
181B ILE 3.1 9.2 + - - +
183B LEU* 1.3 78.2 - - - +
185B GLU* 1.3 62.5 + - - +
187B MSE 3.3 4.3 + - - +
188B ILE* 3.2 25.1 + - - +
197B LEU* 3.8 25.6 - - + +
199B VAL* 3.7 24.7 - - + -
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Residues in contact with GLU 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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5B PHE* 3.9 19.9 - - + -
10B ARG* 2.7 50.9 + - - +
181B ILE 3.0 11.2 + - - +
182B ARG* 2.7 39.4 + - - +
184B ALA* 1.3 78.0 - - - +
186B LEU* 1.3 56.8 + - - +
188B ILE* 3.3 7.8 + - + +
189B GLU* 3.1 23.6 + - - +
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Residues in contact with LEU 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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70B PHE* 3.7 17.2 - - + -
73B LEU* 3.5 18.4 - - + +
74B LEU* 4.4 10.5 - - + -
77B ASN* 3.6 32.1 - - + +
81B LEU* 4.3 21.8 - - + -
182B ARG* 2.9 51.8 + - + +
183B LEU* 3.2 2.0 + - - +
185B GLU* 1.3 73.2 - - - +
187B MSE 1.3 60.9 + - - +
189B GLU* 3.3 21.7 + - - +
190B ALA* 2.8 28.8 + - - +
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Residues in contact with MSE 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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66B VAL* 4.2 10.5 - - + -
67B PHE* 3.6 31.0 - - + -
70B PHE* 3.4 45.5 - - + -
158B PHE* 4.2 5.8 - - + -
162B ILE* 4.1 10.3 - - + -
183B LEU 2.9 17.1 + - - +
184B ALA 3.6 8.5 - - - +
185B GLU 3.3 0.2 - - - -
186B LEU* 1.3 73.4 - - - +
188B ILE* 1.3 64.4 + - - +
190B ALA* 3.1 10.1 + - - +
191B GLY 3.3 0.3 + - - -
192B LEU* 2.9 69.5 + - + +
197B LEU* 3.7 17.7 - - + -
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Residues in contact with ILE 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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5B PHE* 3.7 21.5 - - + -
8B GLY* 3.6 28.7 - - - +
184B ALA 3.2 14.4 + - - +
185B GLU* 3.4 8.3 - - + +
186B LEU 3.3 0.2 - - - -
187B MSE 1.3 75.6 - - - +
189B GLU* 1.3 59.4 + - - +
191B GLY* 3.0 20.6 + - - -
192B LEU* 3.6 24.4 + - + +
193B PRO 4.2 2.7 - - - +
194B ALA* 3.9 16.4 - - + +
195B GLY 5.2 0.4 - - - +
197B LEU 5.7 2.7 - - - +
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Residues in contact with GLU 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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69B LYS* 4.9 6.2 + - - +
73B LEU* 3.5 30.1 - - + +
77B ASN* 5.4 0.7 + - - -
182B ARG* 4.9 6.4 + - - -
185B GLU 3.1 12.9 + - - +
186B LEU* 3.3 23.6 + - - +
188B ILE* 1.3 77.7 - - - +
190B ALA* 1.3 59.8 + - - +
191B GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 190 (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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66B VAL* 3.6 33.7 - - + +
69B LYS* 3.8 19.5 - - + +
70B PHE* 3.7 24.5 - - + +
73B LEU* 3.5 7.6 - - + +
186B LEU 2.8 19.7 + - - +
187B MSE 3.1 9.1 + - - +
189B GLU* 1.3 71.8 - - - +
191B GLY* 1.3 58.4 + - - +
192B LEU 3.6 0.4 - - - -
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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