Contacts of the helix formed by residues 178 - 189 (chain B) in PDB entry 4GTU
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B ASP 4.1 4.2 - - - +
176B ALA 3.8 7.0 - - - +
177B PHE* 1.3 86.9 - - - +
179B ASN* 1.3 59.4 + - + +
181B LYS* 3.7 15.4 - - + +
182B ASP* 3.0 36.0 + - - +
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Residues in contact with ASN 179 (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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138B SER* 2.9 47.6 + - - +
141B LEU* 3.5 25.7 - - - +
142B GLY* 3.3 22.7 + - - -
144B ARG 5.2 0.8 + - - -
177B PHE* 4.6 1.3 - - + -
178B PRO* 1.3 83.2 - - + +
180B LEU* 1.3 61.1 + - - +
182B ASP* 3.4 16.4 + - - +
183B PHE 3.4 8.3 + - - -
186B ARG* 5.4 1.1 + - - +
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Residues in contact with LEU 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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134B MET* 3.3 45.1 - - + +
137B PHE* 3.6 22.4 - - + +
138B SER* 3.1 30.3 + - - +
141B LEU* 4.2 6.1 - - + -
147B PHE* 3.9 17.5 - - + -
163B LEU* 4.4 12.2 - - + +
174B LEU* 4.2 15.7 - - + +
177B PHE* 3.0 16.9 + - + +
179B ASN* 1.3 77.2 - - - +
181B LYS* 1.3 63.1 + - - +
182B ASP 3.3 0.2 - - - -
183B PHE* 3.6 5.8 + - - +
184B ILE* 3.5 24.4 + - - +
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Residues in contact with LYS 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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174B LEU* 3.1 41.1 - - + +
175B ASP* 3.1 37.4 + - - +
177B PHE 3.3 4.5 - - - +
178B PRO* 3.7 12.6 - - + +
179B ASN 3.2 1.0 - - - -
180B LEU* 1.3 74.3 - - - +
182B ASP* 1.3 67.4 + - - +
184B ILE* 3.4 13.6 + - - +
185B SER* 3.1 14.3 + - - -
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Residues in contact with ASP 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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178B PRO 3.0 19.1 + - - +
179B ASN* 3.5 9.7 - - - +
181B LYS* 1.3 76.1 - - - +
183B PHE* 1.3 61.0 + - - +
185B SER* 2.8 32.1 + - - -
186B ARG* 3.3 24.5 + - - +
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Residues in contact with PHE 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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141B LEU* 3.8 17.5 - - + -
145B PRO 3.6 17.5 - - - -
146B TRP* 3.5 21.3 - + - -
147B PHE* 3.5 21.5 - + + -
156B ASP* 3.2 47.3 - - + -
159B ALA* 3.9 4.7 - - + -
160B TYR* 3.7 29.8 - - + -
163B LEU* 3.7 17.3 - - + -
179B ASN 3.4 3.6 + - - -
180B LEU* 3.6 10.3 - - - +
181B LYS 3.3 0.2 - - - -
182B ASP* 1.3 73.6 - - - +
184B ILE* 1.3 56.5 + - + +
185B SER 2.6 17.2 + - - -
186B ARG* 3.1 13.9 + - - +
187B PHE* 3.1 25.5 + + + +
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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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160B TYR* 3.3 32.3 - - + +
163B LEU* 3.6 31.2 - - + -
164B ASP 4.5 1.6 - - - +
167B ARG* 2.9 39.2 + - - +
174B LEU* 3.4 29.2 - - + -
180B LEU 3.5 11.9 + - - +
181B LYS* 3.4 8.8 + - - +
182B ASP 3.3 1.0 - - - -
183B PHE* 1.3 74.7 - - + +
185B SER* 1.3 59.8 + - - +
187B PHE 4.4 0.9 - - - -
188B GLU* 3.6 21.0 - - - +
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Residues in contact with SER 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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181B LYS 3.1 16.1 + - - -
182B ASP* 2.8 19.3 + - - -
183B PHE 2.6 7.3 + - - -
184B ILE* 1.3 75.7 + - - +
186B ARG* 1.3 67.4 + - - -
187B PHE 3.2 0.7 - - - -
188B GLU* 3.1 5.4 + - - +
189B GLY* 2.9 22.0 + - - -
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Residues in contact with ARG 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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141B LEU* 5.3 3.2 - - - +
144B ARG 4.8 1.0 + - - -
145B PRO* 3.2 53.0 + - + +
146B TRP* 3.7 27.4 - - + -
179B ASN* 6.0 1.0 - - - +
182B ASP* 3.3 26.5 + - - +
183B PHE* 3.1 18.1 + - - +
185B SER* 1.3 80.4 - - - +
187B PHE* 1.3 54.3 + - - +
188B GLU 2.7 12.5 + - - -
189B GLY* 3.1 10.8 + - - +
190B LEU* 3.3 18.6 + - + +
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Residues in contact with PHE 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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18B LEU* 4.1 19.5 - - + -
146B TRP* 3.5 24.9 - + + -
152B ILE* 3.7 20.4 - - + -
156B ASP 3.6 14.8 - - - -
157B PHE* 3.1 46.9 - + - -
160B TYR* 3.3 44.0 - + + -
183B PHE* 3.1 19.1 + + + +
184B ILE 4.8 0.2 - - - -
185B SER 4.4 0.4 - - - -
186B ARG* 1.3 75.6 - - - +
188B GLU* 1.3 66.8 + - - +
190B LEU* 4.4 12.6 - - + -
193B ILE* 4.3 16.5 - - + +
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Residues in contact with GLU 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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160B TYR* 2.9 25.8 + - + +
167B ARG* 3.8 13.8 + - - -
184B ILE* 3.6 27.7 - - - +
185B SER* 3.5 8.7 - - - +
186B ARG 2.7 2.6 + - - -
187B PHE* 1.3 81.6 - - - +
189B GLY* 1.3 61.3 + - - +
190B LEU 3.1 8.9 + - - +
193B ILE* 4.3 7.9 - - - +
194B SER* 3.7 24.8 + - - -
197B MET* 3.7 16.7 - - + +
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Residues in contact with GLY 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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185B SER 2.9 15.9 + - - -
186B ARG* 3.1 4.0 + - - -
188B GLU* 1.3 76.4 - - - +
190B LEU* 1.3 61.6 + - - +
191B GLU* 3.3 4.0 + - - -
194B SER* 4.8 4.0 + - - -
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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