Contacts of the helix formed by residues 178 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A LEU 4.6 0.2 - - - -
176A ALA 3.5 11.4 - - - +
177A PHE* 1.3 82.5 - - - +
179A ASN* 1.3 65.4 + - + +
181A LYS* 3.0 17.8 + - + +
182A ASP* 2.9 36.2 + - - +
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER* 2.9 50.1 + - - +
141A LEU* 3.4 33.3 - - - +
142A GLY 2.9 24.3 + - - +
143A LYS* 4.9 0.5 - - - -
144A ARG 4.8 1.9 - - - +
177A PHE 4.6 0.7 - - - -
178A PRO* 1.3 83.8 - - + +
180A LEU* 1.3 60.4 + - - +
182A ASP* 3.7 6.0 + - - +
183A PHE 3.5 9.9 + - - -
186A ARG* 4.7 1.7 + - - -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A MET* 3.8 25.6 - - + +
137A PHE* 3.8 14.4 - - + +
138A SER* 3.7 28.3 - - - +
141A LEU* 4.4 3.8 - - + -
147A PHE* 4.0 18.6 - - + -
163A LEU* 4.2 10.8 - - + -
174A LEU* 3.6 28.3 - - + -
177A PHE* 2.9 29.9 + - + +
179A ASN* 1.3 76.4 - - - +
181A LYS* 1.3 65.9 - - - +
183A PHE* 3.1 21.6 + - - +
184A ILE* 3.1 12.9 + - - +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 5.3 4.4 - - - +
171A PRO 4.8 5.3 + - - -
174A LEU* 3.0 56.3 + - + +
175A ASP* 3.3 30.6 + - - +
177A PHE 3.4 3.8 + - - +
178A PRO* 3.0 18.5 + - + +
180A LEU* 1.3 77.4 - - - +
182A ASP* 1.3 65.3 + - - +
184A ILE* 3.0 16.4 + - - +
185A SER* 3.0 13.3 + - - -
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PRO* 2.9 32.7 + - - +
179A ASN* 4.1 6.7 - - - +
181A LYS* 1.3 75.9 - - - +
183A PHE* 1.3 53.0 + - - +
185A SER* 3.2 8.5 + - - +
186A ARG* 2.7 53.5 + - - +
188D GLU* 4.7 14.0 - - - +
189D GLY* 5.4 0.3 - - - -
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.5 24.2 - - + -
145A PRO 3.7 16.2 - - - -
146A TRP* 3.9 11.2 - + - -
147A PHE* 3.6 32.8 - + - -
156A ASP* 3.1 47.1 - - + -
159A ALA* 4.1 0.2 - - + -
160A TYR* 4.0 24.9 - - + -
163A LEU* 3.8 22.0 - - + -
179A ASN 3.5 2.6 + - - -
180A LEU 3.1 9.3 + - - +
182A ASP* 1.3 77.1 - - - +
184A ILE* 1.3 61.7 + - + +
186A ARG* 3.3 13.9 + - - +
187A PHE* 2.9 32.3 + + + +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.9 14.4 - - + -
163A LEU* 3.5 29.4 - - + -
164A ASP 4.8 0.2 - - - +
167A ARG* 3.1 43.5 - - - +
174A LEU* 3.2 30.5 - - + -
180A LEU 3.5 9.4 - - - +
181A LYS* 3.0 7.3 + - - +
183A PHE* 1.3 80.3 - - + +
185A SER* 1.3 64.6 + - - +
187A PHE* 3.0 10.1 + - - +
188A GLU* 2.9 37.4 + - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS 3.0 11.6 + - - -
182A ASP* 3.7 9.9 - - - -
184A ILE* 1.3 77.7 - - - +
186A ARG* 1.3 62.9 + - - +
188A GLU* 3.5 7.8 + - - +
189A GLY* 3.0 17.5 + - - -
185D SER* 2.7 37.3 + - - -
186D ARG* 3.5 12.3 - - - +
189D GLY* 3.5 11.9 - - - -
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.6 3.8 - - - +
144A ARG 4.0 5.7 + - - -
145A PRO* 3.2 48.5 + - - +
146A TRP* 4.2 21.1 - - + -
179A ASN* 4.7 1.2 + - - -
182A ASP* 2.7 33.3 + - - +
183A PHE* 3.4 29.0 - - - +
185A SER* 1.3 71.3 - - - +
187A PHE* 1.3 67.5 + - - +
189A GLY 2.9 11.4 + - - -
190A LEU* 3.3 12.1 + - - +
188D GLU 4.9 3.0 + - - +
189D GLY* 3.4 15.2 - - - +
191D GLU* 5.8 0.2 - - - -
194D SER* 4.2 24.2 - - - +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.4 5.6 - - + -
146A TRP* 4.2 17.6 - + + -
152A ILE* 4.4 5.6 - - + -
156A ASP* 4.0 11.0 - - + -
157A PHE* 3.3 61.0 - + - -
160A TYR* 3.3 48.2 - + + -
183A PHE* 2.9 16.6 + + + +
184A ILE* 3.0 12.1 + - - +
186A ARG* 1.3 78.3 - - - +
188A GLU* 1.3 62.0 + - - +
190A LEU* 3.2 30.8 + - + +
193A ILE* 3.5 26.5 - - + +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.5 30.6 + - + +
164A ASP* 4.8 4.3 - - - +
167A ARG* 4.6 6.4 + - - -
184A ILE* 2.9 29.4 + - - +
185A SER* 3.9 7.2 - - - +
187A PHE* 1.3 76.1 - - - +
189A GLY* 1.3 51.8 + - - +
190A LEU 3.2 1.3 + - - -
193A ILE* 4.1 7.1 - - - +
194A SER* 2.6 36.7 + - - -
197A MET* 3.6 27.8 - - - +
186D ARG* 6.1 0.7 - - - +
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A SER 3.0 8.1 + - - -
186A ARG 2.9 10.4 + - - -
188A GLU* 1.3 75.1 - - - +
190A LEU* 1.3 64.5 + - - +
191A GLU* 3.1 5.0 + - - +
194A SER* 3.7 7.1 + - - -
189D GLY 3.5 15.9 - - - -
190D LEU* 4.1 16.5 - - - +
191D GLU* 3.3 20.7 + - - +
192D LYS* 6.0 0.5 - - - +
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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