Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 1A4I
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 GLY 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL* 3.7 15.2 - - - +
172A GLY* 3.3 29.5 - - - +
173A ARG* 3.9 0.2 - - - -
174A SER* 3.4 9.2 + - - +
177A VAL* 1.3 81.1 - - - +
179A ALA* 1.3 63.3 + - - +
181A MET* 3.3 3.2 + - - +
182A HIS* 3.1 21.5 + - - +
194A THR* 5.4 0.7 + - - +
215A ALA* 4.7 3.7 - - - +
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Residues in contact with ALA 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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173A ARG* 3.6 20.0 - - + +
174A SER 2.9 21.5 + - - +
175A LYS* 6.0 0.2 - - + -
178A GLY* 1.3 69.0 - - - +
180A PRO* 1.3 65.6 - - + +
182A HIS* 3.2 16.9 + - - +
183A ASP* 3.3 14.6 + - - +
194A THR* 6.2 0.4 - - - -
136B ALA 4.3 6.1 - - - +
137B ARG* 3.7 29.3 + - - +
186B LEU* 5.7 4.3 - - + -
187B TRP* 4.9 4.3 - - + -
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Residues in contact with PRO 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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135A LEU* 3.7 19.8 - - + +
146A PRO* 3.8 12.8 - - + -
149A PRO* 3.6 20.9 - - + -
174A SER 3.3 11.9 - - - +
175A LYS 3.4 21.5 - - - +
176A ILE 3.9 2.9 - - - +
177A VAL 3.2 14.8 - - - +
179A ALA* 1.3 93.3 - - + +
181A MET* 1.4 54.6 + - - -
183A ASP* 3.2 3.4 + - - +
184A LEU* 2.9 31.2 + - - +
137B ARG* 3.5 17.0 - - - +
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Residues in contact with MET 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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149A PRO* 3.8 28.0 - - + +
152A CYS* 3.4 30.7 - - + -
153A LEU* 4.2 7.6 - - + +
156A ILE* 4.5 3.1 - - + -
170A VAL* 4.1 10.1 - - + -
177A VAL* 2.9 24.3 + - + +
178A GLY* 3.5 8.1 - - - +
179A ALA 3.2 0.2 - - - -
180A PRO* 1.4 72.3 - - - +
182A HIS* 1.3 67.1 + - - +
184A LEU* 3.3 11.7 + - + +
185A LEU* 3.0 45.9 + - + +
213A VAL* 3.9 33.0 - - + -
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Residues in contact with HIS 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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170A VAL* 4.1 10.5 - - + +
178A GLY 3.1 12.7 + - - +
179A ALA* 3.4 10.9 + - - +
181A MET* 1.3 77.8 - - - +
183A ASP* 1.3 72.9 + - - +
185A LEU* 3.3 2.3 + - - +
186A LEU* 2.9 50.7 + - + +
192A VAL* 3.4 34.4 + - + +
194A THR* 3.3 28.7 - - + +
182B HIS* 3.4 40.9 + + - -
194B THR* 3.9 10.0 + - - -
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Residues in contact with ASP 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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135A LEU* 3.6 23.8 - - + +
136A ALA* 3.4 24.4 - - - +
179A ALA 3.6 5.9 - - - +
180A PRO 3.2 7.1 + - - +
182A HIS* 1.3 98.5 + - - +
184A LEU* 1.4 63.5 + - - +
186A LEU* 3.2 2.9 + - - +
187A TRP* 2.9 34.5 + - + +
136B ALA* 5.8 0.2 - - - +
137B ARG* 2.8 39.3 + - - -
182B HIS* 5.3 2.1 - - - -
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Residues in contact with LEU 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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135A LEU* 4.1 10.3 - - + -
140A LEU* 5.4 7.4 - - + -
145A ILE* 3.8 40.2 - - + -
149A PRO* 3.4 44.0 - - + +
150A LYS* 3.9 2.7 - - + +
153A LEU* 4.0 30.3 - - + -
180A PRO 2.9 14.5 + - - +
181A MET* 3.3 13.0 + - + +
183A ASP* 1.4 75.8 - - - +
185A LEU* 1.3 63.1 + - - +
187A TRP* 3.5 2.3 + - - +
188A ASN* 2.8 33.9 + - - +
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Residues in contact with LEU 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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153A LEU* 4.7 2.7 - - + -
156A ILE* 4.0 23.3 - - + -
163A ILE* 4.3 23.6 - - + -
168A ALA* 3.9 15.7 - - + -
169A VAL 5.5 0.2 - - - +
170A VAL* 3.7 29.8 - - + -
181A MET* 3.0 31.6 + - + +
182A HIS 3.7 3.4 - - - +
184A LEU* 1.3 72.3 - - - +
186A LEU* 1.4 67.0 + - - +
188A ASN* 3.1 12.1 + - - +
189A ASN 3.2 0.3 + - - -
190A ALA* 3.0 22.8 + - + +
192A VAL* 3.8 12.8 - - + -
211A ILE* 4.4 10.8 - - + -
213A VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 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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136A ALA 5.7 0.9 - - - +
182A HIS* 2.9 37.4 + - + +
183A ASP* 3.2 5.8 + - - +
185A LEU* 1.4 77.2 - - - +
187A TRP* 1.4 83.5 + - + +
189A ASN* 2.8 13.3 + - - -
190A ALA 3.8 7.2 - - - +
192A VAL* 3.6 11.3 - - + +
173B ARG* 2.8 34.3 + - + -
179B ALA* 6.0 3.1 - - + -
194B THR* 3.4 38.6 - - + +
196B HIS* 3.6 23.1 - - + -
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Residues in contact with TRP 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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135A LEU* 3.4 21.9 + - + -
136A ALA* 3.8 9.8 + - - +
137A ARG* 3.7 22.2 - - - -
138A GLY* 3.3 27.4 - - - +
140A LEU* 4.1 25.0 - - + +
183A ASP* 2.9 33.0 + - - +
184A LEU* 3.8 3.1 - - - +
186A LEU* 1.4 96.1 - - + +
188A ASN* 1.3 59.6 + - - +
189A ASN* 3.2 9.8 + - - +
173B ARG* 3.5 58.1 - - + +
179B ALA* 5.0 2.2 - - + -
302B NDP 5.1 1.8 - - - -
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Residues in contact with ASN 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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140A LEU* 5.3 6.3 - - - +
153A LEU* 3.9 25.2 - - - +
157A LYS* 4.4 13.9 + - - -
163A ILE* 3.6 25.3 - - + +
164A ALA* 3.6 17.5 + - - +
184A LEU* 2.8 33.9 + - - +
185A LEU* 3.1 5.1 + - - +
187A TRP* 1.3 78.6 - - - +
189A ASN* 1.3 69.2 + - - +
190A ALA 3.3 3.4 + - - -
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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