Contacts of the helix formed by residues 178 - 192 (chain A) in PDB entry 1IL0
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP* 2.7 24.3 + - - +
153A ARG* 5.4 0.3 - - - +
173A LYS* 4.2 1.5 - - - -
176A MET 3.4 2.3 + - - -
177A THR* 1.3 80.7 - - - +
179A GLN* 1.3 65.0 + - - +
180A LYS* 3.9 10.2 + - - +
181A THR* 2.7 33.3 + - - -
182A PHE* 3.1 19.1 + - - +
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Residues in contact with GLN 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 LYS* 2.6 35.7 + - - +
177A THR 4.1 0.4 + - - -
178A SER* 1.3 73.2 - - - +
180A LYS* 1.3 54.4 + - + +
182A PHE* 3.1 30.6 - - - +
183A GLU* 2.8 57.1 + - - +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.9 36.8 - - + +
178A SER* 3.2 8.7 - - - +
179A GLN* 1.3 76.9 - - + +
181A THR* 1.3 65.7 + - - +
183A GLU* 3.3 12.8 + - - +
184A SER* 2.9 28.0 + - - -
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Residues in contact with THR 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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131A ILE* 3.9 35.7 - - + +
152A ASP 2.5 23.8 + - - -
153A ARG* 3.4 21.6 - - - +
155A ALA* 4.4 2.0 - - + -
177A THR* 3.8 15.5 - - + -
178A SER* 2.7 17.1 + - - -
180A LYS* 1.3 77.3 - - - +
182A PHE* 1.3 63.4 + - - +
184A SER* 3.2 4.0 + - - -
185A LEU* 3.0 31.8 + - + +
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Residues in contact with PHE 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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171A VAL* 3.5 31.9 - - + -
173A LYS* 3.2 39.5 - - + -
177A THR* 4.8 2.0 - - + -
178A SER 3.1 4.4 + - - +
179A GLN* 3.1 32.1 - - - +
181A THR* 1.3 80.1 - - - +
183A GLU* 1.3 61.6 + - + +
185A LEU* 3.1 9.1 + - - +
186A VAL* 2.8 49.6 + - + +
198A SER* 3.7 34.5 - - - -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 2.9 31.9 + - + +
179A GLN* 2.8 48.0 + - - +
180A LYS* 3.3 8.5 + - - +
182A PHE* 1.3 76.2 - - + +
184A SER* 1.3 53.9 + - - +
186A VAL* 3.1 8.2 + - - +
187A ASP* 2.6 40.0 + - - +
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Residues in contact with SER 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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12A LYS* 3.8 3.8 - - - +
13A ILE* 2.9 40.3 + - - +
15A VAL* 4.4 7.9 + - - +
131A ILE* 3.7 19.9 - - - +
180A LYS 2.9 14.4 + - - -
181A THR 3.4 8.5 - - - -
182A PHE 3.2 0.2 - - - -
183A GLU* 1.3 75.9 - - - +
185A LEU* 1.3 59.1 + - - +
187A ASP* 3.4 7.8 + - - +
188A PHE* 2.9 31.4 + - - +
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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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15A VAL* 5.3 1.6 - - + -
103A LEU* 3.8 37.0 - - + -
131A ILE* 4.3 11.2 - - + -
133A ALA* 4.8 6.5 - - + -
155A ALA* 3.6 31.2 - - + -
156A GLY 4.7 5.2 - - - +
157A LEU* 4.3 20.3 - - + +
171A VAL* 4.1 19.3 - - + -
181A THR* 3.0 24.2 + - + +
182A PHE* 3.6 7.4 - - - +
184A SER* 1.3 73.5 - - - +
186A VAL* 1.3 56.3 + - - +
188A PHE* 3.9 5.1 - - + +
189A SER* 2.6 38.1 + - - -
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Residues in contact with VAL 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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171A VAL* 4.5 9.2 - - + -
182A PHE* 2.8 51.4 + - + +
183A GLU* 3.4 11.7 - - - +
185A LEU* 1.3 76.5 - - - +
187A ASP* 1.3 69.4 + - - +
189A SER* 3.3 7.4 + - - -
190A LYS* 3.0 45.3 + - + +
196A PRO* 4.3 10.3 - - + +
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Residues in contact with ASP 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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12A LYS* 2.4 37.4 + - - -
13A ILE 5.5 0.2 - - - +
183A GLU* 2.6 17.9 + - - +
184A SER* 3.8 5.2 + - - +
186A VAL* 1.3 75.0 - - - +
188A PHE* 1.3 62.0 + - - +
190A LYS* 3.2 11.4 + - - +
191A ALA* 2.8 30.1 + - - +
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Residues in contact with PHE 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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15A VAL* 3.4 37.2 - - + -
18A VAL* 3.8 21.3 - - + -
30A ILE* 5.7 3.4 - - + -
34A ALA* 4.4 5.2 - - + -
39A HIS* 3.7 26.5 - + - -
103A LEU* 3.5 24.0 - - + -
105A VAL* 4.8 4.0 - - + -
157A LEU* 4.2 18.8 - - + -
159A PHE* 4.9 1.3 - + - -
184A SER 2.9 17.7 + - - +
185A LEU* 3.9 6.7 - - + +
187A ASP* 1.3 76.8 - - - +
189A SER* 1.3 65.2 + - - +
191A ALA* 3.0 8.1 + - - +
192A LEU* 2.9 59.8 + - + +
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Residues in contact with SER 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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157A LEU* 3.9 8.3 - - - +
169A VAL* 3.8 23.9 - - - +
171A VAL* 4.0 4.3 - - - +
185A LEU 2.6 23.6 + - - -
186A VAL 3.3 5.4 - - - -
188A PHE* 1.3 77.7 - - - +
190A LYS* 1.3 62.4 + - - +
192A LEU* 3.1 24.2 + - - +
194A LYS* 3.2 20.6 + - - +
196A PRO* 3.6 22.7 - - - -
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Residues in contact with LYS 190 (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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186A VAL* 3.0 27.5 + - + +
187A ASP* 3.5 12.3 - - - +
188A PHE 3.2 0.2 - - - -
189A SER* 1.3 73.4 - - - +
191A ALA* 1.3 54.0 + - - +
192A LEU 2.9 4.7 - - - -
193A GLY* 2.6 27.7 + - - -
194A LYS 4.1 8.5 - - - +
196A PRO* 3.9 25.8 - - + -
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Residues in contact with ALA 191 (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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37A THR* 3.3 21.7 - - - +
39A HIS* 3.8 21.7 - - + +
187A ASP 2.8 16.6 + - - +
188A PHE* 3.0 10.7 + - - +
190A LYS* 1.3 72.3 - - - +
192A LEU* 1.3 58.8 + - - +
193A GLY 3.1 1.5 + - - -
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Residues in contact with LEU 192 (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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30A ILE* 5.5 2.9 - - + -
33A VAL* 3.5 22.8 - - + +
34A ALA* 3.5 36.6 - - + +
37A THR* 3.6 18.0 - - - +
39A HIS* 4.0 1.8 - - + -
159A PHE* 3.6 37.2 - - + -
188A PHE* 2.9 47.5 + - + +
189A SER* 3.2 15.7 - - - +
190A LYS 2.9 0.6 - - - -
191A ALA* 1.3 77.3 - - - +
193A GLY* 1.3 60.4 + - - +
194A LYS* 3.6 10.8 + - + +
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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