Contacts of the helix formed by residues 180 - 193 (chain A) in PDB entry 3I0W
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 ARG 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.4 22.4 - - + +
124A ILE* 3.2 24.1 + - - +
126A ALA* 2.9 20.8 + - + -
127A ASN 2.9 27.3 + - - -
128A ASN* 3.5 21.0 - - - +
176A THR 5.5 0.2 + - - -
177A ALA* 2.9 31.0 + - + +
178A GLY 3.0 0.8 - - - -
179A PHE* 1.3 102.1 - - + +
181A ALA* 1.3 65.6 + - - +
182A LYS 3.2 1.3 - - - -
183A TYR* 3.0 29.1 + - + +
184A LEU* 3.0 17.6 + - + +
9C C 3.0 35.4 + - - -
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Residues in contact with ALA 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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169A GLU* 3.6 19.5 - - + +
172A PHE* 3.7 20.8 - - + -
173A GLU* 3.5 26.9 - - + +
177A ALA* 3.9 5.8 - - + +
178A GLY 3.1 15.6 + - - +
179A PHE 3.1 0.6 - - - -
180A ARG* 1.3 77.9 - - - +
182A LYS* 1.3 62.5 + - - +
184A LEU* 3.3 4.2 + - - +
185A LYS* 3.0 23.9 + - - +
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Residues in contact with LYS 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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169A GLU* 3.8 30.2 + - - +
179A PHE* 2.7 42.3 + - - +
181A ALA* 1.3 78.4 - - - +
183A TYR* 1.3 88.8 + - + +
185A LYS* 3.5 4.0 + - - +
186A ASP* 3.0 29.6 + - - +
217A MET* 5.1 7.2 - - + +
8C C 6.1 0.6 - - - -
9C C 3.9 10.9 + - - -
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Residues in contact with TYR 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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123A ILE* 4.0 11.9 - - + -
179A PHE* 4.2 25.6 - + - -
180A ARG* 3.0 24.9 + - + +
182A LYS* 1.3 100.1 - - + +
184A LEU* 1.3 60.5 + - - +
186A ASP* 3.5 1.6 + - - +
187A THR* 2.8 34.8 + - - -
217A MET* 3.4 49.3 - - + +
218A GLY* 3.6 17.9 - - - -
20B G 5.8 0.4 + - - -
21B T 4.7 9.2 + - - -
22B C 3.2 37.7 + - - -
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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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120A LEU* 3.7 39.7 - - + +
123A ILE* 3.7 23.8 - - + -
124A ILE* 3.9 18.4 - - + -
140A ILE* 4.6 1.8 - - + -
172A PHE* 3.7 32.1 - - + -
177A ALA* 3.6 31.6 - - + -
180A ARG* 3.0 13.9 + - + +
181A ALA 3.3 4.9 + - - +
183A TYR* 1.3 76.6 - - - +
185A LYS* 1.3 56.9 + - - +
187A THR* 3.7 3.7 - - - -
188A VAL* 2.9 35.0 + - - +
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Residues in contact with LYS 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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164A LEU 5.8 1.1 - - - +
165A HIS* 5.0 5.6 - - - +
167A PHE 3.2 29.2 - - - +
168A THR* 4.2 9.2 - - - +
169A GLU* 4.5 13.7 - - + +
172A PHE* 3.7 15.0 - - + -
181A ALA 3.0 17.4 + - - +
182A LYS* 3.8 7.2 - - - +
184A LEU* 1.3 77.3 - - - +
186A ASP* 1.3 63.4 + - - +
188A VAL* 3.4 2.7 + - + +
189A ASP* 3.0 57.8 + - - +
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Residues in contact with ASP 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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182A LYS 3.0 19.3 + - - +
183A TYR 3.8 2.9 - - - +
185A LYS* 1.3 76.0 - - - +
187A THR* 1.3 63.1 + - - +
189A ASP* 3.3 12.0 + - - +
190A ARG* 3.1 54.9 + - - +
217A MET* 3.1 42.7 + - + +
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Residues in contact with THR 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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119A LEU* 3.6 26.2 - - + -
120A LEU* 3.9 12.8 - - + -
123A ILE* 3.5 10.8 - - + +
183A TYR 2.8 21.4 + - - -
184A LEU* 3.7 4.3 - - - -
185A LYS 3.3 0.2 - - - -
186A ASP* 1.3 75.2 - - - +
188A VAL* 1.3 66.7 + - - +
190A ARG* 3.2 5.4 + - - +
191A ILE* 3.1 22.6 + - + +
216A PHE* 3.5 30.0 - - + +
217A MET 3.4 18.4 + - - -
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Residues in contact with VAL 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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116A PHE* 4.3 9.4 - - + -
120A LEU* 4.0 29.6 - - + -
161A VAL* 4.2 7.0 - - + +
164A LEU* 3.7 11.7 - - + +
165A HIS* 3.6 38.1 - - + +
172A PHE* 4.2 14.1 - - + -
184A LEU 2.9 21.3 + - - +
185A LYS* 4.0 5.8 - - + +
187A THR* 1.3 75.7 - - - +
189A ASP* 1.3 57.3 + - - +
191A ILE* 3.2 7.1 + - - +
192A TYR* 2.8 28.1 + - - +
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Residues in contact with ASP 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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165A HIS* 3.4 28.6 + - - +
185A LYS* 3.0 58.2 + - - +
186A ASP* 3.4 13.5 - - - +
188A VAL* 1.3 77.1 - - - +
190A ARG* 1.3 59.0 + - + +
192A TYR* 3.3 2.6 + - - +
193A ASN* 2.8 39.9 + - - +
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Residues in contact with ARG 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 ASP* 3.1 41.3 + - - +
187A THR* 3.2 7.6 + - - +
189A ASP* 1.3 75.0 - - + +
191A ILE* 1.3 63.5 + - - +
193A ASN* 3.1 9.3 - - - +
194A GLY 3.4 0.3 + - - -
195A GLU* 2.6 68.7 + - + +
196A LEU* 3.3 26.8 + - + +
215A LYS* 2.8 37.6 + - - +
216A PHE* 4.0 15.2 - - + +
217A MET* 4.1 7.1 - - - +
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Residues in contact with ILE 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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116A PHE* 4.3 19.5 - - + -
119A LEU* 4.1 5.6 - - + -
161A VAL* 3.9 27.8 - - + -
187A THR 3.1 15.7 + - - +
188A VAL* 3.6 7.6 - - - +
190A ARG* 1.3 74.7 - - - +
192A TYR* 1.3 67.3 + - - +
194A GLY* 3.2 12.6 + - - -
196A LEU 3.8 12.4 - - - +
198A LEU* 3.7 29.6 - - + +
216A PHE* 3.6 30.7 - - + -
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Residues in contact with TYR 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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161A VAL* 4.2 14.4 - - + -
162A ASP* 3.4 28.4 - - - -
165A HIS* 3.3 59.1 - + + -
188A VAL 2.8 16.7 + - - +
189A ASP 3.6 4.3 - - - +
191A ILE* 1.3 80.0 - - - +
193A ASN* 1.3 67.2 + - + +
194A GLY 3.3 0.7 + - - -
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Residues in contact with ASN 193 (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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189A ASP* 2.8 27.8 + - - +
190A ARG* 3.1 10.9 - - - +
192A TYR* 1.3 81.7 - - + +
194A GLY* 1.3 59.8 + - - +
195A GLU* 3.0 28.6 + - - +
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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