Contacts of the helix formed by residues 168 - 180 (chain A) in PDB entry 5W4A
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 LEU 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.8 30.7 - - + -
15A ARG* 3.9 9.0 - - + +
16A THR* 3.7 16.4 - - - +
17A TYR* 3.5 39.3 - - + +
140A ILE* 4.4 3.1 - - + -
163A LEU* 3.0 45.9 + - + +
166A LEU* 3.1 21.7 - - + +
167A ASP* 1.3 74.8 - - - +
169A ASP* 1.3 63.9 + - - +
170A PHE 3.1 3.8 - - - +
171A ASP* 3.0 19.0 + - - +
172A ALA 3.1 9.0 + - - -
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Residues in contact with ASP 169 (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 CYS* 3.3 28.1 - - - +
167A ASP* 3.3 14.3 + - - +
168A LEU* 1.3 76.9 - - - +
170A PHE* 1.3 62.5 - - - +
172A ALA* 3.3 0.6 + - - -
173A TYR* 2.9 24.8 + - - +
193A ILE* 3.6 19.4 - - - +
196A ASN* 2.9 37.0 + - + +
197A PHE* 4.0 11.0 - - + +
134C LYS* 2.8 27.3 + - - -
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Residues in contact with PHE 170 (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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14A ILE* 3.5 23.1 - - + -
15A ARG 3.6 14.8 + - - +
16A THR* 3.9 8.7 - - - -
19A PHE* 4.0 21.8 - - + -
22A LEU* 4.0 14.8 - - + -
23A ALA* 4.6 4.0 - - + -
47A VAL* 4.4 4.7 - - + -
48A PHE* 3.9 20.6 - + - -
167A ASP 5.2 0.4 + - - -
168A LEU* 3.1 0.8 - - - +
169A ASP* 1.3 79.0 - - - +
171A ASP* 1.3 70.1 + - - +
173A TYR* 3.2 6.0 + + + +
174A VAL* 2.9 56.8 + - + +
197A PHE* 3.3 53.3 - + + +
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Residues in contact with ASP 171 (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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16A THR* 2.6 30.8 + - - -
17A TYR* 2.8 25.3 + - - +
18A PHE* 3.0 24.9 + - + -
19A PHE* 3.5 17.9 - - + -
163A LEU* 4.1 13.7 - - + -
168A LEU* 3.0 16.1 + - + +
170A PHE* 1.3 78.6 - - - +
172A ALA* 1.3 62.8 + - - +
174A VAL* 3.2 1.6 + - - +
175A PHE* 2.9 32.8 + - + -
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Residues in contact with ALA 172 (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 PHE* 6.4 0.2 - - + -
160A LEU* 3.9 25.5 - - + +
161A SER* 4.8 0.2 - - - -
163A LEU* 4.0 8.8 - - + +
164A CYS* 4.1 13.0 - - - -
168A LEU 3.1 10.8 + - - +
169A ASP 3.3 6.7 + - - +
171A ASP* 1.3 74.6 - - - +
173A TYR* 1.3 58.5 + - - +
175A PHE* 3.5 4.8 + - - +
176A THR* 2.9 33.2 + - - -
193A ILE* 3.9 20.0 - - + -
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Residues in contact with TYR 173 (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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47A VAL* 3.7 28.7 + - + -
169A ASP 2.9 17.5 + - - +
170A PHE* 3.4 7.4 - + - +
172A ALA* 1.3 74.7 - - - +
174A VAL* 1.3 68.6 + - + +
176A THR* 3.2 7.1 + - + -
177A LYS* 2.9 52.1 + - + +
182A GLU* 5.9 0.2 - - - -
190A VAL* 4.6 11.9 - - + -
193A ILE* 3.9 8.9 - - + +
194A ARG* 3.2 68.5 + - + -
197A PHE* 4.7 16.4 - + + -
212A ILE* 3.9 18.2 + - + +
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Residues in contact with VAL 174 (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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19A PHE* 3.4 39.9 - - + -
22A LEU* 3.9 5.2 - - + -
43A PHE* 4.0 20.6 - - + -
47A VAL* 3.8 16.6 - - + -
170A PHE* 2.9 55.4 + - + +
171A ASP 3.2 0.2 + - - -
173A TYR* 1.3 76.9 - - + +
175A PHE* 1.3 64.0 + - - +
177A LYS* 3.1 6.7 + - - +
178A ILE* 2.9 25.3 + - + +
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Residues in contact with PHE 175 (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 PHE* 3.7 39.3 - + - -
19A PHE* 3.7 24.0 - + - -
80A THR* 4.2 3.1 - - + -
83A ALA* 3.5 31.2 - - + -
84A LEU* 3.8 28.0 - - + -
160A LEU* 3.8 38.4 - - + -
163A LEU* 4.2 3.6 - - + -
171A ASP* 2.9 27.4 + - + +
172A ALA* 3.9 4.0 - - - +
174A VAL* 1.3 77.5 - - - +
176A THR* 1.3 58.3 + - - +
178A ILE* 4.8 2.5 - - - -
179A LEU* 2.9 45.6 + - + +
181A LEU* 4.4 1.3 - - - -
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Residues in contact with THR 176 (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 PHE* 3.5 22.3 - - - -
160A LEU* 6.2 0.3 - - - +
172A ALA 2.9 22.3 + - - -
173A TYR* 3.2 9.6 + - + +
175A PHE* 1.3 75.5 - - - +
177A LYS* 1.3 66.1 + - + +
180A GLY* 3.1 4.3 + - - -
181A LEU* 3.0 35.9 + - + +
182A GLU* 3.9 19.7 + - + +
190A VAL* 3.7 37.0 - - + -
193A ILE* 5.1 2.1 - - - +
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Residues in contact with LYS 177 (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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46A TYR* 3.6 69.5 + - + -
47A VAL* 4.4 11.6 + - + +
49A GLY* 5.2 5.7 - - - -
51A SER 5.8 0.4 + - - -
173A TYR* 2.9 53.8 + - + +
174A VAL* 3.6 8.5 - - - +
176A THR* 1.3 80.9 - - + +
178A ILE* 1.3 64.7 + - + +
180A GLY* 3.5 7.6 + - - -
182A GLU* 5.4 7.4 - - - +
194A ARG* 5.5 0.4 - - - +
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Residues in contact with ILE 178 (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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19A PHE* 5.9 0.4 - - + -
43A PHE* 3.5 35.4 - - + -
46A TYR* 4.2 13.5 - - + -
47A VAL* 4.6 3.6 - - + -
55A PRO* 3.6 26.7 - - + -
60A ILE* 4.0 19.1 - - + -
84A LEU* 4.0 26.2 - - + -
88A PHE* 5.6 2.7 - - + -
174A VAL* 2.9 24.0 + - + +
175A PHE 4.2 1.6 - - - +
177A LYS* 1.3 77.6 - - - +
179A LEU* 1.3 64.2 + - + +
180A GLY 3.6 0.7 + - - -
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Residues in contact with LEU 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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83A ALA 4.0 18.8 - - - +
84A LEU* 3.4 38.8 - - + +
88A PHE* 5.6 2.9 - - + -
153A ASN* 4.0 8.7 + - - +
156A LYS* 4.5 20.5 + - + +
160A LEU* 4.4 14.8 - - + -
175A PHE* 2.9 31.7 + - + +
178A ILE* 1.3 81.5 - - + +
180A GLY* 1.3 62.9 + - - +
181A LEU* 3.4 21.1 + - + +
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Residues in contact with GLY 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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153A ASN* 3.8 11.4 + - - -
176A THR 3.1 8.3 + - - -
177A LYS 3.5 5.7 + - - -
178A ILE 3.4 4.4 + - - -
179A LEU* 1.3 78.4 - - - +
181A LEU* 1.3 61.2 + - - +
182A GLU 3.3 9.5 + - - +
183A ASP* 5.6 1.2 - - - +
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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