Contacts of the helix formed by residues 168 - 180 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.9 23.8 - - + -
15C ARG* 3.8 15.0 - - + +
16C THR* 3.7 18.8 - - - +
17C TYR* 3.6 37.5 - - + +
140C ILE* 4.4 2.9 - - + -
163C LEU* 3.0 44.9 + - + +
166C LEU* 3.8 23.1 - - + +
167C ASP* 1.3 74.8 - - - +
169C ASP* 1.3 65.1 + - - +
170C PHE 3.2 3.1 - - - +
171C ASP* 2.9 19.8 + - - +
172C ALA 3.1 9.0 + - - -
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Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 2.9 25.5 + - - -
164C CYS* 3.3 28.4 - - - +
167C ASP* 3.3 14.6 + - - +
168C LEU* 1.3 76.1 - - - +
170C PHE* 1.3 61.6 + - - +
172C ALA* 3.3 0.6 + - - -
173C TYR* 2.9 25.2 + - - +
193C ILE* 3.6 12.9 - - + +
196C ASN* 2.9 44.7 + - + +
197C PHE* 4.2 9.9 - - + +
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Residues in contact with PHE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.5 22.7 - - + -
15C ARG 3.7 14.3 + - - +
16C THR* 3.8 8.5 - - - -
19C PHE* 3.9 27.6 - - + -
22C LEU* 3.9 18.6 - - + -
23C ALA* 4.2 5.6 - - + -
47C VAL* 4.7 2.7 - - + -
48C PHE* 3.8 19.1 - + - -
168C LEU* 3.2 1.0 + - - +
169C ASP* 1.3 77.0 - - - +
171C ASP* 1.3 74.0 + - - +
173C TYR* 3.2 5.1 + + + +
174C VAL* 2.9 53.4 + - + +
197C PHE* 3.3 52.4 - + + -
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Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 2.6 29.9 + - - -
17C TYR* 2.8 27.2 + - - +
18C PHE* 2.9 24.7 + - + -
19C PHE* 3.5 18.8 - - + -
163C LEU* 4.1 13.7 - - + -
168C LEU* 2.9 16.9 + - + +
170C PHE* 1.3 79.7 - - - +
172C ALA* 1.3 63.6 + - - +
174C VAL* 3.3 1.6 + - - +
175C PHE* 2.9 31.6 + - + -
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 6.3 0.2 - - + -
160C LEU* 3.9 25.1 - - + +
161C SER* 4.8 0.2 - - - -
163C LEU* 4.0 9.7 - - + +
164C CYS* 4.0 14.8 - - - -
168C LEU 3.1 8.3 + - - +
169C ASP 3.3 7.6 + - - +
171C ASP* 1.3 74.9 - - - +
173C TYR* 1.3 57.9 + - - +
175C PHE* 3.5 4.8 + - - +
176C THR* 2.9 34.8 + - - +
193C ILE* 4.0 19.7 - - + -
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Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 3.6 28.6 + - + -
169C ASP 2.9 17.7 + - - +
170C PHE* 3.5 7.9 - + - +
172C ALA* 1.3 73.6 - - - +
174C VAL* 1.3 68.9 + - + +
176C THR* 3.2 6.6 + - + -
177C LYS* 3.0 48.1 + - + +
190C VAL* 4.7 10.3 - - + -
193C ILE* 4.0 8.9 - - + +
194C ARG* 3.0 69.7 + - + -
197C PHE* 4.6 22.4 - + + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.5 37.9 - - + -
22C LEU* 3.9 9.4 - - + -
43C PHE* 4.0 21.3 - - + -
47C VAL* 3.9 12.6 - - + -
170C PHE* 2.9 55.6 + - + +
173C TYR* 1.3 77.3 - - + +
175C PHE* 1.3 62.7 + - - +
177C LYS* 3.1 6.7 + - - +
178C ILE* 2.9 24.9 + - + +
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 3.6 43.5 - + - -
19C PHE* 3.7 22.7 - + - -
80C THR* 4.2 3.6 - - + -
83C ALA* 3.6 30.5 - - + -
84C LEU* 3.9 27.4 - - + -
160C LEU* 3.7 37.7 - - + -
163C LEU* 4.2 2.0 - - + -
171C ASP 2.9 28.1 + - - +
172C ALA* 3.8 3.6 - - - +
174C VAL* 1.3 76.8 - - - +
176C THR* 1.3 64.0 + - - +
178C ILE* 4.8 2.2 - - - -
179C LEU* 2.9 40.2 + - + +
181C LEU* 4.1 1.5 - - - +
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Residues in contact with THR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 3.5 23.7 - - - -
160C LEU* 6.2 0.3 - - - +
172C ALA* 2.9 19.6 + - - +
173C TYR* 3.5 9.1 - - + -
175C PHE* 1.3 75.6 - - - +
177C LYS* 1.3 68.0 + - + +
180C GLY* 3.1 4.7 + - - -
181C LEU* 3.0 36.4 + - + +
182C GLU* 3.9 19.1 + - + +
190C VAL* 3.9 36.1 - - + -
193C ILE* 5.1 2.1 - - - +
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Residues in contact with LYS 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C TYR* 3.6 65.9 + - + -
47C VAL* 4.0 13.2 + - + +
49C GLY* 5.2 6.3 - - - -
52C ASP* 5.6 3.6 + - - -
173C TYR* 3.0 52.9 + - + +
174C VAL* 3.6 8.7 - - - +
176C THR* 1.3 81.7 - - + +
178C ILE* 1.3 64.9 + - + +
180C GLY* 3.5 7.1 + - - -
182C GLU* 5.6 3.1 - - - +
194C ARG* 5.3 4.3 - - - +
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Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 5.9 0.2 - - + -
43C PHE* 3.5 39.5 - - + -
46C TYR* 4.1 16.6 - - + -
47C VAL* 4.4 3.6 - - + -
55C PRO* 3.9 19.7 - - + -
60C ILE* 3.9 19.7 - - + -
84C LEU* 4.0 24.9 - - + -
88C PHE* 5.5 3.4 - - + -
174C VAL* 2.9 24.0 + - + +
175C PHE 4.3 1.1 - - - +
177C LYS* 1.3 77.2 - - - +
179C LEU* 1.3 64.0 + - + +
180C GLY 3.6 0.3 + - - -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA 3.9 6.5 - - - +
84C LEU* 3.6 40.2 - - + +
88C PHE* 5.7 1.8 - - + -
153C ASN* 4.2 7.1 + - - +
156C LYS* 3.8 34.1 - - + +
160C LEU* 4.4 2.9 - - + -
175C PHE* 2.9 33.5 + - + +
178C ILE* 1.3 81.1 - - + +
180C GLY* 1.3 63.5 + - - +
181C LEU* 3.4 25.4 + - + +
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASN* 4.1 9.7 + - - -
176C THR 3.1 9.0 + - - -
177C LYS 3.5 5.9 + - - -
178C ILE 3.3 3.8 + - - -
179C LEU* 1.3 78.7 - - - +
181C LEU* 1.3 62.7 + - - +
182C GLU 3.3 9.1 + - - +
183C ASP* 5.7 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