Contacts of the helix formed by residues 156 - 169 (chain C) in PDB entry 5B6N
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 ASN 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 5.4 1.8 - - - +
149C TYR* 4.7 2.4 + - - -
155C ARG* 1.3 73.0 - - - +
157C PHE* 1.3 58.5 + - - +
158C ASP* 3.0 14.0 + - - +
159C GLU* 2.7 39.5 + - + +
160C ILE* 3.2 25.4 + - - +
159D GLU* 3.3 36.9 + - - +
162D ARG* 3.7 10.1 - - - +
180D ASP* 3.3 22.8 + - - +
182D LYS* 4.5 12.1 - - - +
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Residues in contact with PHE 157 (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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35C ILE* 6.0 0.7 - - + -
37C PHE* 4.4 29.6 - + + -
50C GLU* 3.6 42.6 - - + -
53C ARG* 3.9 23.1 - - + -
54C ALA* 3.6 25.4 - - + -
57C LEU* 3.2 20.9 - - + +
61C PHE* 4.8 8.7 - + - -
68C LEU* 5.2 4.5 - - + -
155C ARG* 3.7 6.1 + - + -
156C ASN* 1.3 72.3 - - - +
158C ASP* 1.3 64.6 + - - +
159C GLU 3.3 1.3 - - - -
160C ILE* 3.7 35.7 - - + -
161C LEU* 3.7 10.9 + - - +
179D VAL* 3.8 14.4 - - + -
180D ASP* 2.7 9.6 + - - +
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Residues in contact with ASP 158 (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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53C ARG* 3.0 28.9 + - - -
57C LEU* 3.9 8.1 - - - +
156C ASN* 3.0 9.2 + - - +
157C PHE* 1.3 79.5 - - - +
159C GLU* 1.3 58.6 + - - +
160C ILE 3.4 0.2 - - - -
161C LEU* 3.8 9.0 - - - +
162C ARG* 3.2 26.7 + - - +
180D ASP* 3.6 16.8 + - - +
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Residues in contact with GLU 159 (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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147C ILE* 6.4 2.0 - - + -
149C TYR* 6.1 0.2 - - - +
156C ASN* 2.7 27.5 + - + +
158C ASP* 1.3 78.5 - - - +
160C ILE* 1.3 65.3 + - + +
161C LEU 3.3 0.2 - - - -
162C ARG* 2.8 39.6 + - - +
163C VAL* 3.0 25.9 + - + +
149D TYR* 2.3 32.9 + - - +
156D ASN* 3.4 25.7 + - - +
159D GLU* 4.1 13.9 - - + +
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Residues in contact with ILE 160 (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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35C ILE* 3.7 27.1 - - + -
61C PHE* 4.5 5.8 - - + -
134C VAL* 3.9 36.8 - - + -
136C VAL* 5.3 3.1 - - + -
147C ILE* 4.4 14.4 - - + -
155C ARG* 4.7 4.9 - - + -
156C ASN 3.2 16.8 + - - +
157C PHE* 3.7 41.1 - - + +
158C ASP 3.4 0.2 - - - -
159C GLU* 1.3 80.7 - - + +
161C LEU* 1.3 60.0 + - - +
163C VAL* 3.4 7.8 - - - +
164C VAL* 3.4 22.9 + - + +
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Residues in contact with LEU 161 (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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57C LEU* 3.8 32.1 - - + -
60C GLU* 4.1 17.5 - - + +
61C PHE* 3.7 29.8 - - + -
64C ARG* 4.0 14.6 - - - +
157C PHE 3.7 7.5 + - - +
158C ASP* 3.8 12.6 - - - +
159C GLU 3.3 0.2 - - - -
160C ILE* 1.3 79.1 - - - +
162C ARG* 1.3 61.3 + - - +
164C VAL* 3.2 4.9 + - + +
165C ILE* 3.1 45.0 + - + +
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Residues in contact with ARG 162 (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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158C ASP 3.2 17.5 + - - +
159C GLU* 2.8 43.7 + - - +
160C ILE 3.3 0.2 - - - -
161C LEU* 1.3 79.9 - - - +
163C VAL* 1.3 70.9 + - - +
165C ILE* 3.4 11.6 + - + +
166C SER* 3.0 29.2 + - - -
177C THR* 5.4 0.4 + - - -
180C ASP* 4.7 2.0 - - - +
181C TRP* 3.1 52.7 + - - +
182C LYS* 4.7 6.5 - - - +
183C ASP 5.9 0.4 - - - +
153D THR* 4.9 1.4 - - - +
154D GLY 4.2 12.5 + - - -
155D ARG 4.2 3.0 + - - -
156D ASN* 3.5 23.4 - - - +
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 5.4 3.4 - - + -
145C LEU* 3.7 31.2 - - + -
159C GLU* 3.0 27.1 + - - +
160C ILE* 3.4 12.8 - - + +
162C ARG* 1.3 85.1 - - - +
164C VAL* 1.3 64.2 + - + +
166C SER* 3.8 9.4 - - - -
167C LEU* 3.1 32.3 + - + +
149D TYR* 3.2 33.4 - - + +
153D THR* 4.4 4.4 - - + +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TRP* 5.2 5.4 - - + -
35C ILE* 3.6 26.5 - - + -
61C PHE* 4.8 4.0 - - + -
64C ARG* 5.6 2.7 - - + -
66C VAL* 3.6 29.8 - - + -
136C VAL* 4.3 22.7 - - + -
160C ILE 3.4 14.3 + - - +
161C LEU* 3.2 10.5 + - + +
162C ARG 3.2 0.4 - - - -
163C VAL* 1.3 77.3 - - + +
165C ILE* 1.3 61.6 + - + +
166C SER 3.1 1.3 - - - -
167C LEU* 3.2 5.1 + - - +
168C GLN* 2.9 42.6 + - + +
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Residues in contact with ILE 165 (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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64C ARG* 3.6 35.4 - - - +
161C LEU* 3.1 35.5 + - + +
162C ARG* 3.4 11.0 + - + +
164C VAL* 1.3 76.1 - - + +
166C SER* 1.3 62.1 + - - +
168C GLN* 4.5 7.4 - - - -
169C LEU* 3.3 41.7 + - + +
181C TRP* 5.1 4.7 - - + -
183C ASP* 3.9 33.2 - - + +
223C GLN* 5.0 1.1 - - - +
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Residues in contact with SER 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ARG* 3.0 19.1 + - - -
163C VAL* 3.8 3.8 - - - -
165C ILE* 1.3 76.4 - - - +
167C LEU* 1.3 64.0 + - - -
168C GLN 3.2 0.9 + - - -
169C LEU* 3.2 7.8 + - - +
170C THR* 3.0 22.1 + - - +
177C THR* 3.1 24.4 + - - +
181C TRP* 3.6 21.0 - - - -
153D THR* 3.2 30.2 + - - +
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TRP* 3.6 21.6 - - + -
136C VAL* 4.1 19.5 - - + -
144C LYS* 4.2 24.8 + - + -
145C LEU* 3.7 30.5 - - + -
163C VAL* 3.1 24.1 + - + +
164C VAL* 3.2 6.5 + - - +
166C SER* 1.3 79.0 - - - +
168C GLN* 1.3 58.3 + - - +
170C THR* 2.8 16.8 + - - +
171C ALA* 4.2 5.7 + - - +
150D PRO* 3.6 28.0 - - + -
152D THR* 4.3 6.5 - - - +
153D THR* 3.9 8.5 - - - +
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Residues in contact with GLN 168 (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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106B ARG* 5.1 7.6 + - - +
33C TRP* 3.4 48.7 - - + +
64C ARG* 2.8 42.4 + - - +
66C VAL* 3.4 14.9 - - - +
164C VAL* 2.9 24.8 + - + +
165C ILE* 4.5 2.9 - - - -
167C LEU* 1.3 74.4 - - - +
169C LEU* 1.3 72.0 + - + +
170C THR 3.1 7.8 + - - -
171C ALA* 3.6 3.3 + - - +
172C GLU* 3.4 22.3 + - - +
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Residues in contact with LEU 169 (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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77B GLU* 5.8 3.8 - - - +
165C ILE* 3.3 32.8 - - + +
166C SER* 3.2 6.4 + - - +
168C GLN* 1.3 91.0 - - + +
170C THR* 1.3 59.3 + - - +
171C ALA 3.5 0.9 - - - -
172C GLU* 3.7 31.0 - - - +
173C LYS* 3.3 20.8 + - - +
175C VAL* 3.6 12.9 - - + +
181C TRP* 4.7 5.8 - - + -
183C ASP* 4.9 0.9 - - - +
223C GLN* 3.2 37.7 - - + +
224C PRO* 5.7 2.2 - - + +
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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