Contacts of the helix formed by residues 154 - 166 (chain C) in PDB entry 5SWW
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 THR 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ILE 3.5 13.0 - - - +
153C MET* 1.3 72.9 - - - +
155C TYR* 1.3 68.2 + - - +
156C ASP* 3.6 11.4 + - - +
157C GLU* 2.3 34.1 + - - +
158C PHE* 3.0 28.8 + - - -
179C LEU* 4.4 0.2 - - - -
183C SER* 3.3 21.5 - - - +
187C SER* 4.4 9.2 - - - +
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Residues in contact with TYR 155 (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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154C THR* 1.3 75.1 - - - +
156C ASP* 1.3 71.3 + - - +
158C PHE* 3.9 1.5 - - - +
159C LYS* 2.9 57.6 + - + +
173C PHE* 3.8 34.3 + + - -
175C PRO* 3.9 16.0 - - + +
179C LEU* 3.7 20.1 - - + +
180C ASP* 4.1 1.5 + - - +
183C SER* 5.3 0.4 - - - -
2F G 3.3 90.7 + + + +
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Residues in contact with ASP 156 (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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154C THR* 3.1 10.4 + - - +
155C TYR* 1.3 93.7 - - - +
157C GLU* 1.3 65.1 + - - +
159C LYS* 3.8 6.5 - - - +
160C HIS* 3.0 27.2 + - - +
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Residues in contact with GLU 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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95C PHE* 4.2 9.2 - - + -
125C PHE* 3.8 39.8 - - + -
152C ILE 4.7 2.0 - - - -
153C MET* 3.8 18.8 - - + -
154C THR* 2.3 52.4 + - - +
156C ASP* 1.3 83.3 - - - +
158C PHE* 1.3 65.3 + - - +
160C HIS* 3.2 7.7 + - - +
161C CYS* 3.1 27.9 + - - -
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Residues in contact with PHE 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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18C PHE* 3.7 15.8 - + + -
22C PHE* 3.3 26.2 - - + -
24C ASN* 3.7 25.8 - - + -
127C ALA* 3.9 10.1 - - + -
153C MET* 3.5 55.0 - - + -
154C THR 3.0 25.7 + - - +
155C TYR 3.9 1.3 - - - +
157C GLU* 1.3 75.5 - - - +
159C LYS* 1.3 63.2 + - - +
161C CYS 3.4 1.2 + - - -
162C TRP* 3.1 22.5 + - - +
173C PHE* 3.6 23.5 - - + -
176C TRP* 3.6 15.0 - + - -
179C LEU* 3.6 20.6 - - + -
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Residues in contact with LYS 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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155C TYR* 2.9 45.5 + - + +
156C ASP* 3.8 7.0 - - - +
158C PHE* 1.3 76.7 - - - +
160C HIS* 1.3 62.3 + - - +
162C TRP* 3.4 1.6 + - - +
163C ASP* 3.0 50.4 + - - +
172C PRO* 6.5 0.9 - - - -
173C PHE* 3.8 31.1 - - + +
2F G 6.4 0.9 - - - -
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Residues in contact with HIS 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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36C GLU* 2.8 27.2 + - - -
52C ARG* 5.3 2.5 - - - -
95C PHE* 3.5 30.5 - + - -
156C ASP 3.0 16.8 + - - +
157C GLU* 3.2 8.5 + - - +
159C LYS* 1.3 78.4 - - - +
161C CYS* 1.3 57.5 + - - +
163C ASP* 3.2 6.2 + - - +
164C THR* 2.9 56.9 + - + -
165C PHE* 4.7 2.7 - + - -
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Residues in contact with CYS 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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18C PHE* 3.6 23.3 - - + -
22C PHE* 5.3 1.1 - - - -
34C CYS* 4.8 3.8 - - - -
95C PHE* 3.3 48.5 - - - -
153C MET* 3.9 8.1 - - - -
157C GLU 3.1 20.3 + - - +
158C PHE* 3.9 1.6 - - - +
160C HIS* 1.3 76.9 - - - +
162C TRP* 1.3 57.7 + - - +
165C PHE* 2.8 43.3 + - + +
166C VAL* 3.2 10.1 + - - +
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Residues in contact with TRP 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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15C PRO* 4.2 16.4 - - + -
18C PHE* 3.8 19.9 - + + -
19C THR* 4.1 21.8 - - + -
158C PHE 3.1 16.8 + - - +
159C LYS 3.6 4.5 - - - +
160C HIS 3.2 0.2 - - - -
161C CYS* 1.3 77.2 - - - +
163C ASP* 1.3 73.0 + - - +
166C VAL* 3.3 45.0 - - + +
168C HIS* 3.3 33.7 + - + +
171C CYS* 2.6 36.1 + - + -
172C PRO 4.1 9.0 - - - -
173C PHE* 3.5 40.4 - + + +
174C GLN* 5.7 7.0 - - + -
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Residues in contact with ASP 163 (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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159C LYS* 3.0 48.2 + - - +
160C HIS* 3.8 5.3 - - - +
162C TRP* 1.3 92.6 - - - +
164C THR* 1.3 62.7 + - - +
166C VAL 4.6 0.4 - - - +
168C HIS* 3.3 27.4 + - + -
172C PRO* 5.3 2.8 - - - +
173C PHE 4.8 2.8 + - - -
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Residues in contact with THR 164 (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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12C LEU* 3.9 14.0 - - - +
36C GLU* 5.1 0.2 - - - +
52C ARG* 3.7 40.8 - - + +
160C HIS* 2.9 37.5 + - + +
163C ASP* 1.3 82.5 - - - +
165C PHE* 1.3 73.4 + - + +
166C VAL 3.7 0.9 - - - -
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Residues in contact with PHE 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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12C LEU* 3.8 8.5 - - - -
13C MET* 2.9 33.7 + - + +
34C CYS* 3.7 37.5 - - + -
35C TYR 3.6 3.1 - - - -
36C GLU* 3.5 34.5 - - + -
52C ARG* 3.7 10.3 - - + -
53C GLY* 3.2 44.2 - - - -
54C PHE* 4.9 5.4 - + + -
95C PHE* 3.8 15.9 - + - -
160C HIS* 4.7 0.9 - + - -
161C CYS* 2.8 32.7 + - + +
164C THR* 1.3 83.6 - - + +
166C VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.2 6.6 - - - +
13C MET* 3.7 17.9 - - + +
15C PRO* 4.0 14.8 - - + -
18C PHE* 3.6 33.7 - - + -
161C CYS 3.2 15.1 + - - +
162C TRP* 3.3 42.8 + - + +
163C ASP 4.6 0.9 - - - +
164C THR 5.0 0.2 - - - -
165C PHE* 1.3 81.1 - - - +
167C ASP* 1.3 64.2 + - - +
168C HIS* 2.8 33.9 + - - +
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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