Contacts of the helix formed by residues 156 - 170 (chain C) in PDB entry 5U03
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 SER 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PRO* 4.7 6.5 - - - -
147C LEU* 4.9 11.0 - - - -
148C GLY 4.2 18.6 - - - -
149C GLY* 5.1 0.9 - - - -
150C THR 3.8 15.1 + - - -
151C VAL* 5.3 0.9 - - - -
152C GLY 5.0 1.2 + - - -
153C ASP* 2.9 21.7 + - - +
154C ILE 3.0 0.4 - - - -
155C GLU* 1.3 77.4 - - - +
157C MET* 1.3 63.6 + - - +
158C PRO* 3.3 3.8 - - - -
159C PHE* 2.9 25.2 + - - +
160C ILE* 3.1 18.0 + - - +
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Residues in contact with MET 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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154A ILE* 4.3 16.6 - - + -
157A MET* 5.7 5.2 - - - +
152C GLY* 3.7 27.6 - - - +
153C ASP 3.5 9.9 - - - +
154C ILE* 3.1 31.1 + - + +
156C SER* 1.3 77.2 + - - +
158C PRO* 1.3 71.5 - - + +
160C ILE* 2.9 24.9 + - + +
161C GLU* 3.2 11.8 + - - +
207C LEU* 5.7 13.0 - - + -
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Residues in contact with PRO 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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154A ILE* 5.1 8.7 - - + -
90C THR* 6.4 1.1 - - + -
113C VAL* 4.1 32.3 - - + -
117C ILE* 4.8 7.0 - - + -
118C THR* 3.5 12.7 - - + +
121C ILE* 3.7 14.6 - - + +
154C ILE 3.4 10.8 - - - +
155C GLU 4.0 7.2 - - - +
156C SER 3.3 3.8 - - - -
157C MET* 1.3 94.5 - - + +
159C PHE* 1.3 62.0 + - + +
161C GLU* 3.5 2.9 + - + +
162C ALA* 3.1 21.1 + - - +
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Residues in contact with PHE 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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39C ILE* 3.5 36.8 - - + -
41C PRO* 5.0 3.8 - - + -
88C LEU* 6.3 2.2 - - + -
89C THR 5.7 0.7 - - - -
90C THR* 3.8 31.2 - - + -
93C ILE* 3.9 17.5 - - + -
121C ILE* 3.6 39.0 - - + -
147C LEU* 4.0 15.5 - - + -
155C GLU 3.9 8.3 - - - -
156C SER* 2.9 22.8 + - - +
158C PRO* 1.3 80.7 - - + +
160C ILE* 1.3 67.2 + - - +
161C GLU 3.1 0.4 - - - -
162C ALA* 3.6 4.9 - - - +
163C PHE* 2.8 44.4 + + + -
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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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7C THR* 5.4 3.4 - - + -
147C LEU* 4.4 19.5 - - + -
151C VAL* 5.5 7.0 - - + -
156C SER* 3.1 19.2 + - - +
157C MET* 2.9 16.2 + - + +
159C PHE* 1.3 77.3 - - - +
161C GLU* 1.3 58.4 + - - +
163C PHE* 3.8 3.1 - - + +
164C ARG* 2.8 28.2 + - + +
204C LEU* 4.7 5.4 - - + -
207C LEU* 3.8 50.9 - - + +
209C LEU* 3.8 27.4 - - + +
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Residues in contact with GLU 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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205B ARG* 5.8 0.2 + - - -
235B HIS* 4.1 10.9 + - - -
113C VAL* 5.8 0.4 - - + -
114C VAL* 3.8 30.3 - - + +
118C THR* 3.8 9.4 - - + +
157C MET 3.2 6.4 + - - +
158C PRO* 3.8 9.0 - - + +
159C PHE 3.1 0.6 - - - -
160C ILE* 1.3 78.8 - - - +
162C ALA* 1.3 69.3 + - - +
164C ARG* 2.7 54.0 + - - +
165C GLN* 3.1 13.4 + - + +
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Residues in contact with ALA 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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118C THR* 3.8 25.8 - - - +
121C ILE* 3.6 32.8 - - + -
122C GLN* 3.0 17.3 + - + +
158C PRO 3.1 12.5 + - - +
159C PHE 3.2 7.4 + - - +
161C GLU* 1.3 80.8 - - - +
163C PHE* 1.3 58.7 + - + +
166C PHE* 2.9 25.1 + - - +
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Residues in contact with PHE 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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5C LEU* 3.6 43.3 - - + -
39C ILE* 3.7 26.2 - - + -
121C ILE* 5.1 4.9 - - + -
125C VAL* 4.3 16.4 - - + -
145C ILE* 3.9 22.7 - - + -
147C LEU* 4.3 7.0 - - + -
159C PHE* 2.8 42.9 + + + +
160C ILE* 4.0 3.8 - - + +
162C ALA* 1.3 75.6 - - + +
164C ARG* 1.3 68.6 + - - +
166C PHE* 3.6 13.0 - + + +
167C GLN* 2.9 27.9 + - - +
175C PHE* 4.1 21.2 - + + -
209C LEU* 4.5 5.8 - - + -
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Residues in contact with ARG 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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205B ARG* 4.1 28.1 - - - +
235B HIS* 3.7 12.9 + - - -
160C ILE* 2.8 19.8 + - + +
161C GLU* 2.7 44.8 + - - +
163C PHE* 1.3 77.1 - - - +
165C GLN* 1.3 90.2 + - - +
167C GLN* 3.1 9.5 + - - +
168C PHE* 3.0 47.0 - - + -
207C LEU 4.1 17.9 - - - +
208C GLY* 4.0 20.6 - - - +
209C LEU* 3.6 15.9 - - + -
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Residues in contact with GLN 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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205B ARG* 4.8 0.3 + - - -
235B HIS* 3.3 39.8 - - + +
122C GLN* 4.0 5.2 - - - +
161C GLU* 3.1 11.4 + - + +
162C ALA* 4.0 2.7 - - - +
164C ARG* 1.3 114.3 + - - +
166C PHE* 1.3 57.0 + - - +
168C PHE* 2.8 42.5 + - - +
169C LYS* 3.1 35.0 + - - +
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Residues in contact with PHE 166 (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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3C TYR* 3.7 48.2 - + + -
122C GLN* 3.7 37.0 - - + +
125C VAL* 3.8 19.7 - - + -
126C MET* 4.8 8.3 - - + -
162C ALA 2.9 20.1 + - - +
163C PHE* 3.6 16.6 - + + +
165C GLN* 1.3 76.9 - - - +
167C GLN* 1.3 60.2 + - - +
169C LYS* 2.8 29.2 + - + +
170C VAL* 2.9 33.4 + - + +
175C PHE* 4.1 15.9 - + - -
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Residues in contact with GLN 167 (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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163C PHE 2.9 11.9 + - - +
164C ARG* 3.1 22.8 + - - +
166C PHE* 1.3 76.6 - - - +
168C PHE* 1.3 82.9 + - + +
170C VAL* 2.9 28.4 - - - +
171C LYS 4.0 6.8 - - - +
172C ARG* 4.6 3.3 + - - -
175C PHE* 3.5 40.2 - - + +
177C ASN* 5.4 3.8 + - - +
208C GLY 4.0 7.1 + - - -
209C LEU* 3.5 27.6 - - - +
210C SER 5.5 3.8 + - - +
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Residues in contact with PHE 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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164C ARG* 3.0 47.6 - - + -
165C GLN* 2.8 25.6 + - - +
167C GLN* 1.3 100.2 - - + +
169C LYS* 1.3 62.3 + - - +
170C VAL 3.2 7.2 - - - +
208C GLY 5.5 2.5 - - - -
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Residues in contact with LYS 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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235B HIS* 6.2 0.7 - - - -
119C ASP* 4.1 12.3 + - - -
122C GLN* 2.7 38.9 + - - +
165C GLN* 3.1 27.7 + - - +
166C PHE* 2.8 12.6 + - + +
168C PHE* 1.3 77.1 - - - +
170C VAL* 1.3 63.8 + - + +
171C LYS* 5.5 3.6 - - - +
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Residues in contact with VAL 170 (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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3C TYR* 3.9 12.3 - - + +
126C MET* 6.2 0.7 - - - -
166C PHE* 2.9 52.0 + - + +
167C GLN* 2.9 30.0 - - - +
168C PHE* 3.2 11.6 - - - +
169C LYS* 1.3 79.9 - - + +
171C LYS* 1.3 71.5 + - - +
172C ARG 3.9 0.2 + - - -
174C ASN* 4.2 14.8 - - + +
175C PHE* 3.9 12.3 - - + -
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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