Contacts of the helix formed by residues 148 - 165 (chain C) in PDB entry 1USK
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 GLN 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C CYS 5.4 3.6 - - - +
55C PRO* 5.8 2.9 - - - +
80C SER* 4.6 15.6 + - - +
146C ASP* 3.2 40.9 + - - +
147C LYS* 1.3 80.8 - - - +
149C GLN* 1.3 68.3 + - - +
150C TYR* 3.0 4.6 + - + +
151C GLY 3.1 2.2 + - - +
152C GLU* 2.9 24.9 + - - +
177C ALA* 4.2 16.9 - - + +
202C TYR* 3.7 23.5 - - + -
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Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 3.3 26.2 + - - -
80C SER* 3.5 24.2 - - - +
83C GLN* 2.8 34.7 + - - +
84C PRO* 5.6 0.4 - - - +
103C ASN* 3.3 39.3 + - + +
105C GLU* 4.2 9.9 - - - +
148C GLN* 1.3 71.8 - - - +
150C TYR* 1.3 61.3 + - - +
152C GLU* 5.1 1.3 - - - -
153C GLY* 3.2 16.6 + - - +
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Residues in contact with TYR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 4.4 8.4 - - - -
80C SER* 5.4 1.2 - - - +
102C THR* 3.2 22.4 - - - -
103C ASN* 4.7 4.2 + - - +
121C ASP* 3.5 9.5 - - - +
148C GLN* 3.2 2.5 - - + +
149C GLN* 1.3 79.0 - - - +
151C GLY* 1.3 67.0 + - - +
153C GLY* 4.1 0.3 - - - -
154C LEU* 3.3 43.0 + - + +
201C GLY* 3.7 22.7 - - - -
202C TYR* 3.5 43.7 - + + +
225C PRO* 3.2 14.5 - - + +
226C GLU* 2.5 23.6 + - - -
227C GLY* 3.1 15.5 + - - -
1347C LEU* 3.3 31.0 - - - +
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C HIS* 4.0 0.7 - - - -
146C ASP* 3.9 6.9 + - - -
148C GLN* 3.1 4.9 + - - +
150C TYR* 1.3 79.3 - - - +
152C GLU* 1.3 61.3 + - - +
154C LEU* 3.2 3.4 + - - -
155C ALA* 2.9 29.5 + - - +
200C GLY* 3.2 36.1 - - - -
201C GLY* 3.8 5.2 - - - -
202C TYR* 5.8 0.2 - - - -
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Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C HIS* 3.6 40.6 - - + +
146C ASP* 4.4 1.4 + - - -
147C LYS* 3.7 20.6 - - - +
148C GLN 2.9 18.3 + - - +
149C GLN* 4.8 1.6 - - - +
151C GLY* 1.3 73.5 - - - +
153C GLY* 1.3 62.0 + - - +
155C ALA* 3.4 1.6 + - - +
156C ARG* 3.0 61.2 + - + +
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Residues in contact with GLY 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 4.5 9.4 - - - -
121C ASP* 5.8 2.5 - - - -
149C GLN 3.2 19.5 + - - -
150C TYR 4.1 0.2 - - - -
152C GLU* 1.3 80.2 - - - +
154C LEU* 1.3 56.0 + - - +
156C ARG* 3.5 6.3 + - - +
157C SER* 3.1 26.3 + - - -
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Residues in contact with LEU 154 (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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121C ASP* 3.5 33.4 - - + +
124C GLN* 3.8 10.5 - - + -
125C GLY* 3.8 27.4 - - - +
150C TYR* 3.3 54.6 + - + +
151C GLY* 3.2 6.1 + - - +
153C GLY* 1.3 73.2 - - - +
155C ALA* 1.3 59.6 + - - +
157C SER* 3.2 5.5 + - - -
158C VAL* 3.0 32.4 + - - +
198C TYR* 4.0 17.7 - - + +
200C GLY* 4.9 1.6 - - - -
225C PRO* 3.5 15.9 - - + -
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Residues in contact with ALA 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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143C ILE* 3.5 27.4 - - + +
144C ILE 4.0 5.6 - - - +
145C HIS* 3.8 21.1 - - + -
151C GLY 2.9 17.6 + - - +
152C GLU 3.7 4.5 - - - +
154C LEU* 1.3 74.7 - - - +
156C ARG* 1.3 57.5 + - - +
158C VAL* 3.5 0.7 + - - +
159C GLN* 2.9 29.5 + - - +
172C PHE* 3.9 8.5 - - + -
198C TYR* 4.4 8.8 - - - -
200C GLY* 4.6 1.6 - - - +
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Residues in contact with ARG 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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145C HIS* 5.1 0.8 + - - -
152C GLU* 3.0 46.3 + - - +
153C GLY* 3.8 6.5 - - - +
155C ALA* 1.3 74.1 - - - +
157C SER* 1.3 64.2 + - - +
159C GLN* 3.8 23.6 + - - +
160C ASP* 3.1 33.7 + - - +
172C PHE* 3.7 31.8 - - + -
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Residues in contact with SER 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASP* 4.0 7.6 + - - -
122C SER* 5.2 2.1 - - - -
125C GLY* 3.5 23.2 - - - -
126C PRO* 3.6 14.4 - - - +
129C ALA* 5.3 0.2 - - - +
153C GLY 3.1 14.4 + - - -
154C LEU* 3.4 11.7 - - - -
156C ARG* 1.3 77.6 - - - +
158C VAL* 1.3 57.9 + - - +
160C ASP* 3.4 7.7 + - - +
161C GLY* 2.9 24.1 + - - -
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLY* 3.7 26.2 - - - +
128C ALA* 4.2 3.6 - - + -
129C ALA* 4.3 4.6 - - + +
132C ILE* 4.3 10.1 - - + -
143C ILE* 4.1 7.0 - - + -
154C LEU 3.0 19.0 + - - +
155C ALA 3.9 3.6 - - - +
157C SER* 1.3 73.9 - - - +
159C GLN* 1.3 65.6 + - - +
161C GLY* 3.1 2.1 + - - +
162C LEU* 3.0 43.7 + - + +
198C TYR* 3.7 47.1 - - + +
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Residues in contact with GLN 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 4.5 9.6 - - + -
155C ALA 2.9 18.3 + - - +
156C ARG* 3.8 21.5 + - - +
157C SER 3.4 0.2 - - - -
158C VAL* 1.3 77.1 - - - +
160C ASP* 1.3 62.4 + - - +
162C LEU* 3.4 5.2 + - - +
163C LYS* 2.9 70.3 + - + +
169C VAL* 4.3 13.3 - - + +
172C PHE* 3.5 44.5 - - + +
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Residues in contact with ASP 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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156C ARG* 3.1 22.9 + - - +
157C SER* 3.6 6.8 - - - +
158C VAL 3.3 0.2 - - - -
159C GLN* 1.3 87.5 - - - +
161C GLY* 1.3 62.5 + - - +
163C LYS* 3.3 9.4 + - - +
164C ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 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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126C PRO* 5.9 2.5 - - - -
129C ALA* 4.0 17.7 - - - -
133C LEU* 3.8 12.5 - - - +
157C SER 2.9 15.1 + - - -
158C VAL 3.1 3.3 + - - -
160C ASP* 1.3 77.6 - - - +
162C LEU* 1.3 60.7 + - - +
164C ALA* 3.6 15.9 - - - +
165C ALA* 3.8 1.6 + - - +
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Residues in contact with LEU 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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129C ALA* 4.0 10.3 - - + +
132C ILE* 3.8 25.6 - - + -
133C LEU* 3.7 31.0 - - + -
141C ILE* 4.2 19.5 - - + -
143C ILE* 4.1 17.0 - - + -
158C VAL* 3.0 37.3 + - + +
159C GLN* 3.8 4.0 - - - +
161C GLY* 1.3 73.5 - - - +
163C LYS* 1.3 61.8 + - - +
164C ALA 3.2 0.2 - - - -
165C ALA* 3.1 16.8 + - - +
166C ASN 3.1 8.1 + - - -
167C ALA* 3.2 19.3 + - + +
169C VAL* 4.0 13.9 - - + -
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Residues in contact with LYS 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 GLN* 2.9 55.6 + - + +
160C ASP* 3.8 10.5 - - - +
162C LEU* 1.3 74.5 - - - +
164C ALA* 1.3 65.6 + - - +
166C ASN* 3.1 22.0 + - - +
167C ALA 4.7 4.0 - - - +
169C VAL* 4.3 21.5 - - + -
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Residues in contact with ALA 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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160C ASP 3.0 12.7 + - - +
161C GLY* 3.6 14.8 - - - +
162C LEU 3.2 0.2 - - - -
163C LYS* 1.3 77.5 - - - +
165C ALA* 1.3 57.3 + - + +
166C ASN* 3.4 14.0 + - - -
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Residues in contact with ALA 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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133C LEU* 3.8 33.0 - - + +
161C GLY 3.8 0.9 + - - +
162C LEU 3.1 9.7 + - - +
164C ALA* 1.3 75.7 - - + +
166C ASN* 1.3 72.8 + - - +
167C ALA* 3.2 4.6 + - - +
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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
------------------------------------------------------------
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