Contacts of the helix formed by residues 148 - 165 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS 5.4 3.3 - - - +
80B SER* 5.1 12.5 + - - +
146B ASP* 3.0 37.9 + - - +
147B LYS* 1.3 80.6 - - + +
149B GLN* 1.3 66.0 + - - +
150B TYR* 3.2 4.7 + - + +
151B GLY 3.5 1.5 + - - +
152B GLU* 3.0 25.2 + - - +
177B ALA* 4.5 16.1 - - + +
202B TYR* 3.8 19.9 - - + -
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.3 26.2 + - - -
80B SER* 3.4 23.4 - - - +
83B GLN* 2.7 34.5 + - - +
84B PRO* 5.6 0.2 - - - +
103B ASN* 3.4 33.8 + - + +
105B GLU* 4.4 6.4 - - - +
148B GLN* 1.3 74.9 - - - +
150B TYR* 1.3 62.7 + - - +
152B GLU* 5.1 1.6 - - - -
153B GLY* 3.2 15.6 + - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 4.3 9.5 - - - -
80B SER* 5.4 1.2 - - - +
102B THR* 3.2 22.7 - - - -
103B ASN* 4.9 3.4 + - - +
121B ASP* 3.6 8.0 - - - +
148B GLN* 3.3 1.9 - - + +
149B GLN* 1.3 79.9 - - - +
151B GLY* 1.3 70.9 + - - +
153B GLY* 3.9 0.7 - - - -
154B LEU* 3.2 43.0 + - + +
201B GLY 3.5 22.2 - - - -
202B TYR* 3.3 41.7 - + + +
225B PRO* 3.3 15.0 - - + +
226B GLU* 2.5 24.7 + - - -
227B GLY* 3.1 14.1 + - - -
1347B LEU* 3.1 37.7 - - - +
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B HIS* 4.0 1.1 - - - -
146B ASP* 4.0 8.6 + - - -
148B GLN* 3.5 3.0 + - - +
150B TYR* 1.3 82.1 - - - +
152B GLU* 1.3 60.2 + - - +
154B LEU* 3.4 2.3 + - - -
155B ALA* 2.9 28.6 + - - +
200B GLY* 3.3 38.4 - - - -
201B GLY* 3.6 3.6 - - - -
202B TYR* 5.7 0.2 - - - -
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS* 3.5 42.4 - - + +
146B ASP* 4.4 1.0 + - - -
147B LYS* 3.4 22.2 - - - +
148B GLN 3.0 17.1 + - - +
149B GLN* 4.8 1.5 - - - +
151B GLY* 1.3 73.9 - - - +
153B GLY* 1.3 60.8 + - - +
155B ALA* 3.3 0.7 + - - +
156B ARG* 2.9 65.6 + - + +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 4.4 10.8 - - - -
121B ASP* 5.8 3.1 - - - -
149B GLN 3.2 19.0 + - - -
150B TYR 3.9 0.4 - - - -
152B GLU* 1.3 78.5 - - - +
154B LEU* 1.3 57.0 + - - +
156B ARG* 3.6 6.1 + - - +
157B SER* 3.1 26.9 + - - -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP* 3.6 28.3 - - + +
124B GLN* 3.8 14.1 - - + +
125B GLY* 3.6 33.0 - - - +
150B TYR* 3.2 43.0 + - + +
151B GLY* 3.9 4.7 - - - +
153B GLY* 1.3 72.9 - - - +
155B ALA* 1.3 61.9 + - - +
157B SER* 3.4 4.1 + - - -
158B VAL* 3.0 34.6 + - - +
198B TYR* 4.1 16.2 - - + +
200B GLY* 4.8 1.6 - - - -
225B PRO* 3.5 26.7 - - + -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.7 26.7 - - + +
144B ILE 4.1 5.2 - - - +
145B HIS* 3.8 18.8 - - + -
151B GLY 2.9 19.0 + - - +
152B GLU* 3.3 4.7 + - - +
154B LEU* 1.3 73.5 - - - +
156B ARG* 1.3 59.5 + - - +
158B VAL* 3.4 1.0 + - - +
159B GLN* 2.9 29.6 + - - +
172B PHE* 4.0 9.0 - - + -
198B TYR* 4.4 8.9 - - - -
200B GLY 4.6 2.2 - - - +
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B HIS* 5.7 0.2 + - - -
152B GLU* 2.9 45.5 + - + +
153B GLY* 3.9 5.8 - - - +
155B ALA* 1.3 75.0 - - - +
157B SER* 1.3 58.6 + - - +
159B GLN* 3.8 17.3 + - - +
160B ASP* 3.1 39.4 + - - +
172B PHE* 3.9 31.8 - - + -
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 4.0 7.6 + - - -
122B SER* 5.3 1.6 - - - -
125B GLY* 3.6 6.8 - - - -
126B PRO* 3.5 28.6 - - - +
129B ALA* 5.3 0.3 - - - +
153B GLY 3.1 18.9 + - - -
154B LEU* 3.5 9.6 - - - -
155B ALA 3.2 0.4 - - - -
156B ARG* 1.3 77.6 - - - +
158B VAL* 1.3 57.4 + - - +
160B ASP* 3.3 7.3 + - - +
161B GLY* 3.0 24.4 + - - -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY* 3.7 24.9 - - - +
128B ALA* 4.1 2.2 - - + -
129B ALA* 4.3 10.0 - - + +
132B ILE* 4.0 18.6 - - + -
143B ILE* 4.8 2.0 - - + -
154B LEU 3.0 21.4 + - - +
155B ALA 4.0 3.1 - - - +
157B SER* 1.3 72.4 - - - +
159B GLN* 1.3 61.1 + - - +
161B GLY* 3.4 1.1 + - - +
162B LEU* 2.9 46.7 + - + +
198B TYR* 3.7 40.8 - - + -
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Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 3.5 23.0 - - + +
155B ALA 2.9 18.3 + - - +
156B ARG* 3.8 18.2 + - - +
158B VAL* 1.3 76.1 - - - +
160B ASP* 1.3 58.3 + - - +
162B LEU* 3.2 2.8 + - - +
163B LYS* 2.8 74.8 + - + +
169B VAL* 4.3 10.0 - - + +
172B PHE* 3.3 42.8 - - + +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG* 3.1 27.1 + - - +
157B SER* 3.6 7.9 - - - +
158B VAL 3.3 0.2 - - - -
159B GLN* 1.3 85.5 - - - +
161B GLY* 1.3 61.5 - - - +
163B LYS* 3.3 10.1 + - - +
164B ALA* 3.0 24.9 + - - +
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 6.1 1.8 - - - -
129B ALA* 4.2 16.6 - - - -
133B LEU* 3.9 10.3 - - - +
157B SER 3.0 14.7 + - - -
158B VAL 3.8 2.9 - - - -
160B ASP* 1.3 76.1 - - - +
162B LEU* 1.3 62.1 + - - +
164B ALA* 3.6 16.0 + - - +
165B ALA* 3.7 4.0 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA* 4.1 6.1 - - + +
132B ILE* 3.7 33.4 - - + -
133B LEU* 3.7 27.6 - - + -
141B ILE* 4.2 23.3 - - + -
143B ILE* 4.1 16.4 - - + -
158B VAL* 2.9 37.5 + - + +
159B GLN 3.7 2.9 - - - +
161B GLY* 1.3 75.5 - - - +
163B LYS* 1.3 63.0 + - - +
165B ALA* 3.2 5.9 + - - +
166B ASN 3.1 4.3 + - - -
167B ALA* 3.1 31.6 + - + +
169B VAL* 4.1 12.1 - - + -
196B PHE* 5.6 0.4 - - + -
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLN* 2.8 60.2 + - + +
160B ASP* 3.8 11.0 - - - +
162B LEU* 1.3 70.8 - - - +
164B ALA* 1.3 63.8 + - - +
166B ASN* 3.1 21.8 + - - +
167B ALA 4.7 4.3 - - - +
169B VAL* 4.9 16.8 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ASP 3.0 16.2 + - - +
161B GLY* 3.6 9.6 - - - +
162B LEU 3.2 0.4 - - - -
163B LYS* 1.3 78.1 - - - +
165B ALA* 1.3 56.7 + - - +
166B ASN* 3.3 13.0 + - - -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 3.6 41.4 - - + +
161B GLY 3.7 1.4 + - - +
162B LEU 3.2 4.6 + - - +
164B ALA* 1.3 75.9 - - - +
166B ASN* 1.3 73.2 + - - +
167B ALA* 3.2 2.7 + - - -
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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