Contacts of the helix formed by residues 148 - 165 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D CYS 5.2 4.9 - - - +
55D PRO* 6.0 1.6 - - - +
80D SER* 4.6 15.5 + - - +
146D ASP* 2.8 41.4 + - - +
147D LYS* 1.3 80.0 - - - +
149D GLN* 1.3 62.2 + - - +
150D TYR* 3.4 3.9 + - + +
151D GLY 3.5 1.2 + - - +
152D GLU* 3.0 31.1 + - - +
177D ALA* 4.0 17.4 - - - +
202D TYR* 4.2 19.6 - - + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D SER* 3.7 9.0 + - - -
80D SER* 3.6 37.6 - - - +
83D GLN* 2.6 36.9 + - - +
84D PRO* 5.7 0.2 - - - +
103D ASN* 3.3 36.0 + - - +
105D GLU* 4.2 9.2 - - - +
148D GLN* 1.3 75.5 - - - +
150D TYR* 1.3 63.2 + - - +
152D GLU* 5.1 0.9 - - - -
153D GLY* 3.2 16.5 + - - +
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Residues in contact with TYR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D SER* 4.5 8.5 - - - -
80D SER* 5.4 1.4 - - - +
102D THR* 3.4 11.9 - - - -
103D ASN* 4.6 5.2 + - - +
121D ASP* 3.6 8.6 - - - +
148D GLN* 3.4 1.7 - - + +
149D GLN* 1.3 78.4 - - - +
151D GLY* 1.3 63.2 + - - +
153D GLY* 3.9 0.2 - - - -
154D LEU* 3.1 47.0 + - + +
201D GLY* 3.6 23.3 - - - -
202D TYR* 3.5 34.8 - + + +
225D PRO* 3.2 14.6 - - + +
226D GLU* 2.5 23.0 + - - -
227D GLY* 2.9 17.0 + - - -
1347D LEU* 3.2 52.7 - - - +
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Residues in contact with GLY 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D HIS* 4.1 0.9 - - - -
146D ASP* 3.9 8.5 + - - -
148D GLN* 3.5 4.4 + - - +
149D GLN 3.5 0.2 - - - -
150D TYR* 1.3 81.8 - - - +
152D GLU* 1.3 58.9 + - - +
154D LEU* 3.3 2.2 + - - -
155D ALA* 2.9 30.3 + - - +
200D GLY* 3.3 36.7 - - - -
201D GLY 3.7 3.8 - - - -
202D TYR* 5.9 0.2 - - - -
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D HIS* 3.4 41.4 - - + +
146D ASP* 4.4 1.4 + - - -
147D LYS* 3.7 22.5 - - - +
148D GLN 3.0 19.4 + - - +
149D GLN* 4.8 1.3 - - - +
151D GLY* 1.3 74.8 - - - +
153D GLY* 1.3 56.9 + - - +
155D ALA* 3.8 0.4 - - - +
156D ARG* 3.0 71.4 + - + +
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 4.5 8.7 - - - -
121D ASP* 5.7 3.6 - - - -
149D GLN 3.2 20.9 + - - -
150D TYR 3.9 0.4 - - - -
152D GLU* 1.3 78.9 - - - +
154D LEU* 1.3 56.6 + - - +
156D ARG* 3.6 5.8 + - - +
157D SER* 3.0 27.5 + - - -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 3.6 29.6 - - + +
124D GLN* 3.7 22.0 - - + +
125D GLY* 3.8 19.5 - - - +
150D TYR* 3.1 51.1 + - + +
151D GLY* 3.3 4.7 + - - +
153D GLY* 1.3 73.1 - - - +
155D ALA* 1.3 60.5 + - - +
157D SER* 3.6 4.0 - - - -
158D VAL* 3.0 34.3 + - - +
198D TYR* 3.8 20.6 - - + +
200D GLY* 4.7 1.3 - - - -
225D PRO* 3.5 19.5 - - + -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 3.7 26.8 - - + +
144D ILE 4.0 4.7 - - - +
145D HIS* 3.8 20.6 - - + -
151D GLY 2.9 16.6 + - - +
152D GLU 3.8 4.3 - - - +
154D LEU* 1.3 75.4 - - - +
156D ARG* 1.3 58.1 + - - +
158D VAL* 3.4 0.9 + - - -
159D GLN* 2.8 29.6 + - - +
172D PHE* 4.0 10.5 - - + -
198D TYR* 4.4 8.4 - - - -
200D GLY* 4.6 1.6 - - - +
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D HIS* 5.4 0.6 + - - -
152D GLU* 3.0 49.1 + - - +
153D GLY* 3.9 6.1 - - - +
155D ALA* 1.3 74.4 - - - +
157D SER* 1.3 60.6 + - - +
159D GLN* 3.6 16.2 + - - +
160D ASP* 3.0 40.8 + - - +
172D PHE* 3.8 33.7 - - + -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 4.0 8.4 + - - -
122D SER* 5.4 1.0 - - - -
125D GLY* 3.5 23.3 - - - -
126D PRO* 3.5 14.2 - - - +
129D ALA* 5.3 0.3 - - - +
153D GLY 3.0 18.8 + - - -
154D LEU* 3.6 8.3 - - - -
156D ARG* 1.3 78.0 - - - +
158D VAL* 1.3 58.0 + - - +
160D ASP* 3.4 7.1 + - - +
161D GLY* 3.1 23.9 + - - -
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY* 3.6 26.7 - - - +
128D ALA* 4.2 2.7 - - + -
129D ALA* 4.3 10.2 - - + +
132D ILE* 4.2 13.9 - - + -
143D ILE* 4.6 3.1 - - + -
154D LEU 3.0 21.0 + - - +
155D ALA 3.9 2.9 - - - +
157D SER* 1.3 73.7 - - - +
159D GLN* 1.3 66.8 + - - +
161D GLY* 4.0 0.3 - - - -
162D LEU* 3.1 43.0 + - + +
198D TYR* 3.8 46.0 - - + +
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 3.5 19.7 - - + +
155D ALA 2.8 18.0 + - - +
156D ARG* 3.8 16.5 + - - +
158D VAL* 1.3 77.3 - - - +
160D ASP* 1.3 62.7 - - - +
162D LEU* 3.8 2.3 - - - +
163D LYS* 2.9 59.8 + - + +
169D VAL* 4.1 11.9 - - + +
172D PHE* 3.3 43.3 - - + +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ARG* 3.0 25.9 + - - +
157D SER* 3.6 6.5 - - - +
158D VAL 3.3 0.2 - - - -
159D GLN* 1.3 85.9 - - - +
161D GLY* 1.3 62.5 + - - +
163D LYS* 3.2 9.2 + - - +
164D ALA* 3.0 23.7 + - - +
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Residues in contact with GLY 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 6.1 1.8 - - - -
129D ALA* 4.4 15.0 - - - -
133D LEU* 4.0 8.8 - - - +
157D SER 3.1 15.7 + - - -
158D VAL 4.0 1.1 - - - -
160D ASP* 1.3 75.2 - - - +
162D LEU* 1.3 61.5 + - - +
164D ALA* 3.4 18.6 + - - +
165D ALA* 3.6 4.7 + - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 4.0 8.0 - - + +
132D ILE* 3.7 26.9 - - + -
133D LEU* 3.6 32.5 - - + -
141D ILE* 4.2 24.2 - - + -
143D ILE* 4.1 15.7 - - + -
158D VAL* 3.1 37.1 + - + +
159D GLN 3.8 3.6 - - - +
161D GLY* 1.3 76.6 - - - +
163D LYS* 1.3 60.1 + - - +
165D ALA* 3.2 5.5 + - - +
166D ASN 3.1 4.3 + - - -
167D ALA* 3.1 35.8 + - + +
169D VAL* 4.3 7.4 - - + -
196D PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLN* 2.9 50.9 + - + +
160D ASP* 3.2 8.9 + - - +
162D LEU* 1.3 74.4 - - - +
164D ALA* 1.3 60.8 + - - +
166D ASN* 3.0 27.5 + - - +
167D ALA 4.6 4.9 - - - +
169D VAL* 4.7 19.5 - - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP 3.0 11.9 + - - +
161D GLY* 3.4 14.1 - - - +
162D LEU 3.2 0.4 - - - -
163D LYS* 1.3 77.4 - - - +
165D ALA* 1.3 56.3 + - - +
166D ASN* 3.3 12.7 + - - -
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.7 39.2 - - + +
161D GLY 3.6 1.5 + - - +
162D LEU 3.2 3.5 + - - +
164D ALA* 1.3 76.8 - - - +
166D ASN* 1.3 70.4 + - - +
167D ALA* 3.3 3.1 + - - -
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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