Contacts of the strand formed by residues 149 - 160 (chain D) in PDB entry 2CX9
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 GLY 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D LYS* 3.1 9.8 + - - +
146D VAL* 2.8 25.5 + - - -
147D GLU 3.3 1.4 - - - -
148D GLY* 1.3 78.5 - - - +
150D TRP* 1.3 67.5 + - - -
224D PHE* 3.8 4.5 - - - -
225D VAL 3.1 13.2 - - - -
226D PRO 3.8 7.6 - - - -
227D GLU* 2.6 12.7 + - - -
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Residues in contact with TRP 150 (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 ALA* 4.0 13.0 - - + -
144D GLU 3.2 8.5 - - - -
145D LYS* 3.5 54.7 - - + +
146D VAL* 3.6 2.4 - - - +
149D GLY* 1.3 80.4 - - - -
151D ARG* 1.3 63.8 + - - +
152D LEU* 4.4 6.7 - - + -
174D THR* 3.6 24.9 - - + -
190D PHE* 3.5 29.7 - + + -
223D LEU 3.4 0.7 - - - +
224D PHE* 3.3 9.2 - - - -
225D VAL* 2.8 41.5 + - + -
226D PRO 4.1 12.6 - - - -
227D GLU* 4.6 7.2 + - - -
230D LEU* 4.3 26.6 - - + +
234D ARG* 3.8 33.9 - - + -
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Residues in contact with ARG 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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142D LYS 3.5 1.7 - - - +
143D ALA* 3.4 1.7 - - - -
144D GLU* 2.8 51.1 + - + +
146D VAL* 4.1 25.1 - - + +
150D TRP* 1.3 79.5 - - - +
152D LEU* 1.3 63.0 + - - +
153D ASN* 4.2 1.6 + - - +
222D ASP* 3.3 40.4 + - - +
223D LEU 3.2 1.8 - - - -
224D PHE* 3.1 38.2 - - - +
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Residues in contact with LEU 152 (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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141D THR* 5.0 1.8 - - + -
142D LYS 3.2 3.4 - - - +
143D ALA* 3.2 35.0 - - + -
150D TRP* 4.4 7.6 - - + -
151D ARG* 1.3 75.3 - - - +
153D ASN* 1.3 66.2 + - - +
170D VAL* 4.6 8.3 - - + -
172D ALA* 4.4 4.3 - - + -
190D PHE* 4.0 24.9 - - + -
192D PHE* 4.3 24.5 - - + -
220D LEU* 3.8 21.3 - - + +
222D ASP 3.3 1.7 + - - -
223D LEU* 2.7 51.2 + - + +
225D VAL* 4.4 10.8 - - + -
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Residues in contact with ASN 153 (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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140D LYS 4.2 2.1 - - - +
141D THR* 3.3 3.3 - - - +
142D LYS* 2.8 40.2 + - + +
144D GLU* 4.3 15.2 + - - -
151D ARG* 4.6 4.4 + - - +
152D LEU* 1.3 77.8 + - - +
154D GLY* 1.3 59.2 + - - +
220D LEU 3.3 6.8 - - - +
221D GLU* 3.5 4.9 - - - +
222D ASP* 2.5 49.7 + - - +
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Residues in contact with GLY 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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140D LYS 5.2 0.7 - - - -
141D THR* 3.5 19.7 - - - -
153D ASN* 1.3 75.2 - - - +
155D THR* 1.3 64.4 + - - -
156D LYS 4.3 0.2 - - - -
218D LEU 3.8 0.3 - - - +
219D ILE* 4.9 0.7 - - - +
220D LEU* 2.8 40.3 + - - +
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Residues in contact with THR 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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129D GLU* 3.3 17.6 + - - +
130D PRO* 3.3 29.6 - - + +
141D THR* 3.6 2.6 + - - +
154D GLY* 1.3 78.2 + - - -
156D LYS* 1.3 64.4 + - - +
217D GLN* 3.5 41.1 - - + +
218D LEU 3.2 7.0 + - - +
219D ILE* 4.6 12.0 - - + +
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Residues in contact with LYS 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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126D GLY* 3.4 24.8 + - - +
127D LEU 3.0 19.4 + - - +
128D THR 3.2 12.6 - - - +
129D GLU* 2.8 23.9 + - + -
139D LEU* 3.7 6.7 - - - +
141D THR* 3.2 14.1 - - - +
155D THR* 1.3 75.4 - - - +
157D GLN* 1.3 61.7 + - - +
159D ILE* 3.7 19.3 - - + -
170D VAL* 3.8 14.1 - - + -
171D MET 2.8 26.3 + - - -
217D GLN* 3.1 7.4 - - - +
218D LEU* 2.6 49.0 + - + +
220D LEU* 5.1 5.2 - - + -
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Residues in contact with GLN 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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347C TYR* 3.4 32.0 + - - +
128D THR* 2.9 25.6 + - + -
129D GLU* 4.0 3.3 - - - +
130D PRO* 3.3 35.2 - - + +
156D LYS* 1.3 74.2 - - - +
158D PHE* 1.3 85.7 + - + +
159D ILE* 3.2 10.6 + - - +
205D GLU* 3.3 30.7 + - - -
217D GLN* 3.3 35.3 - - + +
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Residues in contact with PHE 158 (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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346C GLY* 3.5 42.6 - - - -
347C TYR* 3.9 34.8 - + - -
350C VAL* 3.9 14.6 - - + -
128D THR* 4.8 12.2 - - + -
157D GLN* 1.3 86.7 - - + +
159D ILE* 1.3 64.3 + - - +
160D THR* 3.5 6.4 + - - -
205D GLU* 3.4 25.4 - - + -
215D THR* 3.7 26.4 - - + +
216D ALA 3.8 8.2 + - - +
217D GLN* 4.6 0.2 - - - +
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Residues in contact with ILE 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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124D ALA* 3.9 19.3 - - + -
125D TRP 3.4 29.6 - - - +
126D GLY* 3.6 11.7 - - - -
127D LEU 4.0 6.5 - - - +
128D THR* 4.1 5.8 - - - +
156D LYS* 3.7 25.1 - - + -
157D GLN 3.6 14.6 - - - +
158D PHE* 1.3 76.8 - - - +
160D THR* 1.3 70.4 + - - +
161D GLN 3.6 0.3 + - - -
162D GLY* 3.0 16.3 + - - -
215D THR* 4.4 0.9 - - - -
216D ALA 3.0 31.4 + - - +
218D LEU* 3.9 17.7 - - + -
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Residues in contact with THR 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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87D LEU* 4.4 26.8 - - + +
88D THR* 4.8 0.4 - - - -
91D SER* 3.2 24.1 - - - +
95D LEU* 5.9 2.9 - - - +
124D ALA* 3.6 15.2 - - - -
125D TRP 4.4 2.2 + - - +
158D PHE 3.5 6.5 + - - -
159D ILE* 1.3 70.1 - - - +
161D GLN* 1.3 102.3 + - - +
162D GLY 2.9 7.6 + - - -
213D SER* 5.3 2.2 - - - -
214D ASP 3.2 12.8 - - - +
215D THR* 4.6 4.9 + - - +
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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