Contacts of the strand formed by residues 183 - 196 (chain D) in PDB entry 4DQ0
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 ASN 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C THR* 3.5 22.8 - - - +
17C ARG* 4.8 7.0 + - - +
43C ARG* 4.8 0.4 - - - +
176C HIS* 3.6 18.6 - - + +
201C NHE 2.7 44.2 + - - +
176D HIS* 3.5 4.9 - - - +
177D ARG* 3.3 35.1 + - - +
182D GLY* 1.3 76.2 - - - +
184D ARG* 1.3 75.2 + - - +
185D ILE* 4.6 2.0 - - - +
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Residues in contact with ARG 184 (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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16C THR* 4.9 4.7 + - - +
174D GLU* 3.5 32.9 + - + +
175D LEU 3.4 4.3 - - - +
176D HIS* 3.2 38.0 - - - +
177D ARG 5.3 5.3 + - - +
178D THR* 5.8 2.8 - - - +
183D ASN* 1.3 86.2 + - - +
185D ILE* 1.3 66.2 + - - +
186D LYS* 4.0 7.5 + - + +
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Residues in contact with ILE 185 (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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16C THR* 4.1 23.6 - - + +
176C HIS* 4.7 2.7 - - + -
201C NHE 3.4 49.6 - - + +
144D THR* 4.1 19.7 - - - +
145D VAL* 4.8 9.4 - - + -
174D GLU* 3.1 5.1 - - - -
175D LEU* 2.8 50.0 + - + +
183D ASN* 4.6 2.2 - - - +
184D ARG* 1.3 78.3 - - - +
186D LYS* 1.3 70.4 + - - +
187D LEU* 3.3 9.8 - - + +
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Residues in contact with LYS 186 (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 TYR* 3.7 33.9 - - + +
142D PRO 5.7 0.9 - - - +
144D THR* 5.5 1.0 + - - -
172D VAL* 3.9 14.4 - - + -
173D GLY 3.3 13.9 - - - +
174D GLU* 3.3 33.3 + - - -
184D ARG* 4.0 7.6 + - + +
185D ILE* 1.3 78.9 - - - +
187D LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 187 (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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135D ALA* 4.2 19.3 - - + -
136D MET 4.9 8.7 - - - +
141D TYR* 4.3 13.9 - - + +
142D PRO 5.9 2.2 - - - +
143D CYS* 6.0 5.6 - - - -
145D VAL* 5.0 6.1 - - + -
147D PHE* 4.3 13.9 - - + -
172D VAL* 4.5 2.9 - - - +
173D GLY* 2.6 37.7 + - - +
174D GLU* 3.9 1.3 - - - -
175D LEU* 3.7 22.2 - - + +
185D ILE* 3.3 22.0 - - + +
186D LYS* 1.3 75.0 - - - +
188D ARG* 1.3 59.7 + - - +
189D PHE* 3.4 37.6 - - + -
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Residues in contact with ARG 188 (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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135D ALA* 3.9 1.0 - - - -
136D MET* 2.9 42.5 + - + +
138D THR* 3.8 23.6 - - + +
140D ASP* 2.9 34.3 + - - -
141D TYR* 3.8 17.1 + - + +
170D GLU* 2.9 30.7 + - - +
171D ASP* 3.3 8.3 - - - +
172D VAL* 3.6 29.8 - - + +
187D LEU* 1.3 81.8 - - - +
189D PHE* 1.3 63.0 - - - +
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Residues in contact with PHE 189 (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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178C THR* 3.4 39.5 - - + -
103D VAL* 4.8 1.3 - - + -
106D MET* 4.4 6.7 - - + -
133D VAL* 4.9 12.1 - - + -
134D ALA* 3.5 6.3 - - - +
135D ALA* 3.7 32.8 - - + -
136D MET* 3.7 4.0 - - - -
147D PHE* 5.9 0.4 - + - -
169D ASN* 3.4 5.0 - - - +
170D GLU* 3.3 18.9 - - - -
171D ASP 3.2 10.6 + - - +
173D GLY* 4.0 10.5 - - - -
174D GLU 4.0 13.2 - - - -
175D LEU* 3.8 4.5 - - + -
187D LEU* 3.4 44.6 - - + -
188D ARG* 1.3 73.4 - - - +
190D ALA* 1.3 62.4 + - - +
191D THR* 3.5 9.6 + - - +
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Residues in contact with ALA 190 (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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132D ILE 3.5 2.5 - - - +
133D VAL* 3.3 4.9 - - - +
134D ALA 2.8 37.0 + - - +
136D MET* 3.4 23.2 - - + +
151D PHE* 4.3 12.8 - - + -
156D LEU* 3.6 28.3 - - + +
168D TYR* 4.9 1.3 - - - +
169D ASN 3.5 7.2 - - - +
170D GLU* 4.7 4.7 - - + -
189D PHE* 1.3 70.3 - - - +
191D THR* 1.3 61.3 + - - +
192D MET 4.2 0.2 - - - -
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D GLU* 3.7 39.7 + - + +
131D LEU* 5.3 2.5 - - + -
132D ILE 3.5 2.9 - - - -
133D VAL* 3.9 17.8 - - + +
156D LEU* 4.7 0.2 - - - +
167D LYS* 4.0 15.2 - - + +
168D TYR* 3.3 5.5 + - - -
169D ASN* 2.9 53.6 + - - +
189D PHE* 3.5 7.3 + - - +
190D ALA* 1.3 72.3 + - - +
192D MET* 1.3 64.9 + - - +
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Residues in contact with MET 192 (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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130D ASN 3.6 10.7 - - - +
131D LEU* 3.4 9.7 - - - +
132D ILE* 2.9 46.6 + - + +
156D LEU* 3.7 31.9 - - + +
160D TYR* 3.4 62.6 - - + -
165D MET* 3.8 15.5 - - - +
167D LYS 3.3 4.5 - - - +
168D TYR* 3.7 15.5 - - + -
191D THR* 1.3 78.1 - - - +
193D LEU* 1.3 62.0 + - - +
194D ALA* 3.7 16.2 - - + -
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Residues in contact with LEU 193 (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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25D ALA* 4.5 17.5 - - + -
28D VAL* 4.3 25.8 - - + -
29D VAL* 4.2 9.2 - - + -
98D PHE* 4.8 0.4 - - + -
129D TYR* 3.8 29.2 - - + -
130D ASN 3.6 8.5 - - - +
131D LEU* 4.5 19.3 - - + -
165D MET* 3.9 0.3 - - - -
166D VAL* 3.0 47.4 + - + +
167D LYS* 2.8 32.8 + - + +
192D MET* 1.3 72.7 - - - +
194D ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 194 (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 TYR* 3.1 8.9 - - - +
130D ASN 2.9 33.4 + - - +
160D TYR* 4.0 1.3 - - + -
163D TRP* 3.9 17.7 - - + -
164D GLU 3.3 4.3 - - - +
165D MET* 3.6 28.5 - - + -
166D VAL* 4.7 0.2 - - - -
192D MET* 3.7 21.3 - - + -
193D LEU* 1.3 74.5 - - - +
195D ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 195 (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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30D LYS* 4.9 11.7 - - - +
127D GLY* 3.0 31.6 + - - +
128D GLY 3.3 11.2 - - - +
129D TYR* 3.4 37.8 + - + -
163D TRP* 3.5 4.5 - - - +
164D GLU* 2.8 54.3 + - - +
166D VAL* 4.0 10.7 - - + +
194D ALA* 1.3 75.4 - - - +
196D LYS* 1.3 67.8 + - - +
197D LYS* 3.6 1.4 + - + +
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Residues in contact with LYS 196 (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 GLN* 2.9 26.2 + - - -
122D ARG* 4.1 9.1 + - - +
124D THR* 2.9 24.8 + - + +
125D LYS 3.9 13.5 - - - +
126D PRO* 4.2 9.2 - - + +
127D GLY* 2.7 30.5 + - - -
128D GLY 2.8 13.4 + - - +
163D TRP* 3.5 45.8 - - + +
195D ARG* 1.3 75.0 + - - +
197D LYS* 1.3 64.3 + - - +
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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