Contacts of the strand formed by residues 142 - 152 (chain D) in PDB entry 1MWA
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 LYS 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ASN* 6.0 1.6 - - - -
145C ASP* 5.3 1.3 - - - +
170C MET* 3.2 34.6 - - - +
172C ALA* 5.0 4.2 - - - +
175C SER* 6.1 0.4 - - - +
136D GLU 2.5 30.7 - - - +
137D ILE* 4.3 1.8 + - - -
140D LYS* 2.9 45.1 - - + +
141D GLN* 1.3 82.1 - - - +
143D ALA* 1.3 56.2 + - - +
197D ARG* 2.9 47.1 - - + +
198D VAL 3.7 4.5 - - - -
199D SER* 5.2 4.2 + - - +
204D HIS* 5.4 0.4 - - - -
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Residues in contact with ALA 143 (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 PRO* 4.2 18.8 - - + -
136D GLU* 3.8 14.4 - - - +
137D ILE* 5.2 2.2 - - + -
140D LYS* 4.5 0.2 - - - +
142D LYS* 1.3 78.4 - - - +
144D THR* 1.3 61.2 + - - +
145D LEU* 3.2 5.2 - - - +
197D ARG* 3.2 8.6 - - - +
198D VAL* 3.0 50.5 + - + +
203D TRP* 5.3 1.6 - - + -
204D HIS* 4.8 9.0 - - + -
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Residues in contact with THR 144 (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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128C LEU* 5.8 0.3 - - - +
142C LEU* 3.2 42.3 - - + +
143C PHE 3.5 17.5 - - - +
144C THR* 3.1 25.5 + - - +
168C LEU* 3.5 29.8 - - + +
132D PRO* 4.4 11.4 - - - +
136D GLU* 3.6 9.5 + - - -
140D LYS* 5.6 1.4 - - - +
143D ALA* 1.3 70.4 - - - +
145D LEU* 1.3 64.7 + - - +
195D ARG* 4.8 4.3 - - + -
196D LEU 3.7 3.8 - - - +
197D ARG* 4.1 4.9 + - - +
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Residues in contact with LEU 145 (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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128C LEU* 6.4 0.2 - - - -
181C ILE* 4.8 0.9 - - - +
129D LEU* 6.2 1.8 - - + -
130D PHE 4.8 4.3 - - - +
131D GLU* 5.1 1.1 - - + +
132D PRO* 4.1 22.7 - - + -
143D ALA* 3.2 15.7 - - + +
144D THR* 1.3 78.3 - - - +
146D VAL* 1.3 65.1 + - - +
161D TRP* 3.6 31.2 - - + -
195D ARG* 3.1 23.2 - - - +
196D LEU* 2.9 33.8 + - + +
198D VAL* 3.6 31.4 - - + -
203D TRP* 4.8 15.5 - - + -
210D PHE* 4.6 10.3 - - + -
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Residues in contact with VAL 146 (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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128C LEU* 3.6 31.4 - - + -
142C LEU* 5.6 0.2 - - + -
181C ILE* 3.3 24.9 - - + -
183C TRP* 6.2 0.9 - - + -
129D LEU* 3.7 7.6 - - - +
130D PHE* 3.2 41.3 + - + +
144D THR 5.5 0.4 - - - +
145D LEU* 1.3 82.1 - - - +
147D CYS* 1.3 77.8 + - - +
148D LEU* 4.6 4.7 - - + -
161D TRP* 3.6 11.0 - - - -
193D SER* 4.7 4.7 - - - -
194D SER 2.8 27.4 - - - +
195D ARG* 4.0 0.2 - - - +
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Residues in contact with CYS 147 (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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127D VAL* 3.5 16.4 - - - -
128D SER 3.6 7.2 - - - -
129D LEU* 4.4 8.5 - - + +
146D VAL* 1.3 86.5 - - - +
148D LEU* 1.3 76.7 + - - +
159D LEU* 3.4 11.7 - - - +
161D TRP* 3.5 20.0 - - + -
193D SER* 4.1 1.7 - - - -
194D SER* 3.5 13.1 + - - +
212D CYS* 2.0 50.3 - - + -
239D ALA 4.8 0.2 - - - -
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Residues in contact with LEU 148 (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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183C TRP* 3.6 34.1 - - + -
126D LYS 4.9 0.2 - - - +
127D VAL* 3.0 22.5 - - - +
128D SER* 3.3 39.4 + - - +
129D LEU* 3.8 1.1 - - - +
130D PHE* 3.6 36.1 - - + +
146D VAL* 4.6 6.3 - - + -
147D CYS* 1.3 88.9 - - - +
149D ALA* 1.3 67.9 + - - +
150D ARG* 3.9 21.1 - - + +
159D LEU* 3.3 11.8 - - - +
192D LEU 4.5 7.0 - - - +
193D SER* 5.6 0.7 - - - -
214D VAL* 3.4 1.6 - - - +
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Residues in contact with ALA 149 (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 LYS 3.8 8.9 + - - -
148D LEU* 1.3 77.7 - - - +
150D ARG* 1.3 62.4 + - - +
152D PHE* 2.9 23.6 - - - -
157D VAL* 4.1 8.9 - - + +
159D LEU* 3.5 26.2 - - + +
190D TYR 4.7 0.3 - - - +
191D CYS 5.5 0.2 - - - -
192D LEU* 4.2 10.7 + - + +
214D VAL* 3.2 34.1 - - + -
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Residues in contact with ARG 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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183C TRP* 3.2 42.5 - - + +
185C ASN* 5.9 2.9 - - - +
126D LYS* 3.0 21.1 + - - +
128D SER* 5.1 5.5 + - - -
130D PHE* 5.8 2.0 - - - -
148D LEU* 3.9 17.9 - - + +
149D ALA* 1.3 78.3 - - - +
151D GLY* 1.3 65.9 + - - +
152D PHE* 3.7 2.0 - - - -
181D GLU* 3.8 25.0 + - - -
189D SER* 5.9 1.3 - - - -
190D TYR 2.8 25.8 - - - +
191D CYS* 3.2 27.6 - - + -
192D LEU 3.9 9.0 - - - +
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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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123D THR* 4.3 1.6 + - - -
124D PRO 3.7 7.1 - - - +
126D LYS* 3.7 22.7 - - - +
150D ARG* 1.3 92.1 - - - +
152D PHE* 1.3 70.6 + - - +
189D SER* 4.2 9.4 - - - -
190D TYR 3.6 2.6 + - - -
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Residues in contact with PHE 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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123D THR* 2.9 30.3 - - - +
124D PRO 3.0 7.2 - - - +
125D PRO* 3.6 24.0 - - + -
149D ALA 2.9 33.9 - - - -
150D ARG* 3.7 4.7 - - - -
151D GLY* 1.3 83.2 - - - +
153D PHE* 1.3 53.7 + - - +
154D PRO* 3.0 43.3 - - + -
155D ASP* 5.1 2.2 - - - -
157D VAL* 3.5 31.6 - - + -
187D TYR 2.7 11.1 - - - +
189D SER* 2.6 35.6 + - - +
190D TYR* 3.9 8.9 + - + -
216D PHE* 3.8 4.5 - + - -
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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