Contacts of the strand formed by residues 143 - 153 (chain D) in PDB entry 3ARE
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 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C ASP* 5.5 0.4 - - - -
168C MET* 4.0 22.4 - - + -
171C MET* 3.9 23.7 - - + +
173C PHE* 3.8 44.7 - - + -
137D GLU* 3.3 20.3 - - - +
138D ILE* 3.6 4.2 - - - -
141D THR* 2.9 42.0 + - - +
142D GLN* 1.3 82.3 - - - +
144D ALA* 1.3 61.5 + - - +
198D ARG* 3.7 20.6 - - - +
199D VAL 3.6 7.2 - - - +
200D SER* 5.0 1.8 - - - -
201D ALA 4.0 1.8 - - - +
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Residues in contact with ALA 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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133D PRO* 3.6 26.5 - - + -
137D GLU* 3.6 3.1 - - - -
138D ILE* 4.0 8.7 - - + -
143D LYS* 1.3 74.9 - - - +
145D THR* 1.3 62.7 + - - +
146D LEU* 4.0 0.3 - - - +
197D LEU 3.8 0.5 - - - +
198D ARG* 3.3 2.0 - - - -
199D VAL* 2.7 46.6 + - + +
201D ALA* 4.3 3.8 - - - +
204D TRP* 3.9 23.3 - - + -
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Residues in contact with THR 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* 3.2 18.2 - - - +
140C LEU* 3.7 26.5 - - + +
142C THR* 5.4 0.5 + - - -
166C LEU* 5.1 3.1 - - + -
177C SER* 6.1 1.1 - - - -
133D PRO* 3.4 13.5 - - - +
137D GLU* 2.4 37.2 + - - +
144D ALA* 1.3 72.8 - - - +
146D LEU* 1.3 66.0 + - - +
147D VAL* 4.9 0.2 - - + -
196D ARG* 4.1 27.6 - - + -
197D LEU 3.5 7.9 - - - +
198D ARG* 3.1 25.7 + - + +
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Residues in contact with LEU 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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130D VAL* 4.5 13.0 - - + -
131D PHE 3.5 7.2 - - - +
132D GLU* 5.5 0.2 - - - -
133D PRO* 4.0 19.3 - - + -
144D ALA 4.0 8.7 - - - +
145D THR* 1.3 77.7 - - - +
147D VAL* 1.3 62.9 + - - +
162D TRP* 3.6 22.7 - - + -
196D ARG* 3.3 6.6 - - - +
197D LEU* 2.8 48.3 + - + +
199D VAL* 4.1 16.6 - - + -
204D TRP* 4.0 16.8 - - + -
211D PHE* 3.9 36.8 - - + -
242D ALA* 5.0 1.3 - - + -
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Residues in contact with VAL 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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128C LEU* 3.7 18.6 - - + +
138C VAL* 4.1 20.4 - - + -
140C LEU* 3.8 27.1 - - + -
179C VAL* 4.0 27.8 - - + -
130D VAL* 3.5 2.4 - - - +
131D PHE* 2.7 44.0 + - + -
145D THR* 4.9 0.2 - - + -
146D LEU* 1.3 75.2 - - - +
148D CYS* 1.3 71.7 + - - +
149D LEU* 4.2 7.0 - - + -
162D TRP* 4.1 1.8 - - - -
194D SER* 5.0 0.7 - - - -
195D SER 3.4 7.4 - - - +
196D ARG* 4.1 7.9 - - + -
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Residues in contact with CYS 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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128D VAL* 3.7 11.2 - - - -
129D ALA 3.3 11.7 - - - -
130D VAL* 4.6 0.7 - - + +
147D VAL* 1.3 74.3 - - - +
149D LEU* 1.3 71.0 + - - +
150D ALA 4.2 0.4 - - - -
160D LEU* 4.6 5.3 - - - +
162D TRP* 3.4 20.8 - - + -
193D LEU 3.9 0.3 - - - +
194D SER* 3.3 6.1 - - - -
195D SER* 2.8 36.0 + - - +
213D CYS* 2.0 50.5 - - + -
215D VAL* 5.0 0.2 - - - -
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Residues in contact with LEU 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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138C VAL* 4.3 4.0 - - + -
179C VAL* 4.3 2.7 - - + -
181C TRP* 3.5 55.2 - - + +
127D GLU 3.3 2.6 - - - +
128D VAL* 3.3 4.3 - - - -
129D ALA* 2.9 38.5 + - + +
131D PHE* 3.8 25.4 - - + -
147D VAL* 4.2 12.3 - - + -
148D CYS* 1.3 77.8 - - - +
150D ALA* 1.3 60.3 + - - +
151D THR* 4.0 17.4 + - + +
193D LEU 3.6 1.8 - - - +
194D SER* 3.6 28.5 - - - -
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Residues in contact with ALA 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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126D PRO* 4.2 15.3 - - + -
127D GLU 3.3 6.1 - - - +
128D VAL* 4.5 1.1 - - + +
148D CYS* 4.2 1.6 - - - -
149D LEU* 1.3 71.1 - - - +
151D THR* 1.3 61.2 + - - +
153D PHE* 3.6 12.1 - - + -
158D VAL* 5.8 0.4 - - + -
160D LEU* 5.1 4.0 - - + +
192D ALA* 3.2 3.1 - - - -
193D LEU* 2.8 46.5 + - + +
215D VAL* 4.0 30.3 - - + -
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Residues in contact with THR 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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181C TRP* 4.1 10.1 - - + +
125D PRO 4.4 0.2 - - - +
126D PRO* 3.6 1.0 - - - +
127D GLU* 2.9 47.4 + - - +
149D LEU* 4.0 29.5 + - + +
150D ALA* 1.3 78.8 - - - +
152D GLY* 1.3 64.6 + - - +
153D PHE* 3.4 3.5 + - - -
182D GLU* 3.6 7.9 - - - +
191D TYR 3.7 2.5 - - - -
192D ALA* 3.9 15.0 - - + -
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Residues in contact with GLY 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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124D PHE* 3.4 19.8 - - - +
125D PRO 3.4 7.7 - - - +
127D GLU* 5.8 1.6 - - - -
151D THR* 1.3 72.3 - - - +
153D PHE* 1.3 58.1 + - - +
182D GLU* 2.9 30.4 + - - -
190D ARG* 3.4 25.8 + - - -
191D TYR 3.0 2.9 + - - -
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Residues in contact with PHE 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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124D PHE 3.3 11.2 - - - +
126D PRO* 3.7 33.2 - - + -
150D ALA* 3.6 24.9 - - + -
151D THR 4.2 0.2 - - - -
152D GLY* 1.3 78.0 - - - +
154D TYR* 1.3 62.2 + - - +
155D PRO 3.7 11.4 - - - -
156D ASP* 3.8 16.2 - - + -
158D VAL* 3.6 38.8 - - + -
179D PRO* 4.4 4.9 - - + -
190D ARG* 4.4 0.7 - - - -
191D TYR* 2.7 78.6 + - + -
192D ALA* 3.7 3.4 - - - -
193D LEU* 3.8 14.1 - - + -
217D PHE* 4.4 2.2 - + + -
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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