Contacts of the strand formed by residues 165 - 174 (chain D) in PDB entry 5AEW
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 PHE 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.8 1.3 - - + -
26D GLU* 3.9 32.3 - - + -
27D ILE* 3.6 28.5 - - + -
30D PHE* 3.3 43.7 - + + -
49D LEU* 4.3 2.1 - - - +
128D PHE* 4.0 10.8 - + - -
156D LEU* 4.4 10.1 - - + -
157D ARG 3.2 17.5 - - - +
158D ARG* 3.5 42.0 - - + -
159D ALA* 3.9 2.5 - - - +
161D ASN* 2.8 21.0 + - - +
163D LEU 3.3 14.6 - - - -
164D GLY* 1.3 85.4 - - - +
166D SER* 1.3 64.0 + - - +
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Residues in contact with SER 166 (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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48D ALA 5.7 0.4 - - - -
49D LEU 3.2 13.2 - - - -
50D LEU 4.9 0.4 - - - -
51D ASP* 3.3 28.4 + - - -
156D LEU* 3.4 7.3 - - - +
157D ARG* 2.8 45.6 + - - +
158D ARG 4.9 0.2 + - - -
159D ALA* 3.8 13.4 - - - +
161D ASN* 4.2 4.5 - - - -
165D PHE* 1.3 74.8 - - - +
167D ILE* 1.3 63.3 + - - +
168D ALA 3.6 0.3 + - - -
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Residues in contact with ILE 167 (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 PHE* 3.8 23.6 - - + -
34D GLU* 3.8 18.6 - - + +
46D TRP* 4.8 0.9 - - - +
49D LEU* 2.8 22.3 + - + +
50D LEU* 4.0 20.6 - - + -
51D ASP* 2.9 23.9 + - - +
54D ILE* 3.2 26.4 - - + +
56D TYR* 6.1 0.2 - - + -
154D ASP* 4.6 0.2 - - - +
155D VAL 4.0 2.2 - - - -
156D LEU* 3.8 14.6 - - + -
166D SER* 1.3 69.6 - - - +
168D ALA* 1.3 59.2 + - - +
169D LYS 3.8 16.2 - - - +
170D ARG* 3.7 34.5 - - + +
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Residues in contact with ALA 168 (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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51D ASP* 3.8 8.3 - - + -
53D ASP* 3.5 9.4 - - - +
54D ILE* 3.2 22.3 - - - -
55D HIS 3.5 1.4 + - - -
155D VAL* 2.9 24.3 + - + +
157D ARG* 3.7 46.0 - - + +
166D SER 3.6 1.6 + - - -
167D ILE* 1.3 73.6 - - - +
169D LYS* 1.3 63.1 + - + +
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Residues in contact with LYS 169 (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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44B GLU* 4.2 21.9 + - + +
47B PHE* 6.2 2.2 - - - -
90B TYR* 4.9 20.1 + - - -
54D ILE* 3.7 3.6 - - - +
55D HIS* 3.6 23.6 + - + +
57D PHE* 6.3 0.8 - - - +
153D ARG 4.4 2.5 - - - +
154D ASP* 3.2 6.1 - - - +
155D VAL* 2.9 51.7 + - + +
167D ILE* 3.5 3.4 - - - +
168D ALA* 1.3 80.7 - - + +
170D ARG* 1.3 67.1 + - - +
171D THR* 4.7 12.4 + - - +
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Residues in contact with ARG 170 (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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31D TYR* 3.8 3.2 - - - -
34D GLU* 2.7 43.0 + - - -
46D TRP* 4.3 9.1 - - - -
54D ILE* 4.2 1.3 - - + +
55D HIS 3.0 11.7 + - - +
56D TYR* 3.7 27.3 - - + -
57D PHE* 2.8 26.2 + - - +
152D ARG* 3.4 22.8 - - + +
153D ARG 3.5 4.9 - - - -
154D ASP* 2.8 37.4 + - - +
167D ILE* 3.7 24.7 - - + +
169D LYS* 1.3 73.8 - - - +
171D THR* 1.3 67.0 + - - +
172D ILE* 3.8 25.6 - - + -
188D PHE 3.5 14.7 + - - -
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Residues in contact with THR 171 (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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250A GLU* 5.3 4.0 - - + +
57D PHE* 3.1 32.8 - - + +
59D PRO* 4.1 2.7 - - + -
151D GLU 3.8 0.7 - - - +
152D ARG* 3.4 4.0 - - - +
153D ARG* 2.9 48.8 + - + +
169D LYS* 4.7 15.8 + - - -
170D ARG* 1.3 76.3 + - - +
172D ILE* 1.3 64.7 + - - +
173D LEU* 3.7 26.8 + - + -
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Residues in contact with ILE 172 (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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56D TYR* 3.8 32.5 - - + +
57D PHE 2.8 18.1 + - - +
58D MET* 3.5 37.6 - - + +
59D PRO* 3.4 21.0 - - - +
134D PHE* 3.7 34.1 - - + -
151D GLU 3.5 2.5 - - - -
152D ARG* 4.3 6.1 - - + -
170D ARG* 3.8 26.2 - - + +
171D THR* 1.3 75.8 - - - +
173D LEU* 1.3 67.2 + - - +
174D LEU* 3.7 3.3 + - + +
188D PHE* 3.9 14.8 - - + -
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Residues in contact with LEU 173 (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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250A GLU* 4.0 13.2 - - + -
59D PRO* 3.7 20.9 - - + -
61D ARG* 4.6 1.8 - - - +
73D TYR* 3.7 35.7 - - + +
150D GLY* 3.2 4.2 - - - -
151D GLU* 2.9 53.0 + - + +
153D ARG* 3.6 42.6 - - - +
171D THR* 3.7 25.6 - - + +
172D ILE* 1.3 72.7 - - - +
174D LEU* 1.3 61.8 + - - +
175D ASP* 4.5 2.6 - - - +
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Residues in contact with LEU 174 (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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58D MET* 4.0 26.4 - - + +
59D PRO 5.7 2.1 + - - +
61D ARG* 3.0 24.2 + - - +
73D TYR* 5.4 0.4 - - - -
81D HIS* 5.2 2.9 - - + -
134D PHE* 3.9 11.7 - - + -
148D PHE* 4.0 24.5 - - + -
149D ALA 3.7 13.2 - - - +
172D ILE* 3.7 6.5 + - + -
173D LEU* 1.3 73.3 - - - +
175D ASP* 1.3 60.3 + - - +
176D ALA* 3.0 19.4 + - + +
179D LEU* 3.7 30.1 - - + -
184D LEU* 4.9 2.0 - - + -
188D PHE* 3.7 29.2 - - + -
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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