Contacts of the strand formed by residues 47 - 54 (chain D) in PDB entry 2A3W
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 TYR 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D SER* 4.1 17.1 + - - -
43D LEU* 3.7 36.1 + - + -
45D ARG* 3.2 25.6 - - - +
46D ALA* 1.3 76.2 - - - +
48D SER* 1.3 61.6 + - - +
49D LEU* 3.6 27.3 - - + +
64D TYR* 3.6 6.7 - - - -
65D LYS* 2.9 68.5 + - + +
148D GLN* 3.4 7.0 - - - +
149D SER 3.5 24.0 - - - +
150D PHE* 3.6 21.5 - + - -
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Residues in contact with SER 48 (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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47D TYR* 1.3 73.8 - - - +
49D LEU* 1.3 60.7 + - - +
50D PHE 3.6 6.4 + - - -
51D SER* 3.6 12.8 - - - -
62D LEU* 3.4 18.2 - - - +
63D VAL 3.8 1.6 - - - -
64D TYR* 3.8 9.0 - - - -
132D VAL 5.1 0.2 + - - -
134D GLY 5.0 4.0 + - - -
135D GLN 3.8 3.9 + - - +
136D GLU* 3.4 37.5 - - - -
148D GLN 3.0 10.3 + - - +
150D PHE* 3.6 23.9 + - - +
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Residues in contact with LEU 49 (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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37D PHE* 3.5 33.5 - - + -
39D ALA* 4.2 9.4 - - + -
47D TYR* 3.6 24.7 + - + +
48D SER* 1.3 74.0 - - - +
50D PHE* 1.3 62.1 + - - +
63D VAL* 2.8 23.9 + - + +
65D LYS* 4.0 28.5 - - + +
71D TYR* 4.5 7.0 - - + -
94D ILE* 4.1 17.9 - - + -
132D VAL 5.1 0.9 - - - -
133D LEU* 3.9 19.0 - - - +
134D GLY 5.0 0.5 + - - -
150D PHE* 3.7 21.1 - - + -
154D ILE* 4.1 15.9 - - + +
157D LEU* 6.0 0.2 - - - +
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Residues in contact with PHE 50 (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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22D LEU* 4.3 1.6 - - + -
35D LEU* 3.5 44.6 - - + -
37D PHE* 4.6 3.8 - - + -
48D SER* 3.6 2.2 + - - -
49D LEU* 1.3 82.4 - - + +
51D SER* 1.3 60.6 + - - +
52D TYR* 3.8 26.2 - + + -
61D LEU* 4.2 17.5 - - + -
62D LEU* 3.3 8.1 - - - +
63D VAL* 3.0 30.7 + - + -
131D ILE* 3.5 29.2 - - + -
132D VAL 4.1 2.9 - - - -
133D LEU* 4.1 9.2 - - + -
157D LEU* 4.0 15.0 - - + -
159D MET* 4.0 22.9 - - - -
183D LEU* 3.9 12.3 - - + -
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Residues in contact with SER 51 (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 SER* 3.6 8.5 - - - -
50D PHE* 1.3 74.4 - - - +
52D TYR* 1.3 58.2 + - - +
53D ASN* 4.3 2.6 + - - -
62D LEU* 4.1 7.4 - - - +
131D ILE* 3.3 2.3 - - - -
132D VAL 2.9 30.1 + - - +
135D GLN 3.6 22.9 - - - -
136D GLU* 3.9 6.9 + - - -
137D GLN* 2.8 53.0 + - - +
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Residues in contact with TYR 52 (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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26D LEU* 3.8 20.5 - - + +
30D LEU* 4.2 4.4 - - + +
50D PHE* 3.8 15.7 - + + -
51D SER* 1.3 74.6 + - - +
53D ASN* 1.3 67.6 + - - +
54D THR* 3.8 7.6 - - + -
59D ASN* 4.5 0.2 - - - -
60D GLU* 3.3 12.7 + - + -
61D LEU* 2.9 67.5 + - + +
62D LEU* 5.1 0.8 - - - +
125D VAL* 3.8 14.0 - - + +
126D GLU 2.5 30.6 + - - -
127D ALA* 4.0 0.3 - - - -
129D PRO* 3.3 32.7 - - + +
130D LYS 3.5 4.0 - - - -
131D ILE* 3.8 23.6 - - + +
159D MET* 4.7 3.6 - - + -
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Residues in contact with ASN 53 (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 SER* 4.3 3.6 + - - -
52D TYR* 1.3 77.6 + - - +
54D THR* 1.3 65.8 + - - +
57D ARG 3.5 10.4 + - - +
58D ASP* 3.1 26.7 + - - +
59D ASN* 3.1 20.3 + - - +
60D GLU* 4.4 1.1 - - - -
129D PRO* 3.3 4.2 - - - +
130D LYS 2.8 32.7 + - - -
136D GLU* 4.8 0.5 - - - +
137D GLN* 3.4 34.5 + - - +
139D SER 2.9 29.1 + - - +
140D TYR* 3.7 4.0 - - - -
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Residues in contact with THR 54 (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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52D TYR* 3.8 12.6 - - + -
53D ASN* 1.3 79.3 - - - +
55D GLN* 1.3 55.6 + - - +
56D GLY 3.0 1.0 + - - -
57D ARG* 2.7 45.9 + - - +
60D GLU* 3.9 6.0 - - + +
126D GLU* 2.8 46.7 + - + +
127D ALA 3.4 25.4 - - - +
128D GLN 4.4 0.7 - - - -
129D PRO* 4.1 3.4 - - + -
139D SER 5.6 0.2 - - - -
140D TYR* 3.4 16.3 + - - +
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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