Contacts of the strand formed by residues 48 - 53 (chain D) in PDB entry 2PS2
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 GLU 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ARG* 4.0 31.5 + - + -
41D ILE 3.1 4.9 - - - +
42D THR* 3.9 19.7 + - + +
46D GLY 3.5 11.8 + - - +
47D ILE* 1.3 78.4 - - - +
49D GLY* 1.3 60.0 + - - +
50D TRP* 4.4 14.8 + - - +
115D ILE* 3.9 3.3 - - - +
118D LYS* 3.1 29.7 - - - +
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Residues in contact with GLY 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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40D ARG* 3.2 5.7 - - - -
41D ILE 2.8 33.4 + - - -
48D GLU* 1.3 75.2 - - - +
50D TRP* 1.3 64.4 + - - -
111D ALA* 3.5 23.9 - - - +
114D ASP* 3.4 9.6 - - - -
115D ILE* 3.5 7.0 - - - +
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Residues in contact with TRP 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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12D PHE* 3.5 27.6 - + - -
38D ILE* 3.6 19.3 - - + -
39D VAL 3.2 11.0 - - - -
40D ARG* 3.3 43.0 - - + +
48D GLU* 4.4 15.9 + - - +
49D GLY* 1.3 79.6 - - - -
51D GLY* 1.3 58.3 + - - +
110D VAL* 3.5 0.7 - - - +
111D ALA* 3.3 12.7 - - - -
114D ASP* 3.0 17.4 + - - +
118D LYS* 5.7 1.3 - - - -
303D ILE* 4.2 12.1 - - + -
354D LEU* 3.2 24.1 - - - +
356D ILE* 4.5 6.5 - - + -
358D PRO* 3.4 41.0 - - + +
360D LEU* 5.0 11.0 - - + -
363D LEU* 3.3 30.7 - - + -
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Residues in contact with GLY 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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38D ILE* 3.4 5.0 - - - +
39D VAL 2.8 32.9 + - - -
50D TRP* 1.3 76.8 - - - +
52D GLU* 1.3 60.7 + - - +
107D ALA* 3.3 24.7 + - - +
110D VAL* 3.8 13.0 - - - -
303D ILE* 3.8 5.8 - - - +
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Residues in contact with GLU 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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36D ALA* 4.0 4.7 - - - +
37D THR 3.4 11.2 - - - +
38D ILE* 4.0 12.3 - - + +
51D GLY* 1.3 74.6 - - - +
53D SER* 1.3 66.7 + - - +
54D THR* 2.7 26.0 + - - +
106D THR* 3.7 18.7 - - - +
107D ALA* 3.9 5.5 - - - +
110D VAL* 4.8 4.2 - - - +
297D GLU* 4.5 7.4 - - - +
300D GLY* 3.1 2.9 - - - -
301D SER* 2.6 48.5 + - - -
303D ILE* 3.5 16.4 - - + +
304D ALA* 3.2 29.5 + - + +
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Residues in contact with SER 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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37D THR* 3.0 31.9 + - - -
52D GLU* 1.3 74.9 - - - +
54D THR* 1.3 60.2 + - - +
55D PRO* 3.7 8.0 - - - +
68D VAL* 3.8 19.9 - - - +
103D ASP* 2.6 33.0 + - - +
104D ALA 5.7 0.2 - - - -
106D THR* 4.5 2.7 - - - -
107D ALA* 4.2 12.8 - - - +
271D SER* 3.9 14.7 - - - -
297D GLU* 5.4 0.7 - - - -
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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