Contacts of the strand formed by residues 121 - 128 (chain E) in PDB entry 2PY2
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 HIS 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E LEU 3.2 4.2 - - - +
22E GLN* 3.9 9.9 + - - -
23E LEU* 3.0 29.8 + - - +
61E PRO* 4.1 17.6 + - + +
63E TRP* 3.7 36.9 - + + +
103E GLN* 3.0 41.8 + - + -
119E HIS* 3.7 19.7 + - + +
120E LEU* 1.3 89.7 + - - +
122E SER* 1.3 73.2 + - - +
123E SER* 4.8 0.9 - - - -
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Residues in contact with SER 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E PHE* 3.6 23.2 - - - -
19E ASN 3.2 15.9 - - - -
20E PRO* 3.1 8.0 + - - +
21E LEU 3.3 6.1 - - - -
22E GLN* 2.9 21.0 + - - +
60E ILE* 3.6 13.9 - - - +
61E PRO 3.8 6.5 + - - -
62E SER* 3.3 7.5 - - - -
63E TRP* 2.8 20.6 + - - -
121E HIS* 1.3 81.1 - - - +
123E SER* 1.3 62.4 + - - +
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E PHE* 3.6 5.7 - - - -
19E ASN* 2.8 53.4 + - - +
21E LEU 5.1 0.9 + - - -
23E LEU* 5.5 0.3 - - - +
28E ALA* 3.8 21.1 + - - +
39E LEU* 3.5 24.5 - - - +
62E SER* 3.9 1.3 - - - -
63E TRP* 3.5 11.2 - - - +
121E HIS 5.0 0.3 + - - -
122E SER* 1.3 78.0 - - - +
124E ILE* 1.3 65.4 + - - +
125E CYS* 4.8 2.8 - - - -
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Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 4.4 10.8 - - + -
17E LEU 3.6 5.6 - - - +
18E PHE* 3.7 30.5 - - + -
39E LEU* 3.3 10.6 - - - +
40E ALA* 2.8 41.3 + - + -
51E VAL* 3.7 29.8 - - + +
54E LEU* 5.2 3.6 - - + -
55E THR* 3.8 18.8 - - + -
62E SER* 4.0 10.3 - - - -
63E TRP 3.1 13.4 + - - +
64E ILE* 4.0 10.5 - - + -
104E MET* 4.1 2.0 - - - -
123E SER* 1.3 76.2 - - - +
125E CYS* 1.3 66.6 + - - +
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Residues in contact with CYS 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E TRP* 4.1 20.2 - - + -
16E PHE* 3.2 7.6 - - - +
17E LEU* 2.8 44.0 + - + +
19E ASN* 4.7 17.7 - - - -
28E ALA 4.7 0.4 - - - -
31E SER* 4.9 1.1 - - - -
32E CYS* 2.0 53.4 - - + -
37E ALA* 4.4 0.2 - - + -
38E ASN 3.4 4.5 - - - -
40E ALA* 4.3 0.4 - - - -
123E SER* 4.8 1.6 - - - -
124E ILE* 1.3 75.1 - - - +
126E ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E TRP* 4.1 0.7 - - - -
14E ARG* 4.5 9.9 - - - +
15E CYS 3.1 11.9 - - - +
16E PHE* 3.7 26.7 - - + -
37E ALA* 3.0 16.7 - - - +
38E ASN* 2.9 20.9 + - - +
40E ALA* 3.8 15.0 - - + -
41E SER 5.1 0.2 - - - +
79E ASP* 5.9 1.8 - - - +
125E CYS* 1.3 77.2 - - - +
127E LYS* 1.3 61.5 + - - +
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Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PRO* 3.7 34.9 - - - +
8E TRP* 3.8 33.8 - - + +
14E ARG* 3.4 6.0 - - - +
15E CYS* 2.8 34.4 + - + +
35E GLU* 3.0 32.6 + - - +
36E GLY* 3.6 18.2 - - - +
37E ALA* 3.6 1.8 - - + +
126E ALA* 1.3 76.5 - - - +
128E PRO* 1.3 81.3 - - + +
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Residues in contact with PRO 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLY 3.5 11.0 - - - +
14E ARG* 4.2 6.9 - - + -
15E CYS* 4.7 1.3 - - - -
36E GLY 5.3 2.2 - - - +
127E LYS* 1.3 98.0 - - + +
129E LEU* 1.3 67.9 + - - +
130E LYS* 3.6 26.6 + - - +
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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