Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 2P5E
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 29 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ARG* 3.7 22.9 - - - -
100D TYR* 4.1 13.2 + - + -
101D ILE* 4.3 1.9 - - - -
102D PRO* 3.5 22.4 - - + +
27E HIS* 3.9 0.9 - - - +
28E GLU* 1.3 78.8 - - - +
30E MET* 1.4 61.2 + - - +
31E SER* 3.7 32.7 + - - -
33E TYR* 4.8 0.3 + - - -
43E LEU* 4.5 4.5 - - - +
46E TYR* 3.5 33.2 - + + +
47E SER 3.2 12.6 - - - -
48E VAL* 4.4 4.7 - - + +
90E ALA 4.2 2.0 - - - -
91E SER* 3.0 7.6 - - - -
92E SER* 3.0 46.9 + - - +
94E LEU* 3.4 25.6 - - + -
100E LEU* 3.8 17.9 - - + -
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Residues in contact with MET 30 (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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21E CYS* 3.6 36.3 - - - +
23E GLN* 3.5 19.3 - - + +
29E TYR* 1.4 80.7 - - - +
31E SER* 1.3 63.2 + - - +
46E TYR* 3.2 3.3 - - - +
47E SER 2.7 34.0 + - - -
66E ARG* 3.6 22.4 - - - +
69E ILE 3.5 22.4 - - - +
70E GLU 3.5 20.9 - - - +
72E PHE* 3.6 27.5 - - + -
89E CYS* 4.1 2.0 - - - -
90E ALA 3.5 5.6 - - - +
91E SER* 3.9 8.3 - - - -
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Residues in contact with SER 31 (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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29E TYR* 3.7 18.2 - - - -
30E MET* 1.3 77.9 - - - +
32E TRP* 1.3 63.0 + - - +
33E TYR* 3.7 9.2 - - - -
43E LEU* 3.8 8.3 - - - -
45E HIS 3.4 6.1 - - - -
46E TYR* 3.7 16.2 - - - -
72E PHE* 3.6 5.3 - - - -
89E CYS* 3.1 10.9 - - - -
90E ALA* 2.8 55.9 + - - +
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Residues in contact with TRP 32 (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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4E GLN* 3.6 28.5 - - + -
19E LEU* 3.6 36.6 - - + -
20E GLN 3.9 7.6 - - - -
21E CYS* 3.6 18.8 - - + +
31E SER* 1.3 73.2 - - - +
33E TYR* 1.3 57.0 + - - +
43E LEU* 3.4 8.0 - - - +
44E ILE* 2.8 45.4 + - + +
45E HIS 2.9 11.7 + - - +
64E VAL* 4.2 6.3 - - + -
72E PHE* 2.6 48.2 + + - -
74E LEU* 3.5 34.8 - - + +
87E TYR* 3.8 17.3 - - + -
88E PHE 3.3 25.8 - - - -
89E CYS* 4.0 9.0 - - + -
106E SER* 4.8 0.4 - - - -
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Residues in contact with TYR 33 (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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102D PRO* 3.5 33.8 + - - +
104D PHE* 3.6 18.1 - + - -
31E SER* 3.7 20.3 + - - -
32E TRP* 1.3 77.3 - - - +
34E ARG* 1.3 61.0 + - - +
41E LEU* 3.8 36.3 - - + -
42E ARG 3.1 8.7 - - - -
43E LEU* 3.4 40.9 - - + +
44E ILE* 3.7 6.3 - - - +
87E TYR* 3.2 8.0 - - - +
88E PHE* 2.7 37.3 + - + +
90E ALA* 4.2 5.4 - - + -
100E LEU* 4.4 1.4 - - + +
102E PHE* 3.9 28.5 - + - -
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Residues in contact with ARG 34 (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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33E TYR* 1.3 76.2 - - - +
35E GLN* 1.3 60.8 + - - +
36E ASP* 2.9 34.1 + - - -
40E GLY 3.7 0.9 - - - +
42E ARG* 2.9 62.7 + - + +
44E ILE* 3.9 2.5 - - + -
58E VAL* 4.2 18.2 - - + -
62E TYR* 3.0 29.2 + - - -
82E SER 2.8 29.7 + - - -
83E GLN* 3.8 3.3 - - - +
84E THR 3.6 3.0 + - - -
85E SER* 3.6 17.2 + - - +
86E VAL 3.3 5.6 - - - -
87E TYR* 3.8 16.6 - - + -
908E GOL 3.4 19.2 + - - -
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Residues in contact with GLN 35 (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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38D GLN* 2.8 44.0 + - - +
44D LEU* 4.7 0.2 - - - +
89D LEU* 5.1 2.6 - - - +
34E ARG* 1.3 74.4 - - - +
36E ASP* 1.3 70.0 + - - +
37E PRO* 3.7 0.9 - - - +
38E GLY 6.0 0.9 - - - -
39E MET 3.2 27.4 - - - +
40E GLY* 3.9 10.3 - - - +
41E LEU* 4.1 25.7 + - + +
42E ARG* 6.0 0.2 - - - +
85E SER* 3.1 10.4 + - - -
86E VAL* 2.8 32.8 + - - +
88E PHE* 3.3 16.8 - - + -
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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