Contacts of the strand formed by residues 34 - 41 (chain E) in PDB entry 2I3T
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 SER 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E PRO* 4.1 2.4 - - - +
28E ILE 3.7 0.2 - - - +
29E THR* 3.4 4.5 - - - -
30E SER* 3.0 32.2 + - - -
32E ASP* 2.7 30.7 + - - -
33E GLY* 1.3 80.9 - - - +
35E LEU* 1.3 60.5 + - - +
36E THR* 3.9 11.4 - - - +
52E SER* 4.2 13.9 - - - -
53E LEU 3.1 9.9 - - - -
54E ARG* 4.0 9.9 - - - +
59E LEU* 3.5 5.8 - - - +
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Residues in contact with LEU 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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27E LEU* 4.5 14.1 - - + -
28E ILE 3.4 17.5 - - - +
29E THR* 3.7 21.1 - - + -
34E SER* 1.3 72.7 - - - +
36E THR* 1.3 62.8 + - - +
37E VAL* 4.1 5.1 + - + +
52E SER* 3.4 1.6 - - - -
53E LEU* 2.7 38.0 + - + +
59E LEU* 3.9 13.2 - - + +
62E CYS* 4.6 2.7 - - + -
72E ILE* 3.9 22.4 - - + -
74E VAL* 4.1 6.1 - - + -
84E VAL* 3.8 35.7 - - + -
86E LEU* 5.0 5.8 - - + -
92E PHE* 4.7 3.4 - - + -
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Residues in contact with THR 36 (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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10E PRO* 3.7 32.1 - - + -
26E LEU 3.6 2.6 - - - +
27E LEU* 3.9 0.7 - - - -
28E ILE* 2.9 41.1 + - + +
34E SER* 3.9 10.3 - - - +
35E LEU* 1.3 75.1 - - - +
37E VAL* 1.3 62.1 + - - +
38E TYR* 2.8 31.7 + - + +
49E LEU* 4.6 6.1 - - - +
51E GLN 3.6 11.3 + - - -
52E SER* 3.9 11.7 - - - +
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Residues in contact with VAL 37 (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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25E LEU* 4.2 19.1 - - + -
26E LEU 3.4 6.7 - - - +
27E LEU* 3.7 24.7 - - + -
35E LEU* 4.8 8.7 - - + +
36E THR* 1.3 75.1 - - - +
38E TYR* 1.3 74.2 + - - +
49E LEU* 4.0 0.9 - - - +
50E LEU* 2.9 35.8 + - + +
51E GLN* 3.1 22.1 + - + +
72E ILE* 4.8 1.3 - - + -
86E LEU* 4.2 33.2 - - + -
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Residues in contact with TYR 38 (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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6E ILE* 3.2 30.2 - - + +
8E GLN* 2.4 34.9 + - - -
9E ALA* 3.5 11.3 - - - +
10E PRO* 3.8 7.6 - - - +
25E LEU* 3.3 13.1 - - - +
26E LEU* 2.9 43.7 + - + -
28E ILE* 3.9 27.8 - - + -
36E THR* 2.8 34.9 + - - -
37E VAL* 1.3 75.2 - - - +
39E LYS* 1.3 62.2 + - - +
47E VAL* 3.7 20.0 - - + -
48E ASP 3.5 4.5 - - - -
49E LEU* 3.8 25.1 - - + -
50E LEU* 4.6 0.9 - - - -
333E ILE* 4.2 0.7 - - - +
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Residues in contact with LYS 39 (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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23E LYS 3.9 6.3 - - - -
24E SER* 3.4 23.8 + - - +
25E LEU* 4.0 14.1 - - + -
38E TYR* 1.3 76.5 - - - +
40E PHE* 1.3 82.4 + - - +
41E ASP* 4.7 8.8 - - + +
42E ILE* 5.9 0.8 - - - +
46E ASN* 5.4 0.9 + - - -
47E VAL* 3.2 3.4 - - - -
48E ASP* 2.8 34.9 + - + +
50E LEU* 3.6 28.0 - - + -
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Residues in contact with PHE 40 (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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19E ILE* 4.1 10.3 - - + -
21E PRO* 5.0 4.9 - - + -
24E SER* 3.1 53.6 + - - -
25E LEU 3.4 19.1 - - - -
26E LEU* 4.4 10.3 - - + -
39E LYS* 1.3 95.9 + - - +
41E ASP* 1.3 65.1 + - - +
42E ILE* 4.2 21.5 - - + -
46E ASN 3.3 9.4 - - - +
47E VAL* 4.3 2.2 - - + -
303E SER* 5.5 1.8 - - - -
306E ILE* 3.6 33.9 - - + -
335E ILE* 3.9 21.3 - - + -
337E PHE* 4.2 8.5 - + + -
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Residues in contact with ASP 41 (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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353D MET* 3.1 33.5 + - - +
39E LYS* 4.7 7.6 - - + +
40E PHE* 1.3 75.7 - - - +
42E ILE* 1.3 61.8 + - - +
43E GLN* 2.9 23.2 + - - +
44E ALA* 3.2 13.3 - - - +
45E LYS* 2.6 37.8 + - - -
46E ASN* 2.8 24.8 + - - +
337E PHE* 3.6 3.2 - - - -
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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