Contacts of the strand formed by residues 34 - 40 (chain E) in PDB entry 3T0E
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 ILE 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B THR* 5.8 3.8 - - - +
170B GLY 5.9 1.6 - - - +
29E LYS* 3.2 11.3 - - - +
30E ASN* 2.8 45.5 + - - +
32E ASN 3.0 7.5 + - - +
33E GLN* 1.3 82.0 - - - +
35E LYS* 1.3 77.3 + - + +
36E ILE* 3.5 1.0 + - - +
48E PRO* 4.0 21.8 - - + -
49E SER* 3.8 26.0 - - - -
50E LYS* 4.3 8.7 - - - +
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Residues in contact with LYS 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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170B GLY* 4.6 17.3 - - - +
171B VAL 4.7 7.4 - - - +
172B VAL* 6.4 0.4 - - + -
191B GLU* 3.0 39.6 + - - +
27E HIS* 3.9 26.0 + - - +
28E TRP 3.5 8.1 - - - +
29E LYS* 4.5 9.3 - - - +
33E GLN 4.4 0.2 - - - -
34E ILE* 1.3 82.1 - - + +
36E ILE* 1.3 59.9 + - - +
45E TRP* 4.0 28.0 - - + -
47E GLY* 4.3 0.2 - - - -
48E PRO* 3.3 35.2 - - + +
49E SER 3.5 3.1 + - - -
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Residues in contact with ILE 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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28E TRP* 3.0 16.9 + - + +
29E LYS* 3.7 9.4 - - - +
30E ASN* 3.4 29.8 - - + +
34E ILE 3.5 13.7 - - - +
35E LYS* 1.3 73.8 - - - +
37E LEU* 1.3 62.8 + - + +
45E TRP* 4.5 0.7 - - - -
46E LYS* 3.2 3.5 - - - +
47E GLY 2.3 34.9 + - - +
49E SER* 3.6 28.2 - - - +
51E LEU* 4.4 17.5 - - + -
52E ASN 6.0 0.9 - - - +
55E ALA* 4.5 15.0 - - + -
69E LEU* 4.4 13.2 - - + -
82E TYR* 4.7 12.8 - - + -
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Residues in contact with LEU 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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26E PHE* 4.6 12.1 - - + -
27E HIS* 3.4 5.2 - - - +
28E TRP* 3.1 32.6 + - + +
36E ILE* 1.3 81.0 - - + +
38E GLY* 1.3 65.2 + - - +
44E LEU* 3.3 37.7 - - + -
45E TRP* 3.4 15.4 - - - +
46E LYS* 4.4 8.7 - - + -
55E ALA* 5.5 4.0 - - + +
56E ASP* 3.5 16.2 - - - +
57E SER* 3.5 32.5 - - - -
68E PRO 4.5 2.9 - - - +
69E LEU* 4.1 20.4 - - + -
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Residues in contact with GLY 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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26E PHE* 3.8 10.5 - - - -
27E HIS* 4.3 0.4 - - - -
37E LEU* 1.3 79.6 - - - +
39E ASN* 1.3 57.4 + - - -
44E LEU* 3.4 6.9 - - - +
45E TRP* 2.5 71.3 + - - -
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Residues in contact with ASN 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 SER* 5.0 2.6 + - - -
24E ILE 2.8 29.3 + - - +
25E GLN* 3.3 23.5 + - - +
26E PHE* 2.7 52.6 + - + +
38E GLY* 1.3 71.4 - - - -
40E TYR* 1.3 60.4 + - - +
41E GLY 4.1 10.0 + - - +
43E PHE 3.3 5.4 - - - +
45E TRP* 3.2 6.4 + - - +
62E TRP* 3.3 39.1 - - + -
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Residues in contact with TYR 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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131B TYR* 3.9 16.9 + - - -
133B ALA* 3.3 32.7 - - + +
143B LEU* 5.2 3.4 - - + -
145B VAL* 4.0 7.8 - - + +
187B LEU* 4.0 22.7 - - + -
189B MET* 3.2 32.3 - - + -
25E GLN* 4.8 4.5 - - - +
39E ASN* 1.3 73.0 - - - +
41E GLY* 1.3 64.4 + - - +
43E PHE* 2.9 38.2 + + + +
45E TRP* 3.7 16.6 - - + +
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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