Contacts of the helix formed by residues 35 - 43 (chain E) in PDB entry 1JT6
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 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E LEU* 5.4 0.2 - - - +
29E VAL* 3.2 9.6 - - - +
34E SER* 1.3 81.0 + - - +
36E LYS* 1.3 53.2 + - - +
37E GLY* 3.4 4.7 + - - -
38E ASN* 2.7 38.1 + - - +
39E LEU 2.7 31.4 + - - -
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Residues in contact with LYS 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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25E THR* 3.5 29.6 - - + +
26E GLY* 3.9 6.5 - - - -
29E VAL* 3.4 24.4 - - + +
35E SER* 1.3 70.7 - - - +
37E GLY* 1.3 55.5 + - - +
39E LEU* 3.0 3.8 + - - -
40E TYR* 2.7 55.7 + - + -
900E SO4 2.9 33.3 + - - -
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Residues in contact with GLY 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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35E SER* 3.0 6.5 + - - -
36E LYS* 1.3 81.2 - - - +
38E ASN* 1.3 61.7 + - - +
40E TYR* 3.3 6.0 + - - +
41E TYR* 3.0 22.9 + - - +
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Residues in contact with ASN 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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3E LEU* 3.5 24.5 - - + +
7E ILE* 4.7 2.6 - - - +
34E SER* 3.3 21.0 + - - +
35E SER* 2.7 26.8 + - - +
37E GLY* 1.3 68.7 - - - -
39E LEU* 1.3 66.4 + - - +
41E TYR* 3.1 20.4 + - - +
42E HIS* 3.2 45.9 + - - -
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Residues in contact with LEU 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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7E ILE* 3.6 39.0 - - + -
25E THR* 3.7 25.6 - - - +
28E ILE* 3.6 20.9 - - + -
29E VAL* 4.0 15.7 - - + -
34E SER* 4.7 0.6 + - - -
35E SER 2.7 15.5 + - - +
36E LYS* 3.4 8.5 - - - +
38E ASN* 1.3 73.1 - - - +
40E TYR* 1.3 77.7 + - + +
41E TYR 3.1 0.9 + - - -
42E HIS* 3.1 1.3 + - - -
43E PHE* 3.0 38.8 + - + +
45E THR 5.3 5.4 - - - +
46E LYS* 5.5 1.1 - - - +
49E LEU* 4.4 12.6 - - + -
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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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25E THR* 3.0 33.5 - - + +
36E LYS* 2.7 51.0 + - + +
37E GLY* 3.8 5.2 - - - +
39E LEU* 1.3 75.0 - - + +
41E TYR* 1.3 57.6 - - - +
43E PHE 2.4 22.0 - - - +
44E LYS* 3.4 25.9 - - - +
45E THR* 4.5 0.7 - - - -
46E LYS 4.8 0.2 - - - -
249E SO4 2.6 48.9 + - - -
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Residues in contact with TYR 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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37E GLY 3.0 13.2 + - - +
38E ASN* 3.2 16.4 - - - +
39E LEU 3.0 0.2 - - - -
40E TYR* 1.3 81.2 - - - +
42E HIS* 1.3 104.4 + + - +
43E PHE 3.3 1.9 + - - +
44E LYS* 6.0 0.5 - - - +
289E SO4 3.6 15.5 + - - -
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Residues in contact with HIS 42 (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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3E LEU* 4.7 3.0 - - - +
4E LYS* 4.2 30.2 + - + +
7E ILE* 5.2 1.8 - - + -
38E ASN* 3.2 41.2 + - - -
39E LEU 3.1 2.7 + - - +
41E TYR* 1.3 97.6 - + - +
43E PHE* 1.3 89.4 + + + +
48E ASN* 5.1 0.9 + - - -
52E GLU* 4.3 3.1 - - - +
289E SO4 2.7 45.6 + - - +
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Residues in contact with PHE 43 (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 LYS* 3.7 30.7 - - + -
7E ILE* 3.9 24.0 - - + -
8E LEU* 3.9 18.6 - - + -
39E LEU* 3.0 22.8 + - + +
40E TYR* 2.4 35.9 - - - +
41E TYR 4.2 1.6 - - - -
42E HIS* 1.3 89.7 - - + +
44E LYS* 1.3 58.5 + - - +
45E THR 4.0 15.0 - - - +
48E ASN* 3.9 9.9 - - - +
49E LEU* 3.5 35.2 - - + -
52E GLU* 2.8 33.7 - - + -
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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