Contacts of the helix formed by residues 39 - 51 (chain E) in PDB entry 1R4N
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 THR 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E ASN* 3.4 4.5 + - + -
38E ALA* 1.3 74.3 - - - +
40E ALA* 1.3 60.9 + - - +
41E THR 3.7 3.1 + - - -
42E GLY 3.7 5.4 + - - +
43E THR* 2.8 30.9 + - - -
69E ASP* 4.8 6.7 - - - +
73E ASN* 3.4 9.0 - - - +
85E ARG* 3.5 33.0 - - - +
129E THR* 4.0 2.8 + - - -
130E GLN* 3.4 27.4 - - + +
489E GLU* 3.1 25.7 + - - +
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Residues in contact with ALA 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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39E THR* 1.3 77.7 - - - +
41E THR* 1.3 53.4 + - - +
43E THR* 3.5 3.0 - - - -
44E GLU* 2.8 39.3 + - - +
72E ASN* 3.5 30.2 - - - +
73E ASN* 3.6 11.3 - - - +
489E GLU* 3.3 23.6 + - + +
491E HIS* 4.3 6.5 - - - +
494E ALA* 3.6 15.9 - - + -
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E THR* 4.1 2.7 - - - -
40E ALA* 1.3 72.4 - - - +
42E GLY* 1.3 63.2 + - - +
44E GLU* 3.2 2.4 + - - +
45E ILE* 2.9 42.2 + - + +
129E THR* 4.6 7.2 - - + -
130E GLN* 4.0 3.3 + - - -
153E CYS* 4.4 8.1 - - + -
154E ARG 4.9 0.4 - - - +
155E THR* 2.7 32.7 + - - +
489E GLU* 2.5 26.1 + - - -
494E ALA* 3.4 17.7 - - - +
497E LEU* 4.1 19.3 - - + -
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Residues in contact with GLY 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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35E LEU* 3.1 18.8 - - - +
37E ASN 3.7 15.0 - - - -
39E THR* 3.5 8.3 + - - -
40E ALA 3.4 0.2 - - - -
41E THR* 1.3 80.1 - - - +
43E THR* 1.3 61.8 + - - +
45E ILE* 3.2 3.6 + - - +
46E LEU 3.0 19.1 + - - -
129E THR* 3.6 23.5 - - - +
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Residues in contact with THR 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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35E LEU* 4.0 5.3 - - - +
38E ALA* 4.4 4.0 + - - +
39E THR 2.8 24.9 + - - +
40E ALA* 3.7 4.7 - - - +
42E GLY* 1.3 74.0 - - - +
44E GLU* 1.3 72.4 + - - +
46E LEU* 3.3 3.4 + - - +
47E LYS* 2.9 22.3 + - - +
73E ASN* 3.2 29.1 + - - +
74E PHE 4.9 0.7 - - - +
75E PHE* 3.2 32.6 - - + +
89E ALA* 4.3 14.7 - - - +
93E LEU* 3.9 8.9 - - + +
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Residues in contact with GLU 44 (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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40E ALA 2.8 24.5 + - - +
41E THR 3.7 3.4 - - - +
43E THR* 1.3 84.5 - - - +
45E ILE* 1.3 65.9 + - - +
47E LYS* 2.8 33.4 + - - +
48E ASN* 3.0 29.1 + - - +
74E PHE* 4.3 0.9 - - - +
75E PHE* 4.1 5.0 - - - -
491E HIS* 3.2 25.0 + - + -
494E ALA 3.9 12.6 - - - +
495E ALA* 3.9 22.0 - - - +
498E GLY* 4.1 4.5 - - - -
62F GLU* 3.7 2.4 - - - +
65F LYS* 3.2 26.1 + - - +
297F ALA* 5.9 0.3 - - - +
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Residues in contact with ILE 45 (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 LEU* 5.7 0.2 - - + -
41E THR* 2.9 19.8 + - + +
42E GLY* 3.5 5.4 - - - +
44E GLU* 1.3 78.7 - - - +
46E LEU* 1.3 65.5 + - - +
48E ASN* 3.0 11.8 + - - +
49E LEU* 3.3 20.6 + - + +
127E VAL* 3.9 17.7 - - + -
129E THR* 3.8 20.4 - - + -
153E CYS* 3.8 31.6 - - + -
498E GLY* 3.3 25.8 - - - +
501E ALA* 4.0 6.3 - - + -
502E ALA* 3.8 20.4 - - - +
505E VAL* 4.8 3.6 - - + -
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Residues in contact with LEU 46 (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 VAL* 4.3 20.2 - - + -
35E LEU* 3.8 15.9 - - + +
42E GLY 3.0 15.9 + - - +
43E THR 3.7 3.6 - - - +
45E ILE* 1.3 77.0 - - - +
47E LYS* 1.3 52.8 + - - +
49E LEU* 2.9 12.1 + - + +
50E VAL* 2.7 49.3 + - + +
54E ILE* 5.6 0.7 - - + -
57E PHE* 3.4 52.5 - - + -
59E ILE* 3.6 22.9 - - + -
93E LEU* 3.7 12.1 - - + -
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Residues in contact with LYS 47 (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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43E THR 2.9 15.0 + - - +
44E GLU* 2.8 37.2 + - - +
45E ILE 3.1 0.2 + - - -
46E LEU* 1.3 77.0 - - - +
48E ASN* 1.3 80.9 + - - +
49E LEU 2.9 5.5 + - - -
50E VAL* 3.3 1.3 + - - +
51E LEU* 3.0 59.0 + - + +
75E PHE* 3.4 30.6 - - + -
93E LEU* 4.2 2.0 - - + +
96E LEU* 3.6 17.5 - - + -
62F GLU* 2.9 22.4 + - - -
65F LYS* 3.7 9.1 - - - +
92F PHE* 4.2 12.5 - - + -
293F ALA* 5.7 0.2 - - - -
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Residues in contact with ASN 48 (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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44E GLU* 3.0 17.8 + - - +
45E ILE 3.0 2.9 + - - +
47E LYS* 1.3 93.7 - - - +
49E LEU* 1.3 63.2 + - - +
52E PRO* 3.0 21.4 - - - +
495E ALA 4.8 0.4 + - - -
498E GLY* 2.9 30.3 + - - -
499E GLY* 3.5 6.9 - - - +
502E ALA* 3.3 20.5 - - + +
506E ILE* 4.8 1.2 - - - +
62F GLU* 4.6 0.5 - - - +
293F ALA* 3.8 21.2 - - + +
294F SER* 4.4 7.6 + - - +
297F ALA* 3.6 20.3 - - - +
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Residues in contact with LEU 49 (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 LEU* 5.8 1.3 - - + -
33E VAL* 4.1 23.8 - - + -
45E ILE* 3.5 22.4 - - + +
46E LEU* 2.9 15.5 + - + +
48E ASN* 1.3 82.7 - - - +
50E VAL* 1.3 64.2 + - - +
52E PRO* 2.8 20.8 - - - +
54E ILE* 3.1 35.4 + - + +
127E VAL* 5.5 0.4 - - + -
502E ALA* 3.3 29.4 - - + +
505E VAL* 4.0 25.6 - - + -
506E ILE* 3.9 17.3 - - + -
509E ILE* 5.8 1.3 - - + -
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Residues in contact with VAL 50 (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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46E LEU* 2.7 32.6 + - + +
47E LYS* 4.0 4.0 - - - +
49E LEU* 1.3 73.5 - - - +
51E LEU* 1.3 62.9 + - - +
53E GLY* 2.9 10.6 + - - -
54E ILE* 3.5 11.4 - - + -
57E PHE* 3.7 32.8 - - + -
93E LEU* 4.0 13.9 - - + +
94E GLN* 5.4 0.9 - - - +
96E LEU* 3.9 19.7 - - + -
97E ASN* 3.5 15.8 - - + +
100E VAL* 3.4 28.2 - - + +
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Residues in contact with LEU 51 (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 TYR* 3.5 6.6 - - - -
47E LYS* 3.0 45.9 + - + +
50E VAL* 1.3 74.8 - - - +
52E PRO* 1.3 60.5 - - + +
53E GLY 2.7 15.2 + - - -
96E LEU* 4.2 20.9 - - + +
97E ASN* 3.5 17.0 + - - +
62F GLU* 6.1 0.2 - - - +
88F LEU 4.3 15.2 - - - +
89F ASN* 3.7 21.0 - - - +
90F ARG* 4.4 8.5 - - - +
92F PHE* 3.7 35.2 - - + +
293F ALA* 4.3 15.3 - - + -
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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