Contacts of the helix formed by residues 39 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASN* 3.4 4.2 + - + -
38A ALA* 1.3 73.7 - - - +
40A ALA* 1.3 61.8 + - - +
41A THR 3.7 2.9 + - - -
42A GLY 3.7 5.8 + - - +
43A THR* 2.8 30.7 + - - -
69A ASP* 4.7 7.2 - - - +
72A ASN* 5.9 0.4 - - - +
73A ASN* 3.3 8.7 - - - +
85A ARG* 3.5 32.8 - - - +
129A THR* 4.1 2.4 + - - -
130A GLN* 3.4 27.0 - - + +
489A GLU* 3.0 25.9 + - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 1.3 78.6 - - - +
41A THR* 1.3 52.2 + - - +
43A THR* 3.5 1.7 - - - -
44A GLU* 2.7 39.5 + - - +
72A ASN* 3.5 30.6 - - + +
73A ASN* 3.6 12.2 - - - +
489A GLU* 3.3 23.2 + - + +
491A HIS* 4.2 5.8 - - - +
494A ALA* 3.5 16.4 - - + -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 4.1 2.9 - - - -
40A ALA* 1.3 73.4 - - - +
42A GLY* 1.3 65.3 + - - +
44A GLU* 3.7 1.2 - - - +
45A ILE* 2.9 41.8 + - + +
129A THR* 4.6 7.4 - - + -
130A GLN* 4.0 4.4 + - - +
153A CYS* 4.4 7.9 - - + -
154A ARG 4.9 0.4 - - - +
155A THR* 2.7 33.2 + - - +
489A GLU* 2.5 25.3 + - - -
494A ALA* 3.5 18.5 - - - +
497A LEU* 4.0 19.5 - - + -
498A GLY* 4.4 0.2 - - - -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.0 25.5 - - - +
37A ASN 3.7 7.4 - - - -
39A THR* 3.5 7.4 + - - -
40A ALA 3.4 0.4 - - - -
41A THR* 1.3 80.0 - - - +
43A THR* 1.3 62.7 + - - +
45A ILE* 3.2 4.0 + - - +
46A LEU 3.0 19.4 + - - -
129A THR* 3.6 24.0 - - - +
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Residues in contact with THR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.1 5.3 - - - +
38A ALA* 4.4 4.0 + - - +
39A THR 2.8 24.0 + - - +
40A ALA* 3.5 4.5 - - - +
42A GLY* 1.3 73.0 - - - +
44A GLU* 1.3 72.7 + - - +
46A LEU* 3.4 3.7 + - - +
47A LYS* 2.9 22.2 + - - +
73A ASN* 3.3 23.1 + - - +
74A PHE 4.9 0.7 - - - +
75A PHE* 3.2 38.3 - - + +
89A ALA* 4.3 14.7 - - - +
93A LEU* 3.8 8.4 - - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 2.7 23.0 + - - +
41A THR 3.7 3.6 - - - +
43A THR* 1.3 84.0 - - - +
45A ILE* 1.3 63.9 + - - +
47A LYS* 2.9 32.5 + - - +
48A ASN* 2.9 30.0 + - - +
74A PHE* 4.3 0.9 - - - +
75A PHE* 4.1 6.2 - - - -
491A HIS* 3.2 25.6 + - + -
494A ALA 4.0 11.9 - - - +
495A ALA* 3.9 20.8 - - - +
498A GLY* 4.2 5.6 - - - -
62B GLU* 3.8 2.4 - - - +
65B LYS* 3.3 25.3 + - - +
297B ALA* 5.9 0.7 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.6 0.4 - - + -
41A THR* 2.9 25.2 + - + +
42A GLY 3.4 5.4 - - - +
44A GLU* 1.3 75.6 - - - +
46A LEU* 1.3 66.0 + - + +
48A ASN* 2.9 16.3 + - - +
49A LEU* 3.3 20.8 + - + +
127A VAL* 3.9 17.7 - - + -
129A THR* 3.8 20.9 - - + -
153A CYS* 3.7 31.9 - - + -
498A GLY* 3.4 25.3 - - - -
501A ALA* 4.0 5.6 - - + -
502A ALA* 3.8 19.9 - - - +
505A VAL* 4.8 3.6 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.3 15.0 - - + -
35A LEU* 3.7 21.1 - - + +
42A GLY 3.0 13.6 + - - +
43A THR 3.7 3.8 - - - +
45A ILE* 1.3 80.9 - - + +
47A LYS* 1.3 53.5 + - - +
49A LEU* 2.9 12.2 + - + +
50A VAL* 2.7 49.3 + - + +
54A ILE* 5.5 1.1 - - + -
57A PHE* 3.5 46.2 - - + -
59A ILE* 3.6 26.5 - - + -
93A LEU* 3.7 14.4 - - + -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR 2.9 17.7 + - - +
44A GLU* 2.9 32.1 + - - +
45A ILE 3.1 0.2 + - - -
46A LEU* 1.3 76.5 - - - +
48A ASN* 1.3 82.7 + - - +
49A LEU 2.9 5.4 + - - -
50A VAL* 4.0 0.6 - - - +
51A LEU* 3.0 61.3 + - + +
75A PHE* 3.4 32.3 - - + -
93A LEU* 4.2 3.1 - - + +
96A LEU* 3.6 17.4 - - + +
62B GLU* 2.9 23.0 + - - -
65B LYS* 3.8 8.9 - - - +
92B PHE* 4.2 11.1 - - + -
293B ALA* 5.6 0.2 - - - -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 2.9 17.8 + - - +
45A ILE 2.9 3.3 + - - +
47A LYS* 1.3 94.1 - - - +
49A LEU* 1.3 62.7 + - - +
52A PRO* 2.9 22.0 - - - +
495A ALA 4.8 0.4 + - - -
498A GLY* 2.9 30.1 + - - -
499A GLY* 3.5 6.9 - - - +
502A ALA* 3.2 21.3 - - + +
506A ILE* 4.8 1.0 - - - +
62B GLU* 4.7 0.7 - - - +
293B ALA* 3.7 22.4 - - + +
294B SER* 4.5 8.0 + - - +
297B ALA* 3.7 19.8 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.8 1.3 - - + -
33A VAL* 4.2 23.6 - - + -
45A ILE* 3.5 24.2 - - + +
46A LEU* 2.9 15.6 + - + +
48A ASN* 1.3 82.7 - - - +
50A VAL* 1.3 63.6 + - - +
52A PRO* 2.9 18.0 - - - +
54A ILE* 3.1 38.1 + - + +
502A ALA* 3.4 28.0 - - + +
505A VAL* 4.0 26.2 - - + -
506A ILE* 3.8 18.4 - - + -
509A ILE* 5.8 0.9 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 2.7 32.0 + - + +
47A LYS* 4.0 5.2 - - - +
49A LEU* 1.3 72.1 - - - +
51A LEU* 1.3 63.4 + - - +
53A GLY* 2.9 15.2 + - - -
54A ILE* 3.5 10.1 - - + -
57A PHE* 3.8 32.8 - - + -
93A LEU* 3.9 13.2 - - + +
94A GLN* 5.5 0.4 - - - +
96A LEU* 3.8 18.2 - - + -
97A ASN* 3.5 17.8 - - + +
100A VAL* 3.4 23.8 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 5.2 0.2 - - - -
13A TYR* 3.5 6.6 - - - -
47A LYS* 3.0 46.6 + - + +
50A VAL* 1.3 74.3 - - - +
52A PRO* 1.4 58.5 - - + +
53A GLY 2.7 15.4 + - - -
96A LEU* 4.3 21.5 - - + +
97A ASN* 3.4 17.6 + - - +
88B LEU 4.2 16.5 - - - +
89B ASN* 3.9 20.2 - - - +
90B ARG* 4.4 9.4 - - - +
92B PHE* 3.9 31.9 - - + +
293B ALA* 4.3 15.5 - - + -
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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