Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 1URP
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 PRO 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN 3.9 5.6 - - - +
42A ASN* 1.3 88.3 - - - +
44A ALA* 1.3 55.1 + - - +
46A GLU* 3.5 10.2 - - + +
47A LEU* 2.8 30.0 + - - +
66A THR* 3.5 22.6 - - - +
67A ASP* 5.3 2.7 - - + -
70A ALA* 3.9 30.5 - - + +
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Residues in contact with ALA 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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42A ASN* 2.8 21.4 + - - +
43A PRO* 1.3 73.6 - - - +
45A LYS* 1.3 55.0 + - - +
47A LEU* 3.2 12.2 + - - +
48A ALA* 2.9 27.3 + - - +
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Residues in contact with LYS 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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38A ASP 3.8 16.2 - - - +
39A SER 3.5 23.3 - - - +
40A GLN* 3.0 24.4 + - - +
42A ASN* 3.0 18.9 + - - +
44A ALA* 1.3 74.5 - - - +
46A GLU* 1.3 59.4 - - - +
48A ALA* 3.1 11.1 + - + +
49A ASN* 2.8 44.8 + - - +
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Residues in contact with GLU 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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7A VAL* 4.3 2.4 - - + +
39A SER* 3.2 26.1 + - - +
42A ASN 2.9 11.2 + - - +
43A PRO* 3.5 13.5 - - + +
45A LYS* 1.3 75.1 - - - +
47A LEU* 1.3 62.6 + - - +
49A ASN* 3.2 4.2 + - - +
50A VAL* 3.0 29.0 + - - +
63A ILE* 4.0 16.0 - - + +
64A ASN 3.8 3.8 - - - +
65A PRO* 3.2 7.6 - - - +
66A THR* 2.7 41.4 + - + +
70A ALA 4.6 1.6 - - - -
71A VAL* 3.3 36.8 + - - +
74A ALA* 4.5 5.0 - - + +
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Residues in contact with LEU 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 PRO 2.8 14.9 + - - +
44A ALA* 3.3 12.3 - - - +
46A GLU* 1.3 77.9 - - - +
48A ALA* 1.3 61.0 + - - +
50A VAL* 3.4 1.9 + - - +
51A GLN* 3.1 36.5 + - - +
73A ASN* 4.1 14.6 - - + +
74A ALA* 3.6 37.7 - - + +
77A MET* 4.3 16.2 - - + -
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Residues in contact with ALA 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 ALA 2.9 13.4 + - - +
45A LYS* 3.1 16.4 + - + +
47A LEU* 1.3 74.3 - - - +
49A ASN* 1.3 66.8 + - - +
51A GLN* 3.3 13.2 + - - +
52A ASP* 3.0 25.0 + - - +
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Residues in contact with ASN 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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7A VAL* 4.0 9.5 - - + +
37A LEU* 3.5 36.7 + - + +
38A ASP 3.1 33.2 + - - +
39A SER* 3.5 13.5 + - - +
45A LYS* 2.8 30.0 + - - +
46A GLU 3.2 7.8 + - - +
48A ALA* 1.3 75.0 - - - +
50A VAL* 1.3 61.5 + - - +
52A ASP* 3.3 5.5 + - - +
53A LEU* 3.0 28.4 + - - +
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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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7A VAL* 4.2 12.6 - - + -
46A GLU 3.0 16.5 + - - +
47A LEU* 3.9 3.8 - - + +
48A ALA 3.3 0.2 - - - -
49A ASN* 1.3 77.7 - - - +
51A GLN* 1.3 60.4 + - + +
53A LEU* 3.3 8.6 + - + +
54A THR* 3.0 32.6 + - + +
61A LEU* 4.3 18.4 - - + -
63A ILE* 3.8 28.0 - - + -
74A ALA* 3.4 32.3 - - + +
77A MET* 4.5 4.3 - - + -
78A ALA* 4.5 4.5 - - + +
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Residues in contact with GLN 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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47A LEU* 3.1 33.2 + - - +
48A ALA* 3.3 12.2 + - - +
50A VAL* 1.3 75.2 - - - +
52A ASP* 1.3 63.2 + - - +
54A THR* 2.6 25.7 + - - +
55A VAL* 3.3 12.0 + - - +
77A MET* 3.5 37.0 - - + +
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Residues in contact with ASP 52 (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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37A LEU* 4.8 9.6 - - + +
48A ALA 3.0 13.3 + - - +
49A ASN* 3.4 12.3 - - - +
50A VAL 3.3 0.2 - - - -
51A GLN* 1.3 76.3 - - - +
53A LEU* 1.3 62.1 + - - +
55A VAL* 3.1 26.1 - - - +
56A ARG* 3.2 31.5 + - - +
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Residues in contact with LEU 53 (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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5A ALA* 3.5 29.6 - - + -
6A LEU 5.2 0.4 - - - +
7A VAL* 3.5 33.0 - - + -
35A VAL* 4.2 7.6 - - + -
37A LEU* 3.9 9.6 - - + -
49A ASN 3.0 12.2 + - - +
50A VAL* 3.6 7.6 - - + +
51A GLN 3.3 0.2 - - - -
52A ASP* 1.3 79.8 - - - +
54A THR* 1.3 62.1 + - + +
56A ARG* 3.3 38.1 + - - +
57A GLY 3.6 0.2 + - - -
58A THR* 2.8 40.8 + - + +
61A LEU* 3.7 11.9 - - + -
83A ILE* 4.9 0.9 - - + -
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Residues in contact with THR 54 (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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50A VAL* 3.0 24.3 + - + +
51A GLN* 2.6 24.5 + - - +
53A LEU* 1.3 73.9 - - + +
55A VAL* 1.3 70.0 + - - +
57A GLY* 3.2 14.9 + - - -
77A MET* 4.1 29.5 - - + +
78A ALA* 4.3 4.7 - - + -
81A ALA* 4.1 10.0 - - + +
83A ILE* 3.7 28.6 - - + +
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Residues in contact with VAL 55 (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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51A GLN 3.6 8.3 - - - +
52A ASP* 3.1 23.1 - - - +
54A THR* 1.3 88.4 + - - +
56A ARG* 1.3 60.7 + - + +
57A GLY 3.3 3.4 + - - -
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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