Contacts of the helix formed by residues 38 - 53 (chain A) in PDB entry 3URZ
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 GLN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 2.9 20.3 + - - +
36A ALA* 4.0 20.0 + - - +
37A GLY* 1.3 76.3 - - - +
39A ASN* 1.3 64.3 + - - +
40A GLY 3.2 3.7 + - - +
41A GLN* 2.7 44.8 + - + +
42A ALA 3.3 14.9 + - - -
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Residues in contact with ASN 39 (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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34A ILE* 4.2 14.6 - - - +
37A GLY* 3.3 16.9 + - - +
38A GLN* 1.3 72.9 - - - +
40A GLY* 1.3 62.5 + - - +
42A ALA* 3.2 8.7 + - - +
43A VAL* 3.1 30.1 + - + +
70A GLU* 5.3 4.9 - - - +
71A ILE* 3.9 36.7 - - + +
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Residues in contact with GLY 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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38A GLN* 3.2 1.6 - - - +
39A ASN* 1.3 77.8 - - - +
41A GLN* 1.3 59.6 + - - +
43A VAL* 3.5 6.1 + - - +
44A SER* 3.1 23.8 + - - -
47A ARG* 5.3 0.9 + - - -
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Residues in contact with GLN 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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33A ALA* 3.8 16.3 - - + +
38A GLN* 2.7 46.0 + - + +
40A GLY* 1.3 72.9 - - - +
42A ALA* 1.3 59.9 + - - +
44A SER* 3.6 8.9 - - - -
45A TYR* 3.0 52.1 + - + -
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Residues in contact with ALA 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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30A VAL* 3.7 18.9 - - + +
33A ALA* 3.7 22.0 - - + -
34A ILE* 3.8 26.5 - - + +
38A GLN 3.3 8.6 + - - +
39A ASN* 3.2 14.0 + - - +
41A GLN* 1.3 78.3 - - - +
43A VAL* 1.3 56.3 + - - +
45A TYR 3.6 0.2 + - - -
46A PHE* 3.1 27.6 + - - +
71A ILE* 4.7 4.3 - - + -
75A LEU* 5.0 1.3 - - + -
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Residues in contact with VAL 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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39A ASN 3.1 16.6 + - - +
40A GLY* 3.9 5.6 - - - +
41A GLN 3.3 0.2 - - - -
42A ALA* 1.3 73.0 - - - +
44A SER* 1.3 59.8 + - - +
46A PHE* 3.5 6.1 - - - +
47A ARG* 3.0 55.4 + - - +
71A ILE* 3.3 24.9 - - + -
74A LYS* 3.9 22.0 - - + -
75A LEU* 4.5 5.4 - - + -
78A GLU* 3.8 18.2 - - + +
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Residues in contact with SER 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 GLY 3.1 17.1 + - - -
41A GLN* 3.6 12.7 - - - -
42A ALA 3.3 0.6 - - - -
43A VAL* 1.3 76.8 - - - +
45A TYR* 1.3 60.5 + - - +
47A ARG* 3.5 21.7 + - - +
48A GLN* 3.4 33.1 + - - +
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Residues in contact with TYR 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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26A MSE 3.4 25.6 - - + +
29A LYS* 4.3 27.6 - - + -
30A VAL* 3.8 18.4 - - + -
33A ALA* 5.5 0.4 - - + -
41A GLN* 3.0 48.9 + - + +
42A ALA* 5.2 0.4 - - - -
44A SER* 1.3 72.9 - - - +
46A PHE* 1.3 64.1 + - - +
48A GLN* 3.4 21.6 + - - -
49A THR* 3.1 27.0 + - - +
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Residues in contact with PHE 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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27A LEU* 4.8 1.1 - - + -
30A VAL* 3.7 17.2 - - + +
42A ALA 3.1 18.8 + - - +
43A VAL 3.5 5.2 - - - +
45A TYR* 1.3 77.2 - - - +
47A ARG* 1.3 61.1 + - - +
49A THR* 2.6 23.6 + - - -
50A ILE* 3.3 30.2 + - + +
57A THR* 3.4 28.5 - - + -
60A TYR* 4.0 20.2 - + - -
61A TYR* 4.7 4.0 - - + -
75A LEU* 3.3 60.1 - - + -
78A GLU* 4.2 9.2 - - + -
79A LEU* 3.8 17.5 - - + -
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Residues in contact with ARG 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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40A GLY 5.3 0.8 + - - -
43A VAL* 3.0 32.4 + - - +
44A SER* 3.8 25.9 + - - +
45A TYR 3.4 0.2 - - - -
46A PHE* 1.3 75.5 - - - +
48A GLN* 1.3 60.9 + - + +
50A ILE* 3.5 19.0 + - + +
51A ALA* 3.5 11.1 + - - +
78A GLU* 2.7 57.1 + - + +
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Residues in contact with GLN 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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26A MSE 3.2 29.1 - - + +
44A SER* 3.4 17.7 + - - +
45A TYR* 3.4 20.2 + - - +
46A PHE 3.3 0.8 - - - -
47A ARG* 1.3 77.0 - - + +
49A THR* 1.3 61.4 + - - +
51A ALA* 3.3 9.4 + - - +
52A LEU* 3.2 25.1 + - + +
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Residues in contact with THR 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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23A VAL* 4.4 6.9 - - - +
26A MSE 3.3 36.6 - - + +
27A LEU* 4.0 22.3 - - + +
30A VAL* 4.9 0.2 - - + -
45A TYR 3.1 16.2 + - - +
46A PHE* 2.6 22.7 + - - -
48A GLN* 1.3 73.4 - - - +
50A ILE* 1.3 55.4 + - - +
52A LEU* 3.8 7.0 - - - +
53A ASN* 2.8 37.9 + - - +
57A THR* 3.0 24.4 + - - +
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Residues in contact with ILE 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 PHE* 3.3 18.5 + - + +
47A ARG* 3.6 13.2 - - + +
48A GLN 3.3 0.2 - - - -
49A THR* 1.3 75.5 + - - +
51A ALA* 1.3 63.3 + - - +
53A ASN* 4.3 0.2 - - - -
54A ILE* 3.4 34.3 + - + +
57A THR* 3.8 19.1 - - + -
78A GLU* 3.7 42.6 - - + +
79A LEU* 3.8 13.5 - - + -
82A ALA* 3.4 25.1 - - + -
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Residues in contact with ALA 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 ARG 3.5 7.8 + - - +
48A GLN* 3.3 12.5 + - - +
49A THR 3.3 0.6 - - - -
50A ILE* 1.3 79.7 - - - +
52A LEU* 1.3 65.5 + - + +
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Residues in contact with LEU 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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22A SER 5.0 3.8 - - - +
23A VAL* 3.5 23.1 - - + +
26A MSE 4.1 32.1 - - + -
48A GLN* 3.2 15.1 + - + +
49A THR* 3.4 3.6 + - - +
51A ALA* 1.3 81.9 - - + +
53A ASN* 1.3 62.4 + - - +
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Residues in contact with ASN 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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23A VAL* 3.5 24.1 - - + +
49A THR 2.8 12.7 + - - +
52A LEU* 1.3 77.9 - - - +
54A ILE* 1.3 56.9 + - - +
55A ASP* 3.3 19.6 + - - +
56A ARG* 3.3 24.6 + - + +
57A THR* 2.8 31.2 + - - -
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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