Contacts of the helix formed by residues 38 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ALA* 2.8 24.2 + - - +
36B ALA* 4.0 22.6 + - + +
37B GLY* 1.3 73.5 + - - +
39B ASN* 1.3 58.5 + - - +
40B GLY 3.3 3.3 + - - -
41B GLN* 3.4 35.7 - - + +
42B ALA* 3.1 22.5 + - - +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.5 12.8 - - - +
37B GLY* 3.4 18.6 + - - +
38B GLN* 1.3 74.6 - - - +
40B GLY* 1.3 63.8 + - - +
42B ALA* 3.4 2.6 + - - -
43B VAL* 3.1 31.5 + - - +
70B GLU* 5.3 6.7 - - - +
71B ILE* 3.5 34.6 - - + +
74B LYS* 5.8 4.5 - - + -
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN 3.3 0.8 - - - -
39B ASN* 1.3 77.3 - - - +
41B GLN* 1.3 60.5 + - - +
43B VAL* 3.4 8.1 + - - +
44B SER* 3.3 23.6 + - - -
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 3.7 16.3 - - + +
38B GLN* 3.4 38.8 + - + +
40B GLY* 1.3 72.2 - - - +
42B ALA* 1.3 64.8 + - - +
44B SER* 3.4 8.9 + - - -
45B TYR* 3.1 50.6 + - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.9 15.7 - - + +
33B ALA* 3.6 17.7 - - + -
34B ILE* 3.8 26.0 - - + +
38B GLN 3.1 17.9 + - - +
39B ASN* 3.5 8.7 - - - +
40B GLY 3.3 0.2 - - - -
41B GLN* 1.3 77.0 - - - +
43B VAL* 1.3 57.0 + - - +
45B TYR* 3.6 2.8 + - - +
46B PHE* 3.1 28.5 + - - +
71B ILE* 4.4 4.7 - - + -
75B LEU* 4.9 1.8 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN 3.1 18.2 + - - +
40B GLY* 3.8 6.5 - - - +
41B GLN 3.3 0.2 - - - -
42B ALA* 1.3 73.5 - - - +
44B SER* 1.3 59.1 + - - +
46B PHE* 3.2 8.0 + - - +
47B ARG* 3.0 37.0 + - - +
71B ILE* 3.4 21.1 - - + -
74B LYS* 3.9 28.9 - - + +
75B LEU* 4.3 4.9 - - + -
78B GLU* 3.6 30.4 - - + +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY 3.3 14.0 + - - -
41B GLN* 3.7 11.5 - - - -
43B VAL* 1.3 75.8 - - - +
45B TYR* 1.3 64.7 + - - +
47B ARG* 3.2 28.0 + - - +
48B GLN* 3.2 36.3 + - - +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MSE 3.7 24.2 - - + +
29B LYS* 3.5 54.8 + - + +
30B VAL* 3.7 18.2 - - + -
41B GLN* 3.1 51.0 + - + +
42B ALA* 3.9 1.1 - - - +
44B SER* 1.3 79.7 - - - +
46B PHE* 1.3 61.5 + - - +
48B GLN* 3.4 13.0 + - - +
49B THR* 3.0 30.1 + - - +
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.7 1.3 - - + -
30B VAL* 3.7 19.0 - - + +
42B ALA 3.1 18.8 + - - +
43B VAL 3.5 5.2 - - - +
44B SER 3.2 0.2 - - - -
45B TYR* 1.3 78.4 - - - +
47B ARG* 1.3 61.1 + - - +
49B THR* 2.8 20.8 + - - -
50B ILE* 3.2 21.1 + - + +
57B THR* 3.2 33.9 - - + -
60B TYR* 3.9 23.1 - + - -
61B TYR* 4.5 4.5 - - + -
75B LEU* 3.4 56.3 - - + -
78B GLU* 4.1 9.9 - - + -
79B LEU* 3.9 22.4 - - + -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.0 23.3 + - - +
44B SER* 3.2 32.7 + - - +
46B PHE* 1.3 75.7 - - - +
48B GLN* 1.3 64.0 + - + +
50B ILE* 3.3 20.4 + - + +
51B ALA* 3.4 12.3 + - - +
78B GLU* 2.9 51.7 + - + +
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MSE 3.2 30.0 - - + +
44B SER* 3.2 25.6 + - - +
45B TYR* 3.7 13.1 - - - +
47B ARG* 1.3 78.0 - - + +
49B THR* 1.3 61.2 + - - +
51B ALA* 3.5 9.2 + - - +
52B LEU* 3.4 25.0 + - + +
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 4.4 7.6 - - - +
26B MSE 3.2 42.0 - - + +
27B LEU* 3.8 17.6 - - + +
30B VAL* 4.7 0.4 - - + -
45B TYR 3.0 15.9 + - - +
46B PHE* 2.8 20.8 + - - -
48B GLN* 1.3 73.3 - - - +
50B ILE* 1.3 59.1 + - - +
52B LEU* 3.2 9.8 + - - +
53B ASN 2.9 25.6 + - - +
57B THR* 3.2 25.9 + - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.2 22.9 + - + +
47B ARG* 3.3 11.9 + - + +
49B THR* 1.3 75.7 - - - +
51B ALA* 1.3 61.8 + - - +
52B LEU 3.4 0.2 + - - -
53B ASN 3.4 0.3 + - - -
54B ILE* 3.3 33.0 + - + +
57B THR* 3.6 22.0 - - + -
78B GLU* 3.5 45.8 - - + +
79B LEU* 3.9 10.1 - - + +
82B ALA* 3.3 27.6 - - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ARG 3.4 8.6 + - - +
48B GLN* 3.6 12.3 - - - +
49B THR 3.3 0.4 - - - -
50B ILE* 1.3 79.8 - - - +
52B LEU* 1.3 63.5 + - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN* 3.4 26.7 - - + +
23B VAL* 3.5 23.6 - - + -
26B MSE 4.1 21.5 - - + -
48B GLN* 3.4 15.2 + - + +
49B THR* 3.2 7.2 + - - +
50B ILE 4.0 0.2 - - - -
51B ALA* 1.3 79.0 - - + +
53B ASN* 1.3 61.9 + - - +
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.8 21.3 - - + +
49B THR 2.9 13.0 + - - +
50B ILE 3.4 0.4 + - - -
52B LEU* 1.3 77.4 - - - +
54B ILE* 1.3 61.6 + - - +
55B ASP* 3.2 12.3 + - - +
56B ARG* 3.1 28.7 + - + +
57B THR* 2.9 25.6 + - - -
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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