Contacts of the helix formed by residues 34 - 48 (chain B) in PDB entry 4HRE
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 ASP 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 4.3 6.2 - - - +
30B TYR* 5.1 0.8 - - - -
32B ASN 3.6 4.4 + - - +
33B PHE* 1.3 77.1 - - - +
35B ALA* 1.3 66.7 + - - +
36B GLU* 3.2 35.1 - - - +
37B ARG* 3.2 33.4 - - + +
38B ASP* 3.1 28.7 + - - +
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Residues in contact with ALA 35 (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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14B GLU* 3.2 29.9 + - - +
33B PHE* 3.6 23.7 - - + -
34B ASP* 1.3 72.9 + - - +
36B GLU* 1.3 58.1 + - + +
38B ASP* 3.5 1.9 + - - +
39B ALA* 2.9 28.4 + - - +
70B ASP* 3.6 26.2 - - + +
71B ILE* 4.0 5.4 - - - -
74B ALA* 3.6 6.7 - - + +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 5.9 0.2 - - - +
34B ASP* 3.2 30.6 - - - +
35B ALA* 1.3 71.4 - - - +
37B ARG* 1.3 56.6 + - - +
38B ASP 3.1 1.3 - - - -
39B ALA* 3.2 4.5 + - - +
40B LEU* 2.9 37.0 + - + +
74B ALA* 4.0 14.5 - - + +
77B ARG* 6.3 0.9 - - - +
78B ARG* 4.9 2.7 + - - +
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Residues in contact with ARG 37 (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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32B ASN 5.9 1.0 + - - -
34B ASP* 3.2 33.2 + - + +
35B ALA 3.5 0.2 - - - -
36B GLU* 1.3 78.5 + - - +
38B ASP* 1.3 62.5 + - - +
40B LEU* 3.2 14.9 - - + +
41B ASN* 3.0 43.4 + - - +
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Residues in contact with ASP 38 (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 TYR* 5.4 0.3 - - - -
33B PHE* 3.7 9.7 - - - -
34B ASP 3.1 20.9 + - - +
35B ALA 3.8 3.6 - - - +
36B GLU 3.1 0.6 - - - -
37B ARG* 1.3 82.4 - - - +
39B ALA* 1.3 65.6 - - - +
40B LEU 3.1 1.3 - - - -
41B ASN* 3.4 7.0 + - - +
42B ILE* 3.0 31.5 + - - +
59B ILE* 3.7 27.9 - - + +
63B ARG* 3.1 34.0 + - - -
71B ILE* 4.1 15.5 - - + -
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Residues in contact with ALA 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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35B ALA 2.9 15.3 + - - +
36B GLU* 3.4 9.2 - - - +
38B ASP* 1.3 74.6 - - - +
40B LEU* 1.3 63.6 + - - +
42B ILE* 3.3 1.4 + - - +
43B GLU* 3.0 24.5 + - - +
71B ILE* 3.9 11.3 - - - +
74B ALA* 3.8 9.0 - - + +
75B TYR* 3.6 45.1 - - + +
78B ARG* 5.4 6.5 - - + -
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Residues in contact with LEU 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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36B GLU* 2.9 18.2 + - + +
37B ARG* 3.2 19.1 - - + +
39B ALA* 1.3 78.5 - - - +
41B ASN* 1.3 68.6 + - - +
43B GLU* 3.2 7.2 + - - +
44B THR* 2.8 35.4 + - - +
78B ARG* 3.0 42.8 - - - +
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Residues in contact with ASN 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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37B ARG* 3.0 36.9 + - - +
38B ASP* 3.4 3.6 + - - +
40B LEU* 1.3 83.4 - - - +
42B ILE* 1.3 57.2 + - - +
44B THR* 3.1 12.6 + - - +
45B ALA* 2.8 30.1 + - - +
55B THR* 4.5 8.5 - - + +
59B ILE* 3.9 22.2 - - + +
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Residues in contact with ILE 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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38B ASP 3.0 19.2 + - - +
39B ALA* 3.7 3.8 - - - +
41B ASN* 1.3 75.7 - - - +
43B GLU* 1.3 57.3 + - - +
45B ALA* 3.1 6.9 + - - +
46B VAL* 2.8 33.9 + - + +
55B THR* 5.3 0.2 - - - -
56B ILE* 3.8 28.5 - - + -
59B ILE* 4.3 19.5 - - + -
60B LEU* 4.0 24.9 - - + -
71B ILE* 3.6 24.7 - - + -
75B TYR* 4.7 3.8 - - + -
83B LEU* 4.1 28.0 - - + -
87B LEU* 4.8 0.7 - - + -
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Residues in contact with GLU 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 ALA 3.0 10.7 + - - +
40B LEU* 3.5 9.5 - - - +
42B ILE* 1.3 74.9 - - - +
44B THR* 1.3 64.6 + - - +
46B VAL* 3.3 3.1 + - + +
47B LYS* 3.0 61.2 + - + +
75B TYR* 3.6 26.1 - - + +
78B ARG* 4.2 28.2 + - + +
79B THR* 3.1 30.4 - - + +
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Residues in contact with THR 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 LEU* 2.8 26.3 + - - +
41B ASN* 3.3 15.2 + - - +
43B GLU* 1.3 79.0 + - - +
45B ALA* 1.3 53.0 + - - +
47B LYS* 3.6 6.1 + - - +
48B THR* 2.7 34.1 + - - +
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Residues in contact with ALA 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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41B ASN 2.8 15.7 + - - +
42B ILE 3.1 5.6 + - - +
44B THR* 1.3 76.0 - - - +
46B VAL* 1.3 63.5 - - - +
48B THR* 3.7 8.9 + - - -
51B VAL* 3.5 4.3 - - - -
52B ASP* 3.2 49.8 + - + +
55B THR* 3.9 19.3 - - + -
56B ILE* 3.9 11.2 - - + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 2.8 21.7 + - + +
43B GLU* 3.9 6.7 - - + +
45B ALA* 1.3 76.7 - - - +
47B LYS* 1.3 70.0 + - + +
48B THR 3.3 6.0 - - - +
51B VAL* 4.3 12.1 - - - +
56B ILE* 4.1 15.5 - - + -
75B TYR* 4.4 14.8 - - - +
83B LEU* 6.2 0.4 - - + -
86B ALA* 4.8 11.4 - - + +
87B LEU* 4.4 10.3 - - + -
90B ALA* 3.8 28.5 - - + +
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Residues in contact with LYS 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 GLU* 3.0 51.2 + - + +
44B THR* 3.6 6.3 + - - +
46B VAL* 1.3 81.4 - - + +
48B THR* 1.3 65.0 + - - +
49B LYS* 3.5 3.3 + - - +
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 2.7 26.2 + - - +
45B ALA* 3.7 12.6 + - - -
46B VAL 3.3 4.2 - - - +
47B LYS* 1.3 79.7 - - - +
49B LYS* 1.3 72.1 + - + +
50B GLY 3.2 0.3 + - - -
51B VAL* 2.8 23.0 + - - +
52B ASP* 4.2 16.7 - - + +
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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