Contacts of the helix formed by residues 27 - 43 (chain A) in PDB entry 3BRU
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 LEU 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 2.9 43.9 + - + +
26A SER* 1.3 85.7 - - - +
28A ALA* 1.3 61.3 + - - +
29A HIS* 3.4 2.9 - - - -
30A GLN* 3.4 31.9 + - + +
31A SER* 2.9 35.2 + - - +
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Residues in contact with ALA 28 (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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24A ASP 4.0 1.9 + - - +
25A ALA* 3.5 17.1 + - - +
26A SER 3.5 1.8 - - - -
27A LEU* 1.3 75.9 - - - +
29A HIS* 1.3 58.2 + - - +
31A SER* 3.3 4.0 + - - -
32A LEU* 3.1 35.4 + - + +
59A VAL* 3.9 16.9 - - + +
60A PRO* 6.2 0.4 - - + -
63A SER* 4.3 25.1 - - - +
67A TYR* 4.7 10.1 - - + +
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Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 5.3 1.0 + - - +
27A LEU 3.4 0.2 - - - -
28A ALA* 1.3 73.3 - - - +
30A GLN* 1.3 69.1 + - - +
32A LEU* 3.2 6.0 + - - +
33A ILE* 3.0 42.7 + - + +
67A TYR* 3.9 47.2 + + + +
68A PHE* 4.0 28.3 - + - -
77A ALA* 5.9 0.4 - - - +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.4 38.1 + - + +
29A HIS* 1.3 82.8 + - - +
31A SER* 1.3 69.8 + - - +
33A ILE* 3.4 5.5 + - - +
34A ARG* 2.9 45.8 + - - +
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Residues in contact with SER 31 (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* 2.9 28.1 + - - +
28A ALA* 3.5 5.1 - - - -
30A GLN* 1.3 90.2 + - - +
32A LEU* 1.3 57.8 + - - +
34A ARG* 3.5 3.8 - - - +
35A ALA* 3.0 31.5 + - - +
57A ALA* 3.6 28.1 + - - +
59A VAL* 3.8 7.7 - - - +
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Residues in contact with LEU 32 (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 ALA 3.1 24.0 + - - +
29A HIS* 3.6 5.2 - - - +
31A SER* 1.3 74.7 - - - +
33A ILE* 1.3 59.3 + - - +
35A ALA* 3.7 2.1 - - - +
36A GLY 2.8 25.1 + - - -
53A ILE* 4.0 17.0 - - + +
54A LEU* 4.0 10.8 - - + -
57A ALA* 3.9 14.6 - - + -
59A VAL* 3.5 27.8 - - + -
63A SER* 4.2 5.6 - - - +
64A PHE* 3.8 31.2 - - + +
67A TYR* 4.7 5.4 - - + -
68A PHE* 4.0 18.2 - - + -
74A PHE* 3.4 21.8 - - + -
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Residues in contact with ILE 33 (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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29A HIS* 3.0 39.2 + - + +
30A GLN* 3.8 5.4 - - - +
32A LEU* 1.3 75.9 - - - +
34A ARG* 1.3 53.0 + - - +
36A GLY* 3.1 1.7 + - - -
37A LEU* 2.8 54.1 + - + +
68A PHE* 4.2 20.2 - - + -
74A PHE* 4.6 0.9 - - + -
77A ALA* 4.4 20.0 - - + +
78A LEU* 3.5 19.3 - - + +
81A ALA* 3.9 16.6 - - + -
85A TYR* 5.1 6.3 - - + -
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Residues in contact with ARG 34 (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 GLN* 2.9 34.0 + - - +
31A SER* 3.5 6.1 - - - +
33A ILE* 1.3 78.1 - - - +
35A ALA* 1.3 58.9 + - - +
37A LEU* 3.3 27.8 + - - +
38A GLU* 2.9 76.0 + - - +
85A TYR* 6.2 0.4 - - - -
123A ARG* 4.9 4.9 - - - +
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Residues in contact with ALA 35 (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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31A SER 3.0 18.6 + - - +
32A LEU 3.8 2.9 - - - +
34A ARG* 1.3 78.7 - - + +
36A GLY* 1.3 62.7 + - - +
38A GLU* 4.6 5.2 - - - -
39A HIS* 3.0 35.4 + - + +
53A ILE* 3.9 27.4 - - + +
56A ALA* 4.1 12.1 - - + -
57A ALA* 4.0 12.8 - - + +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 2.8 15.6 + - - -
33A ILE 3.1 4.2 + - - -
35A ALA* 1.3 76.9 - - - +
37A LEU* 1.3 56.0 + - - +
40A LEU* 3.0 37.4 + - - +
53A ILE* 4.0 9.5 - - - +
74A PHE* 4.0 7.0 - - - -
78A LEU* 3.8 23.1 - - - -
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Residues in contact with LEU 37 (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 ILE* 2.8 38.4 + - + +
34A ARG* 3.8 27.1 - - - +
36A GLY* 1.3 68.2 - - - +
38A GLU* 1.3 57.5 + - + +
40A LEU* 5.2 1.6 - - - -
41A THR* 2.7 44.3 + - + +
78A LEU* 3.8 29.8 - - + +
81A ALA* 4.7 1.8 - - + -
82A TYR* 4.1 27.6 - - + +
85A TYR* 4.7 18.4 - - + -
126A LEU* 4.3 9.2 - - + -
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Residues in contact with GLU 38 (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 ARG* 2.9 63.9 + - - +
35A ALA* 4.0 7.7 - - - +
37A LEU* 1.3 77.0 - - - +
39A HIS* 1.3 67.7 + - + +
41A THR* 3.2 16.4 + - - -
42A GLU* 3.3 19.8 + - - +
56A ALA* 6.1 0.7 - - - +
123A ARG* 3.9 35.1 + - - +
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Residues in contact with HIS 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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35A ALA* 3.0 32.6 + - - +
36A GLY 4.1 0.2 - - - +
38A GLU* 1.3 86.4 + - + +
40A LEU* 1.3 60.5 + - - +
42A GLU* 4.6 2.7 - - - -
43A LYS* 2.8 37.5 + - - +
44A GLY 3.9 0.2 + - - -
48A VAL* 4.0 11.0 - - + +
52A GLU* 2.6 43.9 + - + +
53A ILE* 3.9 16.2 - - + -
56A ALA* 3.3 29.2 - - + +
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Residues in contact with LEU 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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36A GLY* 3.0 22.6 + - - +
39A HIS* 1.3 78.2 - - + +
41A THR* 1.3 52.5 + - - +
42A GLU 3.3 0.7 - - - -
43A LYS 3.7 5.5 - - - +
44A GLY* 3.7 6.7 - - - +
45A TYR* 3.9 31.4 - - + +
48A VAL* 4.1 26.9 - - + +
53A ILE* 4.8 2.5 - - + -
71A LYS* 6.5 0.7 - - - -
74A PHE* 5.8 1.1 - - + -
75A GLY* 5.3 2.2 - - - -
78A LEU* 3.8 24.7 - - + -
126A LEU* 3.5 19.6 - - + +
129A ASN* 2.7 32.7 + - - +
130A LEU* 4.0 23.3 - - + +
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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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37A LEU* 2.7 30.9 + - + +
38A GLU* 3.2 8.7 + - - -
40A LEU* 1.3 75.8 - - - +
42A GLU* 1.3 59.3 + - - +
82A TYR* 4.6 10.5 - - + -
122A ARG 3.9 0.9 - - - +
123A ARG* 3.5 19.1 - - - -
124A GLY 3.0 45.1 + - - +
126A LEU* 3.9 26.7 - - + +
129A ASN* 3.1 15.8 + - - +
194A LYS* 4.0 2.3 - - - +
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Residues in contact with GLU 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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38A GLU* 3.3 17.5 + - - +
39A HIS* 3.9 4.2 - - - +
41A THR* 1.3 80.7 - - - +
43A LYS* 1.3 70.1 + - + +
122A ARG* 3.6 49.1 + - + +
123A ARG* 3.8 23.6 + - + -
129A ASN* 4.7 0.4 + - - -
194A LYS* 4.7 5.7 + - - +
132B GLN 5.6 0.5 - - - +
135B GLY* 3.5 23.2 + - - +
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Residues in contact with LYS 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 HIS* 2.8 16.1 + - - +
40A LEU 3.9 1.6 - - - -
42A GLU* 1.3 88.2 - - + +
44A GLY* 1.3 61.3 + - - +
47A SER* 3.9 21.5 + - - -
48A VAL* 3.8 10.1 - - + -
52A GLU* 3.2 37.7 + - - -
129A ASN* 3.4 19.2 + - - +
132B GLN 4.5 8.3 - - - +
133B GLU* 5.0 6.6 - - - -
135B GLY* 3.9 18.8 - - - +
136B ALA* 3.9 21.9 - - + +
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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