Contacts of the helix formed by residues 34 - 45 (chain B) in PDB entry 3BQT
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 VAL 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ILE* 4.5 11.2 - - + -
30B GLU 3.6 16.4 - - - +
31B LEU* 3.8 8.1 - - - +
33B ASP* 1.3 87.1 - - + +
35B GLY* 1.3 74.5 + - - +
37B LYS* 4.8 0.5 + - - +
38B GLU* 3.4 50.3 + - + +
39B ALA* 4.1 15.7 - - + +
42B ARG* 4.9 9.2 - - - +
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Residues in contact with GLY 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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31B LEU 3.4 15.5 + - - -
32B LYS 3.6 6.3 + - - -
33B ASP 3.2 6.4 + - - -
34B VAL* 1.3 90.1 - - - +
36B SER* 1.3 63.5 + - - -
37B LYS 3.5 1.1 - - - -
39B ALA* 3.3 13.0 + - - +
59B GLU* 5.6 0.2 - - - -
62B VAL* 4.4 8.3 - - - -
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Residues in contact with SER 36 (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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31B LEU* 4.9 1.8 - - - -
35B GLY* 1.3 69.2 - - - -
37B LYS* 1.3 75.0 + - - +
38B GLU 3.2 1.8 - - - -
39B ALA* 3.6 6.4 - - - +
40B PHE* 2.9 27.7 + - - +
55B LEU* 4.3 10.7 - - - +
58B LEU* 3.8 12.3 - - - +
59B GLU* 2.9 55.9 + - - +
62B VAL* 4.3 4.1 - - - +
78B LEU* 4.5 3.5 - - - +
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Residues in contact with LYS 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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34B VAL 5.6 0.4 - - - +
35B GLY* 3.5 0.6 - - - -
36B SER* 1.3 85.4 + - - +
38B GLU* 1.3 58.9 + - - +
40B PHE* 3.8 1.2 - - - +
41B LEU* 3.1 28.4 + - - +
55B LEU* 4.3 7.2 - - + -
77B GLU* 3.3 33.7 + - - +
78B LEU* 4.3 13.7 - - + +
81B PHE* 3.5 56.6 - - + +
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Residues in contact with GLU 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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34B VAL* 3.4 43.8 + - + +
35B GLY 3.9 1.4 + - - -
36B SER 3.2 0.2 - - - -
37B LYS* 1.3 78.1 - - - +
39B ALA* 1.3 66.6 + - - +
41B LEU* 3.7 16.4 - - + +
42B ARG* 3.0 44.5 + - - -
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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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20B LEU* 4.3 12.5 - - + +
25B ILE* 4.1 13.4 - - + +
31B LEU* 3.6 25.4 - - + -
34B VAL* 4.1 6.1 - - + -
35B GLY 3.3 18.4 + - - +
36B SER* 3.1 6.4 + - - +
38B GLU* 1.3 78.9 - - - +
40B PHE* 1.3 62.4 + - - +
42B ARG* 3.1 18.5 + - - +
43B ILE* 3.4 14.2 + - - +
58B LEU* 4.5 4.3 - - + -
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Residues in contact with PHE 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 SER 2.9 15.8 + - - +
37B LYS 3.8 0.4 - - - +
39B ALA* 1.3 73.2 - - - +
41B LEU* 1.3 69.0 + - - +
42B ARG 3.0 2.0 - - - -
43B ILE* 3.1 16.6 + - + +
44B TRP* 2.9 25.1 + + + +
50B VAL* 3.6 24.7 - - + -
51B CYS 3.4 21.1 - - - -
54B GLU* 4.3 5.8 - - + -
55B LEU* 3.3 44.4 - - + -
58B LEU* 4.1 8.8 - - + +
81B PHE* 4.1 13.9 - + - -
82B HIS* 3.5 32.5 - + - -
85B LEU* 4.2 18.4 - - + -
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Residues in contact with LEU 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 LYS 3.1 14.9 + - - +
38B GLU* 3.7 18.4 - - + +
40B PHE* 1.3 83.0 - - - +
42B ARG* 1.3 66.2 + - + +
44B TRP* 3.3 23.3 + - + +
45B GLU* 3.3 23.3 + - + +
81B PHE* 4.4 16.6 - - + -
85B LEU* 4.9 8.7 - - + -
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Residues in contact with ARG 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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23B ALA* 2.5 37.7 + - + +
24B GLY* 4.3 9.7 + - - -
25B ILE* 2.9 34.2 - - + +
34B VAL* 4.9 6.8 - - - +
38B GLU* 3.0 48.2 + - - +
39B ALA 3.1 11.4 - - - +
40B PHE 3.0 0.6 - - - -
41B LEU* 1.3 81.6 - - + +
43B ILE* 1.3 58.1 + - - +
45B GLU* 2.9 34.9 - - - +
46B ASN* 3.4 8.0 - - - +
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Residues in contact with ILE 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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16B LEU* 5.0 10.3 - - + -
19B ASP* 2.9 37.5 - - + +
20B LEU* 4.3 17.5 - - + -
23B ALA* 3.3 17.3 - - + -
39B ALA 3.4 5.8 + - - +
40B PHE* 3.3 31.2 - - + +
42B ARG* 1.3 73.8 - - - +
44B TRP* 1.3 56.9 + - - +
45B GLU 3.0 1.8 - - - -
46B ASN* 2.7 11.3 + - + +
47B ASP* 2.5 38.9 + - + +
50B VAL* 4.3 21.1 - - + -
54B GLU* 6.2 0.7 - - + -
58B LEU* 4.8 7.4 - - + -
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Residues in contact with TRP 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 PHE* 2.9 17.5 + + + +
41B LEU* 3.4 22.7 - - + +
43B ILE* 1.3 78.2 - - - +
45B GLU* 1.3 80.0 + - + +
47B ASP 2.9 6.9 - - - -
48B SER* 2.8 62.9 + - - +
50B VAL* 4.1 13.2 - - + -
82B HIS* 6.1 2.7 - + - -
85B LEU* 3.2 46.7 - - + +
86B GLU* 3.7 43.3 - - + +
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Residues in contact with GLU 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 LEU* 3.3 9.8 + - + +
42B ARG* 2.9 42.4 - - - +
43B ILE 3.0 0.4 - - - -
44B TRP* 1.3 93.3 - - + +
46B ASN* 1.3 66.0 + - - +
48B SER* 4.9 1.0 + - - -
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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