Contacts of the helix formed by residues 39 - 51 (chain B) in PDB entry 4BSX
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 GLY 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLN* 1.3 74.7 - - - +
40B GLN* 1.3 53.4 + - - +
41B ASP* 3.1 4.4 - - - +
42B LEU* 3.0 13.3 + - - +
43B LEU* 2.8 34.1 + - - +
98B ARG* 4.7 8.0 - - - +
99B LEU* 3.8 9.8 - - - +
102B LEU* 3.8 8.1 - - - -
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Residues in contact with GLN 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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30B LEU* 3.8 33.2 + - + +
32B THR 3.7 7.9 + - - -
33B PRO* 3.6 12.1 - - - +
34B ARG* 3.1 44.6 + - - +
37B CYS* 3.0 44.2 + - + +
38B GLN 3.4 0.2 - - - -
39B GLY* 1.3 77.8 - - - +
41B ASP* 1.3 63.0 + - - +
43B LEU* 3.4 2.7 + - - +
44B HIS* 2.8 29.6 + - - +
102B LEU* 3.6 18.6 - - + +
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Residues in contact with ASP 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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30B LEU 4.6 8.1 - - - +
31B LYS* 5.0 5.2 - - - +
33B PRO* 5.6 8.9 - - - +
39B GLY 3.1 1.7 - - - +
40B GLN* 1.3 82.5 + - - +
42B LEU* 1.3 63.7 + - - +
44B HIS* 3.2 11.0 + - - +
45B ALA* 3.2 20.3 + - - +
60B SER* 5.5 1.0 - - - -
64B LEU* 3.9 32.1 - - + +
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Residues in contact with LEU 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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8B LEU* 5.6 0.4 - - + -
39B GLY* 3.0 14.1 + - - +
41B ASP* 1.3 77.8 - - - +
43B LEU* 1.3 64.2 + - - +
45B ALA* 3.0 7.2 + - - +
46B MSE 3.0 30.4 + - - +
61B LEU* 4.2 12.6 - - + -
64B LEU* 3.9 10.0 - - + +
67B ASP* 5.2 3.8 - - - +
69B VAL* 4.0 25.8 - - + -
70B ALA* 4.1 21.8 - - + +
73B VAL* 4.0 25.4 - - + -
95B ALA* 4.6 7.6 - - + -
99B LEU* 4.1 23.1 - - + -
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Residues in contact with LEU 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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15B LEU* 4.0 24.2 - - + -
26B LEU* 5.6 3.6 - - + -
30B LEU* 3.7 20.9 - - + -
39B GLY 2.8 16.1 + - - +
40B GLN 3.8 4.5 - - - +
42B LEU* 1.3 76.4 - - - +
44B HIS* 1.3 64.6 + - - +
46B MSE 4.4 11.9 - - + -
47B VAL* 2.9 31.3 - - + +
99B LEU* 3.7 20.8 - - + +
102B LEU* 3.7 34.1 - - + -
103B LEU* 4.3 25.8 - - + +
106B GLU* 6.2 1.6 - - + -
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Residues in contact with HIS 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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27B LYS* 3.4 36.8 + - + -
30B LEU* 3.8 18.1 - - + +
31B LYS* 3.6 40.7 + - + +
40B GLN 2.8 21.9 + - - +
41B ASP* 3.2 12.3 + - - +
43B LEU* 1.3 72.9 - - - +
45B ALA* 1.3 62.6 + - - +
47B VAL* 3.3 5.0 - - - +
48B LEU* 3.1 54.1 + - + +
56B GLU* 4.3 4.6 + - - -
60B SER* 3.9 15.8 + - - -
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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 ASP 3.2 8.7 + - - +
42B LEU* 3.0 10.6 + - + +
44B HIS* 1.3 81.0 - - - +
46B MSE 1.3 56.9 + - + +
48B LEU* 3.3 15.3 + - - +
49B LEU* 3.0 32.3 + - - +
57B ALA* 3.7 2.4 - - - +
60B SER* 4.2 13.5 - - - -
61B LEU* 3.7 37.0 - - + -
64B LEU* 4.9 1.3 - - + -
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Residues in contact with MSE 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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8B LEU* 3.8 24.5 - - + -
11B ALA* 4.0 20.0 - - + -
12B PHE* 3.5 43.9 - - + +
15B LEU* 4.1 10.1 - - + -
42B LEU* 3.0 29.6 + - + +
43B LEU* 3.3 12.3 + - + +
45B ALA* 1.3 72.7 - - - +
47B VAL* 1.3 60.7 + - - +
49B LEU* 3.2 6.0 + - - +
50B LYS* 2.9 30.8 + - - +
73B VAL* 4.4 13.5 - - + -
99B LEU* 3.5 33.4 - - + -
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Residues in contact with VAL 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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15B LEU* 3.9 27.4 - - + +
23B LEU* 3.4 32.8 - - + +
26B LEU* 3.9 18.4 - - + -
27B LYS* 3.6 21.5 - - + +
30B LEU* 4.1 7.4 - - + -
43B LEU* 2.9 22.8 - - + +
44B HIS* 3.4 7.0 - - - +
45B ALA 3.3 0.2 - - - -
46B MSE 1.3 76.9 + - - +
48B LEU* 1.3 62.8 + - - +
50B LYS* 3.2 5.4 - - - +
51B LEU* 3.0 25.7 - - + -
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Residues in contact with LEU 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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27B LYS* 3.9 26.9 - - + -
44B HIS* 3.1 38.5 + - + +
45B ALA* 3.3 8.9 + - - +
47B VAL* 1.3 74.8 + - + +
49B LEU* 1.3 60.5 + - - +
51B LEU* 3.2 10.6 + - + +
53B GLN* 2.9 53.5 + - + +
56B GLU* 3.8 34.3 - - + +
57B ALA* 3.8 10.3 - - + -
60B SER* 3.8 16.8 - - - +
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Residues in contact with LEU 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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12B PHE* 4.1 17.0 - - + -
45B ALA 3.0 18.9 + - - +
46B MSE 3.2 8.7 + - - +
48B LEU* 1.3 76.0 - - - +
50B LYS* 1.3 58.6 + - - +
52B GLY* 3.1 18.1 + - - +
53B GLN 4.8 2.2 - - - +
54B GLU* 4.3 21.6 - - + +
57B ALA* 3.3 21.1 - - + -
61B LEU* 4.5 3.4 - - + -
73B VAL* 4.2 13.7 - - + -
77B TRP* 3.8 38.1 - - + +
78B ALA* 4.0 20.9 - - + -
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Residues in contact with LYS 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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12B PHE* 3.5 31.8 + - + +
13B ASP* 5.0 7.2 + - - +
15B LEU* 4.1 11.4 - - + -
16B GLY* 3.4 39.0 - - - +
20B GLN* 4.6 5.9 + - - +
23B LEU* 4.0 15.9 - - + +
46B MSE 2.9 15.0 + - - +
47B VAL* 3.2 5.4 - - - +
49B LEU* 1.3 76.6 - - - +
51B LEU* 1.3 58.0 + - - +
52B GLY 3.2 1.9 + - - -
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Residues in contact with LEU 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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20B GLN* 3.8 25.8 - - + +
23B LEU* 3.8 42.4 - - + +
24B LEU* 4.1 17.5 - - + +
27B LYS* 4.1 15.0 - - + -
47B VAL* 3.0 22.1 - - + -
48B LEU* 3.2 9.8 + - - +
50B LYS* 1.3 76.6 - - - +
52B GLY* 1.3 59.4 + - - +
53B GLN* 3.2 34.2 + - - +
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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