Contacts of the helix formed by residues 50 - 68 (chain B) in PDB entry 3SF4
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 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B THR* 3.0 9.6 + - - +
49B GLU* 1.3 75.2 - - - +
51B LEU* 1.3 53.1 + - - +
52B LYS* 2.7 21.4 + - - +
53B THR* 2.7 47.7 + - - +
54B LEU* 2.9 6.9 + - - -
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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
----------------------------------------------------------
48B THR 5.5 0.2 - - - +
49B GLU* 3.1 30.5 + - - +
50B ASP* 1.3 73.1 - - - +
52B LYS* 1.3 56.8 + - - +
54B LEU* 3.5 21.5 - - + +
55B SER* 2.9 30.7 + - - -
84B LEU* 3.5 30.3 - - + +
87B THR* 4.8 2.9 - - - +
88B ILE* 3.3 39.4 - - + +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 2.7 14.6 + - - +
51B LEU* 1.3 77.3 - - + +
53B THR* 1.3 62.2 + - + +
55B SER* 3.6 8.2 - - - -
56B ALA* 3.6 15.2 + - - +
88B ILE* 3.6 22.9 - - + -
90B ASP* 3.1 36.1 + - - -
50E LYS* 5.9 0.2 - - - +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 4.7 4.0 + - - +
50B ASP* 2.7 44.1 + - - +
52B LYS* 1.3 74.3 - - + +
54B LEU* 1.3 59.4 + - - -
55B SER 3.2 0.7 - - - -
56B ALA* 3.3 9.7 + - - +
57B ILE* 2.9 32.5 + - - +
51E PRO 5.8 0.2 - - - -
52E ILE* 4.5 27.4 - - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA 6.0 1.6 - - - +
44B VAL* 6.2 4.3 - - + -
47B GLY* 5.5 2.9 - - - -
48B THR* 3.6 36.3 - - + +
50B ASP 2.9 6.2 + - - +
51B LEU* 3.5 35.0 - - + +
53B THR* 1.3 79.2 + - - +
55B SER* 1.3 60.8 + - - +
57B ILE* 3.0 24.1 - - + +
58B TYR* 3.0 54.0 - - + +
84B LEU* 3.5 19.1 - - + -
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU 2.9 17.3 + - - -
52B LYS* 3.6 11.9 - - - -
54B LEU* 1.3 73.4 - - - +
56B ALA* 1.3 57.6 + - - +
57B ILE 2.9 10.1 + - - -
58B TYR* 3.1 4.2 + - - -
59B SER* 2.9 14.1 + - - -
81B ASP* 2.5 36.7 + - - +
84B LEU* 3.8 17.3 - - - -
85B ALA* 5.3 3.4 - - - +
88B ILE* 5.8 2.7 - - - -
90B ASP* 5.2 2.6 + - - -
50E LYS* 2.9 22.0 + - - +
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Residues in contact with ALA 56 (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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52B LYS 3.6 9.0 + - - +
53B THR* 3.3 12.9 + - - +
55B SER* 1.3 78.7 + - - +
57B ILE* 1.3 58.4 + - - +
59B SER* 3.8 1.1 - - - -
60B GLN* 3.1 34.0 + - - +
50E LYS* 3.1 38.3 - - + +
51E PRO 3.6 14.1 - - - +
52E ILE* 4.1 10.6 - - + +
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Residues in contact with ILE 57 (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 ALA* 3.7 24.5 - - + -
40B PHE* 4.0 20.8 - - + +
43B ALA* 4.3 11.4 - - + -
44B VAL* 4.2 25.4 - - + +
48B THR* 5.6 2.7 - - + -
53B THR* 2.9 28.3 - - - +
54B LEU* 3.0 25.1 - - + +
55B SER 2.9 0.4 - - - -
56B ALA* 1.3 75.6 - - - +
58B TYR* 1.3 57.4 + - + +
60B GLN* 4.0 0.7 - - - +
61B LEU* 2.8 38.2 + - + +
52E ILE* 4.1 17.5 - - + -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 4.8 25.6 - - + +
54B LEU* 3.0 63.0 - - + +
55B SER* 3.1 5.3 + - - +
57B ILE* 1.3 76.0 - - + +
59B SER* 1.3 55.0 + - - +
61B LEU* 3.5 5.9 - - - -
62B GLY* 2.7 32.2 + - - -
77B TYR* 3.6 38.3 - + - +
78B HIS* 4.6 0.3 + - - -
80B HIS* 4.2 22.4 - + + -
81B ASP* 3.8 13.9 - - + -
84B LEU* 3.3 21.0 - - + +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER 2.9 16.3 + - - -
56B ALA 3.7 1.6 - - - -
58B TYR* 1.3 78.6 - - - +
60B GLN* 1.3 57.6 + - - +
62B GLY 3.2 0.2 + - - -
63B ASN* 3.0 30.5 + - - -
78B HIS* 3.6 8.7 - - - -
81B ASP* 4.0 13.1 + - - -
100B ASN* 4.7 4.9 + - - -
48E GLN 4.0 10.4 + - - -
49E ALA* 4.4 0.7 - - - -
50E LYS* 3.3 46.9 + - - +
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Residues in contact with GLN 60 (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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25B GLU* 3.2 40.6 + - - +
28B CYS* 5.2 2.8 - - - +
40B PHE* 3.9 20.9 - - + -
56B ALA 3.1 14.5 + - - +
57B ILE 4.3 0.2 - - - +
59B SER* 1.3 73.1 - - - +
61B LEU* 1.3 63.7 + - - +
62B GLY 3.1 0.7 - - - -
63B ASN* 3.9 7.7 - - - +
64B ALA* 3.1 25.1 + - - +
49E ALA* 5.1 9.7 - - + +
50E LYS 3.2 32.2 + - - +
51E PRO* 4.3 1.4 - - - +
52E ILE* 3.2 18.1 - - - +
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Residues in contact with LEU 61 (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 VAL* 5.2 2.9 - - + +
40B PHE* 4.3 25.3 - - + -
41B GLU* 5.9 0.9 - - - +
57B ILE* 2.8 23.6 + - + +
58B TYR 3.6 0.7 - - - +
60B GLN* 1.3 78.0 - - - +
62B GLY* 1.3 59.8 + - - +
64B ALA* 3.9 3.7 - - - +
65B TYR* 3.0 34.8 + - + -
77B TYR* 3.6 29.2 - - + -
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Residues in contact with GLY 62 (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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58B TYR 2.7 16.9 + - - -
59B SER 3.6 2.0 - - - -
61B LEU* 1.3 78.8 - - - +
63B ASN* 1.3 62.8 + - - +
64B ALA 3.2 0.2 - - - -
65B TYR 3.4 1.0 + - - -
66B PHE* 3.3 5.4 + - - +
74B ALA* 3.2 30.1 - - - +
77B TYR* 3.9 13.7 - - - -
78B HIS* 3.4 18.4 + - - -
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Residues in contact with ASN 63 (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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59B SER* 3.0 17.9 + - - +
60B GLN* 3.6 7.3 + - - +
62B GLY* 1.3 73.4 - - - +
64B ALA* 1.3 65.9 + - - +
66B PHE* 3.1 8.3 + - - +
67B TYR* 3.0 21.3 + - - +
78B HIS* 2.7 38.9 + - - -
100B ASN* 4.1 7.1 - - - +
47E LEU* 3.9 28.4 - - + +
48E GLN 3.1 25.1 - - - +
49E ALA* 4.2 8.8 - - - +
63E ILE* 5.3 5.8 - - + +
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Residues in contact with ALA 64 (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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28B CYS* 4.2 20.4 - - - -
33B CYS* 4.2 9.0 - - + +
37B VAL* 4.0 20.4 - - + -
40B PHE* 5.4 1.1 - - + -
60B GLN 3.1 20.5 + - - +
61B LEU* 3.9 7.2 - - - +
62B GLY 3.2 0.2 - - - -
63B ASN* 1.3 76.1 - - - +
65B TYR* 1.3 63.7 + - - +
67B TYR* 3.0 19.1 + - - +
68B LEU* 3.0 17.9 + - - +
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Residues in contact with TYR 65 (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 VAL* 3.2 31.3 - - + +
41B GLU* 2.9 25.5 + - - -
61B LEU* 3.0 24.1 + - + -
62B GLY 3.4 5.0 + - - +
63B ASN 3.3 0.2 - - - -
64B ALA* 1.3 78.8 - - - +
66B PHE* 1.3 60.1 + - - +
68B LEU* 3.2 11.5 + - + +
69B HIS 3.0 4.2 + - - -
70B ASP* 2.8 60.0 + - + +
73B LYS* 3.5 17.9 - - + -
74B ALA* 3.7 19.3 - - - +
77B TYR* 3.9 19.8 + + - -
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Residues in contact with PHE 66 (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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62B GLY 3.3 9.8 + - - +
63B ASN* 3.1 16.0 + - - +
65B TYR* 1.3 78.1 - - - +
67B TYR* 1.3 59.4 - - - +
69B HIS* 2.9 24.8 + - - -
71B TYR* 3.4 37.2 + + - -
74B ALA* 3.7 6.0 - - + +
78B HIS* 5.5 0.7 - - - +
103B ASN 4.6 3.6 - - - -
104B THR* 3.9 28.5 - - - -
107B VAL* 3.5 27.8 - - + -
45E CYS* 3.9 27.6 - - + -
47E LEU* 3.4 29.2 - - + -
65E ALA* 4.2 12.8 - - + -
66E GLY 4.9 0.7 - - - -
67E GLY* 4.2 11.2 - - - -
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 3.9 26.3 + - - -
33B CYS* 3.6 24.2 - - + -
63B ASN 3.0 7.2 + - - +
64B ALA* 3.0 11.5 + - - +
66B PHE* 1.3 83.1 - - - +
68B LEU* 1.3 68.4 + - + +
69B HIS* 3.4 16.7 + - - -
65E ALA* 5.7 9.4 - - + -
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Residues in contact with LEU 68 (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 CYS* 4.0 9.0 - - + +
34B ARG* 3.6 65.4 + - + +
37B VAL* 4.2 12.6 - - + -
64B ALA 3.0 16.7 + - - +
65B TYR* 3.2 15.2 + - + +
66B PHE 3.1 0.2 - - - -
67B TYR* 1.3 90.4 - - + +
69B HIS* 1.3 75.6 + - - +
70B ASP* 3.3 7.2 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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