Contacts of the helix formed by residues 50 - 68 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C THR* 3.0 14.1 + - - +
49C GLU* 1.3 75.4 - - - +
51C LEU* 1.3 58.4 + - - +
52C LYS* 3.0 15.4 + - - +
53C THR* 2.9 36.7 + - - +
54C LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C THR 4.7 5.8 - - - +
49C GLU* 3.1 14.4 + - - +
50C ASP* 1.3 73.2 + - - +
52C LYS* 1.3 56.7 + - - +
54C LEU* 4.0 24.2 - - + -
55C SER* 2.8 30.8 + - - -
84C LEU* 3.6 18.5 - - + +
87C THR* 5.5 4.3 - - + -
88C ILE* 3.7 33.4 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASP* 3.0 11.6 + - - +
51C LEU* 1.3 78.0 - - - +
53C THR* 1.3 63.2 + - - +
55C SER* 3.4 5.0 - - - -
56C ALA* 3.3 18.5 + - - +
88C ILE* 4.0 18.9 - - + +
90C ASP* 3.3 29.6 + - - +
92C LEU* 6.4 0.4 - - - +
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C CYS* 5.4 4.5 - - - -
18C LEU* 4.7 14.9 - - + +
21C ALA* 5.2 2.2 - - + -
48C THR* 5.1 7.2 - - + +
50C ASP* 2.9 34.7 + - - +
52C LYS* 1.3 75.5 - - - +
54C LEU* 1.3 66.6 + - - +
56C ALA* 3.1 9.8 + - + +
57C ILE* 3.0 38.1 + - + +
52F ILE* 4.7 16.4 - - + -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 4.6 16.2 - - + -
47C GLY* 6.1 1.1 - - - -
48C THR* 4.0 23.3 - - + +
50C ASP 2.9 13.1 + - - +
51C LEU* 3.2 25.8 + - + +
53C THR* 1.3 76.0 - - - +
55C SER* 1.3 63.5 + - - +
57C ILE* 3.0 20.2 + - + +
58C TYR* 3.0 60.9 + - + +
84C LEU* 4.0 9.0 - - + -
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU 2.8 17.3 + - - -
52C LYS* 3.4 9.2 - - - -
53C THR 3.1 0.2 - - - -
54C LEU* 1.3 77.3 - - - +
56C ALA* 1.3 63.1 + - - +
58C TYR* 3.2 6.5 + - - +
59C SER* 3.0 19.4 + - - -
81C ASP* 2.5 34.5 + - - +
84C LEU* 3.7 19.5 - - - +
85C ALA* 4.6 4.5 - - - +
88C ILE* 5.0 5.4 - - - -
90C ASP* 5.4 3.8 + - - -
50F LYS* 3.2 12.4 + - - +
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS 3.3 8.5 + - - +
53C THR* 3.1 12.9 + - + +
55C SER* 1.3 78.3 + - - +
57C ILE* 1.3 63.2 + - - +
59C SER* 3.3 1.2 + - - -
60C GLN* 2.9 30.2 + - - +
50F LYS* 3.6 37.9 - - + +
51F PRO 4.4 4.7 - - - +
52F ILE* 4.1 14.1 - - + -
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C CYS* 5.1 6.5 - - - -
21C ALA* 3.2 36.1 - - + -
40C PHE* 4.0 23.0 - - + +
43C ALA* 4.8 4.3 - - + -
44C VAL* 3.6 29.6 - - + +
53C THR* 3.0 25.7 + - + +
54C LEU* 3.1 21.5 - - + +
56C ALA* 1.3 77.2 - - - +
58C TYR* 1.3 63.2 + - + +
60C GLN* 3.3 2.6 + - - +
61C LEU* 3.0 26.8 + - + +
52F ILE* 3.7 10.3 - - + -
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.4 19.6 - - + +
54C LEU* 3.0 53.1 + - + +
55C SER* 3.6 5.6 - - - +
57C ILE* 1.3 80.1 - - - +
59C SER* 1.3 57.6 + - - +
61C LEU* 3.1 6.5 + - + -
62C GLY* 2.8 26.2 + - - -
77C TYR* 3.4 53.5 - + + +
80C HIS* 3.9 31.4 - + + -
81C ASP* 3.9 4.7 - - + -
84C LEU* 4.0 16.6 - - + -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER 3.0 10.7 + - - -
56C ALA 3.5 8.1 - - - -
58C TYR* 1.3 76.1 - - - +
60C GLN* 1.3 58.1 + - - +
62C GLY 3.3 0.9 + - - -
63C ASN* 2.9 28.2 + - - -
78C HIS* 3.4 10.7 - - - -
81C ASP* 3.3 27.1 + - - +
100C ASN* 3.7 16.8 + - - -
48F GLN 4.1 4.9 + - - -
50F LYS* 3.6 27.0 + - - +
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.2 35.0 + - - +
28C CYS* 5.0 5.8 - - - +
40C PHE* 3.4 37.2 - - + -
56C ALA 2.9 20.6 + - - +
57C ILE 3.8 1.6 - - - +
59C SER* 1.3 74.5 - - - +
61C LEU* 1.3 62.3 + - - +
63C ASN* 4.0 7.1 - - - +
64C ALA* 2.9 29.8 + - - +
49F ALA* 5.4 7.3 - - + +
50F LYS 2.7 34.3 + - - +
51F PRO* 4.0 0.2 - - - +
52F ILE* 3.5 12.0 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 4.0 9.6 - - + +
40C PHE* 3.5 35.9 - - + -
41C GLU* 4.0 15.3 - - + +
44C VAL* 4.1 11.2 - - + -
57C ILE* 3.0 26.9 + - + +
58C TYR* 3.5 8.1 - - - +
60C GLN* 1.3 73.8 - - - +
62C GLY* 1.3 62.0 + - - +
64C ALA* 3.4 3.6 + - - +
65C TYR* 2.8 60.6 + - + -
77C TYR* 3.6 35.2 - - + +
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Residues in contact with GLY 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR 2.8 13.8 + - - -
61C LEU* 1.3 77.7 - - - +
63C ASN* 1.3 55.4 + - - +
65C TYR* 3.4 0.6 + - - -
66C PHE* 2.8 30.1 + - - +
74C ALA* 3.6 12.1 - - - +
77C TYR* 3.7 14.1 - - - +
78C HIS* 3.3 24.6 + - - -
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Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 2.9 20.2 + - - +
60C GLN* 4.0 6.6 - - - +
62C GLY* 1.3 75.0 - - - +
64C ALA* 1.3 58.5 + - - +
66C PHE* 3.1 4.2 + - - +
67C TYR* 2.8 29.6 + - - +
78C HIS* 2.8 28.4 + - - -
100C ASN* 3.6 8.4 + - - +
47F LEU* 3.5 33.8 - - + +
48F GLN 2.9 26.5 - - - +
49F ALA* 4.1 8.1 - - - +
63F ILE* 4.8 6.7 - - + +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C CYS* 4.1 20.9 - - - -
33C CYS* 4.2 9.1 - - + +
37C VAL* 4.0 20.6 - - + -
40C PHE* 5.4 1.3 - - + -
60C GLN 2.9 20.8 + - - +
61C LEU* 3.6 4.7 - - - +
63C ASN* 1.3 76.9 - - - +
65C TYR* 1.3 62.4 + - - +
67C TYR* 3.1 10.7 + - - +
68C LEU* 3.0 27.3 + - - +
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 5.0 9.6 - - - -
37C VAL* 3.0 33.9 - - + +
41C GLU* 2.7 23.4 + - - -
61C LEU* 2.8 45.8 + - + +
62C GLY 3.9 2.9 - - - +
64C ALA* 1.3 69.7 - - - +
66C PHE* 1.3 66.0 + - - +
68C LEU* 3.1 14.4 + - + +
70C ASP* 2.8 59.6 + - + +
73C LYS* 3.2 35.5 - - + +
74C ALA* 4.0 7.4 - - - +
77C TYR* 4.0 15.5 - + - -
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY 2.8 15.4 + - - +
63C ASN* 3.2 13.9 - - - +
65C TYR* 1.3 75.7 - - - +
67C TYR* 1.3 59.9 + - - +
69C HIS* 2.8 22.5 + - - -
71C TYR* 3.4 33.6 + + - -
74C ALA* 3.8 9.6 - - + +
78C HIS* 4.9 1.3 - - - +
103C ASN* 4.3 3.1 - - + -
104C THR* 3.4 42.2 - - - -
107C VAL* 3.8 22.0 - - + -
45F CYS* 3.9 28.7 - - + -
47F LEU* 3.8 25.1 - - + -
65F ALA* 4.0 13.9 - - + -
66F GLY 5.2 0.7 - - - -
67F GLY* 4.6 5.8 - - - -
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLY* 4.6 15.2 + - - -
33C CYS* 3.4 32.8 - - + -
63C ASN 2.8 12.6 + - - +
64C ALA* 3.2 9.9 - - - +
66C PHE* 1.3 81.5 - - - +
68C LEU* 1.3 63.9 - - + +
69C HIS* 3.2 20.9 + - - -
47F LEU* 5.9 0.9 - - + -
63F ILE* 5.5 8.7 - - + -
64F LEU 6.1 0.4 - - - -
65F ALA* 5.1 17.5 - - + -
66F GLY 6.1 0.7 - - - -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C CYS* 3.9 35.9 - - + +
34C ARG* 3.3 54.7 + - + +
37C VAL* 4.2 11.4 - - + -
64C ALA 3.0 19.8 + - - +
65C TYR* 3.1 10.7 + - + +
67C TYR* 1.3 82.4 - - + +
69C HIS* 1.3 74.1 + - - +
70C ASP* 3.1 6.2 + - + +
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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