Contacts of the helix formed by residues 41 - 62 (chain C) in PDB entry 1SCF
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 SER 41 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PRO* 1.3 69.4 - - - +
42C HIS* 1.3 59.2 + - - +
43C CYS 2.9 3.6 + - - -
44C TRP* 3.0 18.4 + - - +
45C ILE* 2.9 34.6 + - - +
121C ARG* 5.7 0.4 - - - +
125C ALA* 3.5 40.9 + - - -
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Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PRO* 3.1 17.6 + - + +
41C SER* 1.3 78.9 + - - +
43C CYS* 1.3 84.9 + - - +
45C ILE* 4.2 10.1 - - - -
46C SER* 3.9 11.5 + - - -
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Residues in contact with CYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 5.3 2.3 - - - +
39C LEU* 4.0 20.0 - - + -
40C PRO* 2.9 25.3 + - - +
42C HIS* 1.3 102.5 - - - +
44C TRP* 1.3 59.8 + - + +
46C SER* 4.5 3.5 + - - -
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Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.1 20.8 - - + +
35C GLY 5.1 1.3 - - - +
36C MSE 3.5 45.7 + - + -
39C LEU* 3.0 27.5 + - + -
40C PRO 3.0 27.6 + - - -
41C SER* 3.0 17.5 + - - -
43C CYS* 1.3 79.0 - - + +
45C ILE* 1.3 95.5 + - + +
46C SER* 3.1 5.6 + - - -
47C GLU* 3.4 7.9 + - - +
48C MSE 3.2 32.4 + - + +
121C ARG* 3.7 42.4 - - + -
122C SER* 3.6 15.9 - - - -
125C ALA* 3.8 11.2 - - + -
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 2.9 27.2 + - - +
42C HIS* 4.2 7.6 - - - -
43C CYS 3.9 0.2 - - - -
44C TRP* 1.3 103.9 - - + +
46C SER* 1.3 65.5 + - - +
48C MSE 3.2 1.0 + - + +
49C VAL* 2.9 38.3 + - + +
90C VAL* 5.1 4.9 - - + -
122C SER* 3.2 33.9 - - - +
125C ALA* 3.9 11.2 - - + +
126C PHE* 3.6 28.5 - - + -
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C HIS 3.9 17.2 + - - -
43C CYS 4.5 3.5 + - - -
44C TRP 4.2 2.1 - - - -
45C ILE* 1.3 81.9 + - - +
47C GLU* 1.3 59.8 + - - +
49C VAL* 3.5 14.9 - - - +
50C VAL* 4.1 8.3 + - - +
90C VAL* 4.1 29.6 - - - +
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Residues in contact with GLU 47 (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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33C VAL* 4.0 18.6 - - + -
44C TRP* 3.4 4.8 + - - +
46C SER* 1.3 76.5 + - - +
48C MSE 1.3 57.8 + - - +
50C VAL* 3.2 12.6 + - - +
51C GLN* 2.9 46.1 + - + +
104C SER* 3.8 18.7 + - - -
105C PRO* 3.7 23.9 - - + +
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Residues in contact with MSE 48 (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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30C LEU* 3.6 25.1 - - + -
31C LYS 3.9 8.3 - - - +
32C TYR* 3.8 13.5 - - + -
33C VAL* 3.7 25.8 - - - -
36C MSE 3.5 15.5 - - - +
44C TRP* 3.2 37.1 + - + +
45C ILE* 3.7 3.8 - - + +
47C GLU* 1.3 77.2 - - - +
49C VAL* 1.3 56.9 + - - +
51C GLN* 4.3 2.5 - - - +
52C LEU* 2.8 32.7 + - + +
118C ILE* 3.5 28.3 - - + -
122C SER* 4.0 17.0 - - - +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 2.9 40.4 + - + +
46C SER 3.5 11.4 - - - +
48C MSE 1.3 70.1 - - - +
50C VAL* 1.3 64.2 + - + +
52C LEU* 4.6 2.7 - - + -
53C SER* 2.9 27.5 + - - -
83C VAL* 3.2 15.8 - - + +
86C LEU* 4.2 19.5 - - + +
87C VAL* 3.4 19.5 - - + +
90C VAL* 4.2 17.9 - - + -
122C SER* 5.0 6.5 - - - -
123C ILE* 5.5 0.9 - - + -
126C PHE* 4.1 16.4 - - + -
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Residues in contact with VAL 50 (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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31A LYS* 4.8 7.4 - - - +
104A SER 5.8 8.1 - - - +
46C SER 4.2 10.8 - - - +
47C GLU* 3.2 15.6 + - - +
49C VAL* 1.3 79.0 - - + +
51C GLN* 1.3 64.8 + - - +
53C SER* 3.1 6.9 + - - -
54C ASP* 2.8 39.9 + - - +
87C VAL* 3.6 30.1 - - + -
90C VAL* 5.9 1.8 - - + -
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Residues in contact with GLN 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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30C LEU* 3.4 8.6 - - + +
31C LYS* 3.4 58.7 + - + +
47C GLU* 2.9 43.1 + - + +
48C MSE 3.4 6.5 + - - +
50C VAL* 1.3 77.7 - - - +
52C LEU* 1.3 63.5 + - - +
54C ASP* 3.1 25.2 + - - +
55C SER* 3.0 27.0 + - - -
104C SER* 5.1 3.2 - - - +
105C PRO* 4.1 10.6 - - + +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.7 22.4 - - + -
48C MSE 2.8 29.0 + - + +
49C VAL* 4.9 2.2 - - - -
51C GLN* 1.3 71.7 - - - +
53C SER* 1.3 57.7 + - - +
55C SER* 3.3 3.0 + - - -
56C LEU* 2.9 35.4 + - + +
83C VAL* 4.3 12.6 - - + -
115C PHE* 3.6 28.9 - - + -
118C ILE* 4.3 6.5 - - + +
119C PHE* 3.8 28.9 - - + +
122C SER* 3.3 35.0 - - - +
123C ILE* 5.5 1.3 - - + -
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Residues in contact with SER 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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49C VAL 2.9 24.2 + - - -
50C VAL* 3.1 10.1 + - - -
52C LEU* 1.3 73.8 - - - +
54C ASP* 1.3 63.8 + - - +
56C LEU* 4.4 3.0 - - - +
57C THR* 3.1 27.2 + - - -
80C VAL* 4.9 2.5 + - - +
83C VAL* 3.7 15.2 - - - +
84C ASP* 2.8 27.1 + - - -
87C VAL* 4.2 6.2 - - - +
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Residues in contact with ASP 54 (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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31A LYS* 3.0 35.9 + - - -
50C VAL* 2.8 25.6 + - - +
51C GLN* 3.1 28.2 + - - +
52C LEU 3.4 0.2 - - - -
53C SER* 1.3 74.0 - - - +
55C SER* 1.3 58.9 + - - +
57C THR* 3.2 4.2 + - - -
58C ASP* 2.9 43.5 + - - +
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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
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28C ILE* 4.8 5.4 - - - +
29C THR 2.6 28.4 + - - -
30C LEU* 3.6 9.5 - - - +
31C LYS 4.8 0.3 + - - -
51C GLN 3.0 17.0 + - - -
52C LEU 3.3 4.5 + - - -
54C ASP* 1.3 77.6 - - - +
56C LEU* 1.3 58.3 + - - +
58C ASP* 3.5 5.3 + - - +
59C LEU* 2.9 29.5 + - - +
115C PHE* 3.8 20.9 - - - -
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Residues in contact with LEU 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 LEU 2.9 19.2 + - - +
53C SER* 4.4 2.9 - - - +
55C SER* 1.3 74.5 - - - +
57C THR* 1.3 61.6 + - - +
59C LEU* 3.5 6.6 + - + +
60C LEU* 3.0 28.1 + - - +
76C ILE* 3.6 29.0 - - + +
79C LEU* 3.9 16.2 - - + -
80C VAL* 3.8 13.5 - - + +
83C VAL* 3.9 16.8 - - + -
115C PHE* 4.2 10.5 - - + -
116C PHE* 3.9 29.2 - - + -
119C PHE* 3.8 32.5 - - + -
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Residues in contact with THR 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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107A PRO* 5.9 7.2 - - + -
53C SER* 3.1 18.5 + - - -
54C ASP* 3.2 5.9 + - - -
56C LEU* 1.3 76.1 - - - +
58C ASP* 1.3 66.9 + - - +
60C LEU* 3.4 18.9 + - + +
61C ASP* 3.2 18.4 - - - +
80C VAL* 3.3 27.7 - - + +
84C ASP* 5.2 0.2 + - - -
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Residues in contact with ASP 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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107A PRO* 5.9 3.1 - - - +
54C ASP* 2.9 28.5 + - - +
55C SER* 3.9 5.1 - - - +
57C THR* 1.3 80.1 - - - +
59C LEU* 1.3 63.4 + - - +
61C ASP* 3.3 21.9 + - - +
62C LYS* 3.0 27.0 + - - +
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Residues in contact with LEU 59 (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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22C LEU* 4.8 5.6 - - + -
26C TYR* 3.6 37.0 - - + +
28C ILE* 4.2 30.7 - - + -
55C SER 2.9 21.9 + - - +
56C LEU* 3.7 22.7 - - + +
57C THR 3.4 0.2 - - - -
58C ASP* 1.3 71.6 - - - +
60C LEU* 1.3 62.2 + - - +
62C LYS* 3.0 17.4 + - - +
63C PHE* 3.2 30.8 - - + -
76C ILE* 3.9 18.2 - - + -
115C PHE* 5.3 1.1 - - + -
116C PHE* 4.4 9.9 - - + -
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Residues in contact with LEU 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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56C LEU 3.0 17.5 + - - +
57C THR* 3.5 13.2 - - + +
58C ASP 3.2 0.2 - - - -
59C LEU* 1.3 76.0 - - - +
61C ASP* 1.3 63.6 + - - +
63C PHE* 3.2 22.2 + - - +
73C TYR* 3.2 65.3 - - + +
76C ILE* 3.7 13.7 - - + -
77C ASP* 3.6 27.6 - - + +
80C VAL* 5.0 8.3 - - + -
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 3.2 21.9 - - - +
58C ASP* 3.3 15.3 + - - +
59C LEU 3.1 0.6 - - - -
60C LEU* 1.3 81.6 - - - +
62C LYS* 1.3 60.7 + - + +
63C PHE 3.1 6.5 - - - -
73C TYR* 5.9 0.4 - - - -
24D LYS* 2.9 27.0 + - - +
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Residues in contact with LYS 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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26C TYR* 3.6 21.5 + - - +
58C ASP* 3.0 28.1 + - - +
59C LEU* 3.0 16.8 + - + +
61C ASP* 1.3 80.6 - - + +
63C PHE* 1.3 64.9 + - + +
22D LEU 3.7 2.3 - - - +
23D PRO* 3.3 6.7 - - + +
24D LYS* 2.9 40.3 + - + +
25D ASP* 3.8 29.4 - - + +
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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
------------------------------------------------------------
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