Contacts of the helix formed by residues 46 - 62 (chain B) 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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS 5.4 0.4 + - - -
44B TRP 3.1 0.4 + - - -
45B ILE* 1.3 77.5 - - - +
47B GLU* 1.3 64.7 + - - +
49B VAL* 3.4 16.2 - - - +
50B VAL* 3.5 15.4 - - - +
90B VAL* 3.4 32.3 - - - +
91B LYS* 5.8 1.6 - - - +
98B LEU* 4.1 7.6 - - - -
99B LYS 3.2 23.6 + - - -
100B LYS* 3.6 19.8 + - - +
102B PHE* 4.2 0.4 - - - -
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.6 20.2 - - + -
44B TRP 3.2 3.3 + - - +
46B SER* 1.3 76.5 + - - +
48B MSE 1.3 64.5 + - - +
50B VAL* 3.5 12.2 + - - +
51B GLN* 2.8 54.4 + - - +
100B LYS 4.7 3.6 - - - +
102B PHE* 3.5 53.5 + - + +
104B SER* 4.9 2.4 - - - -
105B PRO* 3.9 14.3 - - + +
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Residues in contact with MSE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.4 30.5 - - + -
31B LYS 4.8 0.2 - - - +
32B TYR* 4.4 5.6 - - - -
33B VAL* 3.6 29.5 - - + +
36B MSE 4.3 11.0 - - + +
44B TRP* 3.0 34.0 + - + +
45B ILE* 3.2 5.6 + - + +
47B GLU* 1.3 73.9 - - - +
49B VAL* 1.3 59.5 + - - +
51B GLN* 3.3 3.2 + - + -
52B LEU* 2.9 62.8 + - + +
118B ILE* 3.8 13.7 - - + -
122B SER* 3.1 23.8 - - - +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 2.8 29.9 + - + +
46B SER* 3.4 15.5 - - - +
48B MSE 1.3 75.7 - - - +
50B VAL* 1.3 55.9 + - + +
52B LEU* 3.7 6.1 - - + +
53B SER* 2.9 29.6 + - - -
83B VAL* 3.9 28.9 - - + +
86B LEU* 4.2 9.9 - - + +
87B VAL* 3.9 25.1 - - + +
90B VAL* 4.7 3.4 - - + -
122B SER* 5.2 2.5 - - - +
123B ILE* 5.9 0.4 - - + -
126B PHE* 3.6 31.0 - - + -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.5 18.1 + - - +
47B GLU* 3.9 20.0 - - - +
48B MSE 3.4 0.4 - - - -
49B VAL* 1.3 75.0 - - + +
51B GLN* 1.3 65.1 + - - +
53B SER* 3.3 7.6 - - - -
54B ASP* 3.0 46.4 + - - +
87B VAL* 4.2 22.7 - - + -
91B LYS* 4.5 15.7 - - - +
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.8 10.5 - - + -
31B LYS* 3.3 53.2 + - + +
33B VAL* 4.7 0.4 - - + -
47B GLU* 2.8 45.2 + - + +
48B MSE 3.7 5.6 - - + +
50B VAL* 1.3 81.0 - - - +
52B LEU* 1.3 62.1 + - - +
54B ASP* 3.3 19.9 + - - +
55B SER* 3.0 26.2 + - - -
104B SER* 5.0 2.8 - - - +
105B PRO* 3.3 16.8 - - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.1 4.3 - - + -
48B MSE 2.9 43.7 + - + +
49B VAL* 3.7 7.6 - - - +
51B GLN* 1.3 74.3 - - - +
53B SER* 1.3 58.9 + - - +
55B SER* 3.4 1.7 + - - +
56B LEU* 2.9 34.9 + - - +
83B VAL* 4.3 14.1 - - + -
115B PHE* 3.4 31.6 - - + +
119B PHE* 4.0 37.2 - - + +
122B SER* 3.7 27.1 - - - +
123B ILE* 6.1 0.4 - - + -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL 2.9 18.4 + - - -
50B VAL 3.3 7.4 - - - -
52B LEU* 1.3 75.3 - - - +
54B ASP* 1.3 59.3 + - - +
56B LEU* 3.9 1.0 - - - +
57B THR* 2.8 39.2 + - - -
80B VAL* 5.9 0.9 - - - -
83B VAL* 3.7 17.0 - - - +
84B ASP* 2.7 30.5 + - - -
87B VAL* 4.1 8.9 - - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 5.6 0.5 - - - +
50B VAL* 3.0 31.2 + - - +
51B GLN* 3.3 22.7 + - - +
53B SER* 1.3 80.2 + - - +
55B SER* 1.3 58.0 + - - +
57B THR* 3.7 5.8 - - - -
58B ASP* 2.8 39.2 + - - +
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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
----------------------------------------------------------
28B ILE* 4.6 6.2 - - - +
29B THR 2.8 27.0 + - - -
30B LEU* 3.2 20.8 - - - +
31B LYS 4.8 0.3 + - - -
51B GLN 3.0 9.4 + - - -
52B LEU 4.0 0.2 - - - -
54B ASP* 1.3 77.5 - - - +
56B LEU* 1.3 59.5 + - - +
58B ASP* 3.4 7.8 + - - +
59B LEU* 2.9 28.8 + - - +
115B PHE* 3.8 21.8 - - - -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 2.9 21.3 + - - +
53B SER 4.0 2.0 - - - +
55B SER* 1.3 73.4 - - - +
57B THR* 1.3 60.4 + - - +
59B LEU* 3.2 6.1 + - + +
60B LEU* 2.9 26.3 + - - +
76B ILE* 3.3 25.2 - - + +
79B LEU* 3.9 23.1 - - + +
80B VAL* 3.9 14.4 - - + -
83B VAL* 4.1 7.4 - - + -
115B PHE* 3.9 14.4 - - + -
116B PHE* 3.9 30.3 - - + -
119B PHE* 3.6 34.8 - - + -
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Residues in contact with THR 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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53B SER* 2.8 29.0 + - - -
54B ASP* 3.7 5.8 - - - +
56B LEU* 1.3 76.5 - - - +
58B ASP* 1.3 62.9 + - - +
60B LEU* 3.3 15.7 + - + +
61B ASP* 3.5 10.2 + - - +
80B VAL* 3.6 25.6 - - + +
84B ASP* 4.7 1.7 + - - -
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 2.8 26.8 + - - +
55B SER* 3.6 8.0 - - - +
57B THR* 1.3 75.7 - - - +
59B LEU* 1.3 63.8 + - - +
61B ASP* 3.2 24.2 + - - +
62B LYS* 3.3 25.3 + - - +
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Residues in contact with LEU 59 (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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22B LEU* 4.8 7.4 - - + -
26B TYR* 3.9 32.1 - - + +
28B ILE* 4.3 31.2 - - + -
55B SER 2.9 18.1 + - - +
56B LEU* 3.5 9.9 - - + +
58B ASP* 1.3 76.3 - - - +
60B LEU* 1.3 62.9 + - - +
62B LYS* 2.9 24.6 + - + +
63B PHE* 3.5 16.5 - - + -
76B ILE* 3.6 30.5 - - + -
116B PHE* 4.3 16.2 - - + -
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Residues in contact with LEU 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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56B LEU 2.9 15.8 + - - +
57B THR* 3.3 11.8 + - + +
59B LEU* 1.3 72.5 - - - +
61B ASP* 1.3 62.7 + - - +
62B LYS 3.0 1.4 + - - -
63B PHE* 3.2 19.4 + - - +
73B TYR* 3.4 59.9 - - + +
76B ILE* 3.9 13.2 - - + +
77B ASP* 3.4 38.1 - - + +
80B VAL* 4.2 12.1 - - + -
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Residues in contact with ASP 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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24A LYS* 2.6 35.4 + - - +
57B THR 3.5 5.8 + - - +
58B ASP* 3.2 25.7 + - - +
59B LEU 3.1 0.4 + - - -
60B LEU* 1.3 75.6 - - - +
62B LYS* 1.3 76.0 + - - +
63B PHE 3.3 2.0 - - - -
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Residues in contact with LYS 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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22A LEU 3.6 2.6 - - - +
23A PRO* 3.5 13.0 - - + +
24A LYS* 3.0 41.3 + - + +
25A ASP* 3.2 35.2 - - + +
26B TYR* 3.5 16.2 - - - +
58B ASP* 3.3 19.8 + - - +
59B LEU* 2.9 20.5 + - + +
61B ASP* 1.3 101.0 + - - +
63B PHE* 1.3 69.4 + - + +
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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
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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