Contacts of the helix formed by residues 46 - 62 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS 5.4 2.6 + - - -
44A TRP 3.3 1.0 - - - -
45A ILE* 1.3 85.2 - - - +
47A GLU* 1.3 63.9 - - - +
49A VAL* 3.7 6.6 - - - +
50A VAL* 3.5 21.1 - - - +
90A VAL* 3.6 29.9 - - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.1 15.9 - - + -
44A TRP* 3.3 10.5 + - - +
46A SER* 1.3 79.0 - - - +
48A MSE 1.3 58.2 + - - +
50A VAL* 3.5 9.7 + - - +
51A GLN* 2.8 66.8 + - + +
104A SER 4.3 2.8 - - - +
105A PRO* 3.4 26.3 - - + +
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Residues in contact with MSE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 33.7 - - + -
31A LYS 3.6 20.9 - - - +
32A TYR* 4.4 3.1 - - + -
33A VAL* 3.7 28.5 - - + -
36A MSE 3.8 22.4 - - - +
44A TRP* 2.9 44.4 + - + +
45A ILE* 4.2 2.0 - - - +
46A SER 3.3 0.2 - - - -
47A GLU* 1.3 76.4 - - - +
49A VAL* 1.3 60.4 + - - +
51A GLN* 3.9 2.6 - - - +
52A LEU* 2.9 35.2 + - + +
118A ILE* 3.9 9.0 - - + -
122A SER* 4.0 10.5 - - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.3 21.9 + - + +
46A SER 3.7 8.3 - - - +
48A MSE 1.3 71.9 - - - +
50A VAL* 1.3 61.7 + - + +
52A LEU* 4.4 0.7 - - + -
53A SER* 2.9 31.0 + - - -
83A VAL* 3.4 27.7 - - + +
86A LEU* 4.1 21.1 - - + +
87A VAL* 3.5 21.0 - - + +
90A VAL* 4.2 11.0 - - + -
122A SER* 4.7 9.2 - - - -
123A ILE* 5.4 0.7 - - + -
126A PHE* 3.9 25.6 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A SER 3.5 14.1 + - - +
47A GLU* 3.5 14.3 + - - +
48A MSE 3.3 0.2 - - - -
49A VAL* 1.3 74.1 - - + +
51A GLN* 1.3 69.9 + - - +
53A SER* 3.4 2.9 + - - -
54A ASP* 3.0 43.2 + - - +
87A VAL* 4.0 27.8 - - + -
90A VAL* 6.0 2.7 - - + -
104C SER* 4.6 13.0 - - - +
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.8 8.5 - - + -
31A LYS* 3.4 58.4 + - + +
47A GLU* 2.8 54.0 + - + +
48A MSE 4.0 7.2 - - - +
50A VAL* 1.3 83.8 - - - +
52A LEU* 1.3 57.2 + - - +
54A ASP* 3.4 12.8 + - - +
55A SER* 3.0 33.6 + - - -
105A PRO* 4.4 1.1 - - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.0 19.3 - - + -
48A MSE 2.9 26.4 + - + +
49A VAL* 3.9 5.8 - - + +
51A GLN* 1.3 72.8 - - - +
53A SER* 1.3 65.9 + - - +
55A SER* 4.0 1.6 - - - +
56A LEU* 3.0 31.4 + - - +
83A VAL* 4.3 8.7 - - + -
115A PHE* 3.5 31.9 - - + +
118A ILE 4.2 1.1 - - - +
119A PHE* 3.9 37.0 - - + +
122A SER* 3.4 34.8 - - - +
123A ILE* 6.1 0.4 - - + -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL 2.9 19.5 + - - -
50A VAL* 3.6 5.6 - - - -
52A LEU* 1.3 77.7 - - - +
54A ASP* 1.4 59.2 + - - +
56A LEU* 3.8 2.3 - - - +
57A THR* 2.8 40.9 + - - -
80A VAL* 4.9 1.3 - - - +
83A VAL* 4.3 11.1 - - - +
84A ASP* 2.6 30.5 + - - -
87A VAL* 4.4 8.2 - - - +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.0 27.7 + - - +
51A GLN* 3.9 15.4 + - - +
53A SER* 1.4 76.4 + - - +
55A SER* 1.3 67.2 + - - +
57A THR* 4.1 4.1 - - - -
58A ASP* 3.1 24.1 + - - +
31C LYS* 4.0 16.7 + - - +
104C SER* 3.5 32.3 + - - -
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.8 3.5 - - - +
29A THR 2.8 27.5 + - - -
30A LEU* 3.5 10.6 - - - +
31A LYS 4.6 0.7 + - - -
51A GLN* 3.0 19.1 + - - -
52A LEU 4.1 0.7 - - - -
54A ASP* 1.3 78.6 - - - +
56A LEU* 1.3 56.8 + - - +
58A ASP* 3.5 8.0 + - - +
59A LEU* 3.2 29.2 + - - +
115A PHE* 3.8 21.3 - - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU 3.0 20.5 + - - +
53A SER* 4.1 1.8 - - - +
55A SER* 1.3 73.0 - - - +
57A THR* 1.3 66.2 + - - +
59A LEU* 3.1 28.7 + - + +
60A LEU* 3.4 1.4 + - - +
76A ILE* 3.4 32.5 - - + +
79A LEU* 3.9 19.5 - - + +
80A VAL* 3.7 13.8 - - + +
83A VAL* 4.0 8.3 - - + -
115A PHE* 4.1 10.8 - - + -
116A PHE* 3.9 27.6 - - + -
119A PHE* 3.7 35.9 - - + -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 2.8 25.7 + - - -
54A ASP* 4.1 4.9 - - - -
56A LEU* 1.3 70.8 - - - +
58A ASP* 1.3 62.1 + - - +
60A LEU* 3.2 31.2 + - + +
61A ASP* 4.1 1.9 + - - +
80A VAL* 3.5 26.0 - - + +
84A ASP* 5.0 0.2 + - - -
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP 3.1 18.4 + - - +
55A SER* 3.7 7.6 - - - +
56A LEU 3.2 0.2 - - - -
57A THR* 1.3 77.8 - - - +
59A LEU* 1.3 63.7 + - - +
61A ASP* 3.2 19.1 - - - +
62A LYS* 2.8 34.5 + - - -
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Residues in contact with LEU 59 (chain A).
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* 5.6 4.7 - - + -
26A TYR* 4.1 31.0 - - + +
28A ILE* 4.2 35.0 - - + -
55A SER 3.2 13.4 + - - +
56A LEU* 3.1 33.6 + - + +
58A ASP* 1.3 77.8 + - - +
60A LEU* 1.4 63.0 - - - +
62A LYS* 2.9 25.0 + - + +
63A PHE* 3.4 20.7 - - + -
76A ILE* 4.1 19.5 - - + -
115A PHE* 5.4 1.1 - - + -
116A PHE* 5.2 3.8 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 3.4 7.6 + - - +
57A THR* 3.2 28.9 + - + +
59A LEU* 1.4 76.4 - - - +
61A ASP* 1.3 56.7 + - - +
62A LYS 3.1 5.7 + - - -
63A PHE* 3.2 15.9 + - - +
73A TYR* 3.3 75.3 - - + +
76A ILE* 3.8 16.2 - - + -
77A ASP* 4.0 14.8 - - + +
80A VAL* 4.5 11.2 - - + -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR 4.1 1.4 + - - +
58A ASP* 3.2 22.5 + - - +
60A LEU* 1.3 75.9 - - - +
62A LYS* 1.3 71.0 + - + +
63A PHE 3.5 1.1 - - - -
24B LYS* 3.8 17.0 + - - +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.5 19.5 + - - +
58A ASP* 2.8 43.1 + - - -
59A LEU* 2.9 22.1 + - + +
61A ASP* 1.3 92.1 - - - +
63A PHE* 1.3 68.3 + - + +
22B LEU 3.5 2.6 - - - +
23B PRO* 3.4 7.8 - - + +
24B LYS* 2.9 44.0 + - + +
25B ASP* 3.6 31.0 - - + +
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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