Contacts of the helix formed by residues 12 - 21 (chain D) 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 VAL 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ASN* 1.4 72.3 - - + +
13D LYS* 1.3 69.2 + - - +
15D VAL* 3.6 8.1 - - - +
16D THR* 3.1 29.6 + - - +
120D ASN* 3.6 25.8 - - + +
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Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN 3.6 2.0 - - - +
12D VAL* 1.3 83.7 - - - +
14D ASP* 1.3 65.7 + - - +
16D THR* 3.8 11.2 + - - +
17D LYS* 3.9 14.7 + - - +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 2.8 18.1 + - - +
13D LYS* 1.3 77.1 - - - +
15D VAL* 1.3 63.1 + - - +
17D LYS* 3.0 31.8 + - - +
18D LEU* 3.0 24.3 + - - +
75D ILE* 3.9 29.5 - - + +
78D LYS* 4.2 17.0 + - - +
79D LEU* 5.9 2.0 - - + -
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 2.8 22.5 + - - +
12D VAL* 3.1 11.0 + - - +
14D ASP* 1.3 76.2 - - - +
16D THR* 1.3 60.8 + - - +
18D LEU* 3.4 8.6 + - - +
19D VAL* 3.0 29.7 + - + +
75D ILE* 5.5 0.2 - - - -
79D LEU* 4.2 15.9 - - + -
116D PHE* 3.7 26.0 - - + -
119D PHE* 4.0 26.0 - - + -
120D ASN* 3.6 26.5 - - - +
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.1 18.3 + - - +
13D LYS* 4.0 7.2 - - - +
14D ASP 3.3 0.2 - - - -
15D VAL* 1.3 80.0 - - - +
17D LYS* 1.3 56.0 + - - +
19D VAL* 3.7 9.8 + - - +
20D ALA* 3.2 24.4 + - - +
120D ASN* 5.9 0.2 + - - -
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ILE* 3.5 29.7 - - + +
68C GLU 4.3 12.7 + - - +
13D LYS 3.9 9.4 + - - +
14D ASP* 3.0 33.4 + - - +
15D VAL 3.3 0.2 - - - -
16D THR* 1.3 76.7 - - + +
18D LEU* 1.3 64.7 + - - +
20D ALA* 3.4 8.5 - - - +
21D ASN* 3.1 24.1 + - - +
70D LEU* 4.1 28.5 - - + -
75D ILE* 4.5 5.2 - - + -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP 3.0 13.6 + - - +
15D VAL* 3.6 8.7 - - - +
17D LYS* 1.3 72.2 - - - +
19D VAL* 1.4 65.2 + - - +
21D ASN* 2.9 14.6 + - - +
22D LEU* 3.0 30.4 + - + +
72D ASN* 3.8 41.5 - - + +
75D ILE* 4.1 21.1 - - + +
76D ILE* 3.6 26.2 - - + -
79D LEU* 4.3 6.7 - - + -
116D PHE* 3.6 33.0 - - + -
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.0 27.5 + - + +
16D THR* 3.8 10.5 - - - +
17D LYS 3.5 0.2 - - - -
18D LEU* 1.4 69.8 - - - +
20D ALA* 1.3 62.4 + - - +
21D ASN 3.3 0.2 + - - -
22D LEU* 3.3 20.0 + - - +
24D LYS* 5.9 2.1 - - - +
112D PRO* 4.3 11.0 - - + +
113D GLU* 3.8 36.1 - - + +
116D PHE* 4.2 28.7 - - + -
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C PHE* 4.0 6.4 - - - +
64C SER* 3.0 52.1 + - - +
65C ASN 4.7 0.4 - - - +
66C ILE* 3.7 22.4 - - + -
16D THR 3.2 12.0 + - - +
17D LYS* 3.4 11.7 - - - +
19D VAL* 1.3 80.1 - - - +
21D ASN* 1.3 56.9 + - - +
22D LEU 3.5 0.8 - - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASN* 4.0 16.4 - - - +
63C PHE* 3.4 7.2 - - - -
64C SER 5.1 0.2 - - - +
66C ILE* 3.7 7.8 - - + +
70C LEU 4.9 0.2 + - - -
71C SER* 3.5 12.6 - - - +
72C ASN* 3.1 47.8 + - - +
17D LYS 3.1 14.9 + - - +
18D LEU* 2.9 6.7 + - - +
20D ALA* 1.3 77.2 - - - +
22D LEU* 1.3 59.9 + - - +
23D PRO* 4.5 0.3 - - - +
70D LEU* 4.1 17.5 - - + +
72D ASN* 2.8 43.3 + - - +
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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