Contacts of the helix formed by residues 12 - 21 (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 VAL 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ASN* 1.4 72.2 - - + +
13C LYS* 1.3 62.6 + - + +
14C ASP 3.2 1.3 - - - -
15C VAL* 3.6 12.9 - - + +
16C THR* 3.1 29.7 + - - +
120C ASN* 4.4 25.6 - - - +
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Residues in contact with LYS 13 (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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11C ASN 3.5 2.0 + - - +
12C VAL* 1.3 82.3 - - + +
14C ASP* 1.4 64.7 + - - +
16C THR* 3.4 9.2 + - - +
17C LYS* 3.1 32.1 + - - +
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Residues in contact with ASP 14 (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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11C ASN* 2.9 14.0 + - - +
13C LYS* 1.4 80.6 - - - +
15C VAL* 1.3 62.9 + - - +
16C THR 3.3 0.2 - - - -
17C LYS* 3.2 26.7 + - - +
18C LEU 3.1 18.4 + - - -
70C LEU* 3.3 30.8 - - - +
75C ILE* 3.6 26.5 - - + +
78C LYS* 5.7 1.6 + - - -
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Residues in contact with VAL 15 (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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11C ASN* 2.9 23.8 + - + +
12C VAL* 3.7 13.9 - - + +
13C LYS 3.5 0.2 - - - -
14C ASP* 1.3 74.2 - - - +
16C THR* 1.3 57.0 + - - +
18C LEU* 3.3 7.1 + - - +
19C VAL* 2.9 31.8 + - + +
75C ILE* 4.6 0.9 - - - +
79C LEU* 4.0 25.8 - - + -
116C PHE* 3.9 31.0 - - + -
119C PHE* 4.0 16.2 - - + -
120C ASN* 4.1 18.4 - - - +
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Residues in contact with THR 16 (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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12C VAL* 3.1 17.9 + - - +
13C LYS* 3.5 11.0 - - - +
14C ASP 3.3 0.4 - - - -
15C VAL* 1.3 76.3 - - - +
17C LYS* 1.3 62.8 + - + +
19C VAL* 3.6 6.5 + - - +
20C ALA* 3.2 22.2 + - + +
66D ILE* 6.4 0.2 - - + -
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Residues in contact with LYS 17 (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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13C LYS* 3.1 15.3 + - - +
14C ASP* 3.2 30.9 + - - +
16C THR* 1.3 72.7 - - + +
18C LEU* 1.3 59.0 + - - +
20C ALA* 3.3 2.6 + - - +
21C ASN* 2.9 35.1 + - - +
70C LEU* 4.0 16.6 - - + -
75C ILE* 4.4 8.3 - - + -
66D ILE* 4.0 28.4 - - + +
67D SER* 3.4 14.9 + - - +
68D GLU* 2.7 55.7 + - - +
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Residues in contact with LEU 18 (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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14C ASP 3.1 12.4 + - - +
15C VAL* 3.3 8.5 + - - +
17C LYS* 1.3 72.9 - - - +
19C VAL* 1.3 59.2 + - - +
21C ASN 3.1 3.5 + - - -
22C LEU* 2.8 44.3 + - + +
72C ASN* 3.5 42.2 - - + +
75C ILE* 4.1 20.7 - - + +
76C ILE* 3.8 26.7 - - + -
79C LEU* 4.2 5.4 - - + -
116C PHE* 3.4 36.6 - - + -
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Residues in contact with VAL 19 (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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15C VAL* 2.9 24.6 + - + +
16C THR* 4.0 6.7 - - - +
17C LYS 3.4 0.4 - - - -
18C LEU* 1.3 73.3 - - - +
20C ALA* 1.3 59.9 + - - +
22C LEU* 3.2 23.2 + - - +
24C LYS* 5.9 2.3 - - - +
112C PRO* 4.3 7.9 - - + +
113C GLU* 4.0 35.2 - - + +
116C PHE* 3.9 36.8 - - + -
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Residues in contact with ALA 20 (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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16C THR* 3.2 15.3 + - + +
17C LYS 3.3 0.6 + - - +
19C VAL* 1.3 75.9 - - - +
21C ASN* 1.3 58.0 + - - +
22C LEU 3.5 0.4 - - - -
24C LYS* 6.5 0.4 - - - +
63D PHE* 3.4 11.8 - - - +
64D SER* 3.0 52.1 + - - +
65D ASN 3.9 2.7 - - - +
66D ILE* 3.4 29.4 - - + -
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Residues in contact with ASN 21 (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 LYS* 2.9 19.4 + - - +
18C LEU 3.2 2.7 - - - +
20C ALA* 1.3 77.5 - - - +
22C LEU* 1.3 57.5 + - - +
23C PRO* 4.6 0.3 - - - +
63C PHE* 5.3 0.2 - - - -
70C LEU 4.9 4.6 + - - -
72C ASN* 3.0 29.0 + - - +
75C ILE* 5.7 1.8 - - - +
21D ASN* 4.0 11.4 - - - +
63D PHE* 3.5 6.4 - - - -
64D SER 4.9 0.5 - - - +
66D ILE* 4.3 10.2 - - - +
70D LEU 3.1 24.7 + - - -
71D SER* 3.7 4.6 + - - +
72D ASN* 3.0 50.4 + - - +
73D TYR 4.4 1.4 + - - -
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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