Contacts of the helix formed by residues 12 - 21 (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 VAL 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ASN* 1.4 67.4 - - - +
13B LYS* 1.3 67.7 + - + +
14B ASP 3.2 2.6 + - - -
15B VAL* 3.8 7.7 + - + +
16B THR* 3.6 23.6 + - - +
120B ASN* 5.3 15.3 - - - +
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Residues in contact with LYS 13 (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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11B ASN 3.6 0.4 - - - -
12B VAL* 1.3 82.8 - - + +
14B ASP* 1.3 66.9 + - - +
16B THR* 3.7 9.3 - - - +
17B LYS* 3.3 23.0 + - - +
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Residues in contact with ASP 14 (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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11B ASN* 3.5 14.9 + - + +
12B VAL 3.2 0.6 - - - -
13B LYS* 1.3 81.1 - - - +
15B VAL* 1.3 65.5 + - + +
17B LYS* 3.5 6.7 + - - +
18B LEU* 3.0 23.0 + - - +
70B LEU* 4.0 34.6 - - - +
75B ILE* 3.6 22.2 - - + +
78B LYS* 3.5 30.5 + - + +
79B LEU* 5.7 2.7 - - + -
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Residues in contact with VAL 15 (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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11B ASN 3.8 9.8 + - - +
12B VAL* 3.8 8.5 + - + +
13B LYS 3.6 0.2 - - - -
14B ASP* 1.3 73.8 - - - +
16B THR* 1.3 53.0 + - - +
18B LEU* 3.3 6.9 + - - +
19B VAL* 2.8 36.3 + - + +
75B ILE* 5.0 0.4 - - - -
79B LEU* 4.0 29.8 - - + -
116B PHE* 3.5 37.7 - - + -
119B PHE* 4.2 9.0 - - + -
120B ASN* 3.9 28.9 - - - +
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Residues in contact with THR 16 (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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66A ILE* 5.8 5.6 - - + +
12B VAL* 3.6 14.1 + - - +
13B LYS* 3.7 12.1 - - - +
14B ASP 3.3 0.4 - - - -
15B VAL* 1.3 76.8 - - - +
17B LYS* 1.3 57.3 + - - +
19B VAL* 3.5 6.2 + - - +
20B ALA* 2.9 29.1 + - + +
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Residues in contact with LYS 17 (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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67A SER* 4.2 8.3 - - - +
68A GLU* 3.4 28.5 + - + +
69A GLY* 4.9 1.3 - - - -
70A LEU* 3.6 23.4 + - - +
13B LYS 3.3 13.5 + - - +
14B ASP* 3.8 9.0 - - - +
16B THR* 1.3 76.0 - - + +
18B LEU* 1.3 65.0 + - - +
20B ALA* 4.2 5.6 - - - -
21B ASN* 2.9 38.4 + - - +
70B LEU* 3.2 58.6 + - + +
72B ASN* 4.6 0.4 - - - +
75B ILE* 4.1 8.5 - - + +
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Residues in contact with LEU 18 (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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14B ASP 3.0 17.8 + - - +
15B VAL* 3.5 4.7 - - - +
17B LYS* 1.3 74.3 - - - +
19B VAL* 1.3 61.6 + - - +
21B ASN 3.1 4.3 + - - -
22B LEU* 3.1 41.9 + - + +
72B ASN* 3.4 41.7 - - + +
75B ILE* 3.8 13.3 - - + +
76B ILE* 3.8 22.2 - - + -
79B LEU* 3.8 21.1 - - + -
116B PHE* 3.5 29.4 - - + -
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Residues in contact with VAL 19 (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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15B VAL* 2.8 25.4 + - + +
16B THR* 3.8 6.3 - - - +
18B LEU* 1.3 69.3 - - - +
20B ALA* 1.3 62.5 + - - +
22B LEU* 3.1 26.0 + - - +
24B LYS* 6.0 1.0 - - - +
112B PRO* 3.8 9.1 - - + +
113B GLU* 4.0 29.6 - - + +
116B PHE* 3.8 36.1 - - + -
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Residues in contact with ALA 20 (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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63A PHE* 4.1 5.9 - - - +
64A SER* 3.3 40.3 + - - +
66A ILE 3.6 24.9 - - - +
67A SER* 4.0 9.9 - - - +
16B THR* 2.9 18.6 + - + +
17B LYS* 3.6 7.9 - - - +
18B LEU 3.3 0.2 - - - -
19B VAL* 1.3 75.2 - - - +
21B ASN* 1.3 62.2 + - - +
22B LEU 3.5 0.6 + - - -
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Residues in contact with ASN 21 (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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21A ASN* 4.1 8.0 - - - +
63A PHE* 3.5 7.6 - - - -
64A SER 5.3 0.9 - - - +
67A SER* 2.8 26.9 + - - -
70A LEU 3.6 10.2 + - - -
71A SER* 3.4 5.7 + - - -
72A ASN* 2.9 53.3 + - - +
73A TYR 4.7 0.5 + - - -
17B LYS* 2.9 29.1 + - - +
18B LEU 3.1 3.1 + - - -
20B ALA* 1.3 79.8 - - - +
22B LEU* 1.3 57.5 + - - +
23B PRO* 4.4 0.9 - - - +
72B ASN* 3.4 28.0 + - - +
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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