Contacts of the helix formed by residues 15 - 26 (chain A) in PDB entry 1KI1
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 GLY 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA 3.2 1.8 - - - -
14A VAL* 1.3 81.2 - - - +
16A LYS* 1.3 63.0 + - - +
17A THR 3.4 1.8 - - - -
18A CYS* 3.9 13.4 - - - +
19A LEU* 3.0 28.9 + - - +
115A THR* 4.8 0.7 + - - -
116A GLN* 4.5 9.6 - - - +
159A ALA* 5.4 0.7 - - - +
4001A SO4 2.8 15.5 + - - -
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Residues in contact with LYS 16 (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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8A VAL* 3.8 23.5 - - + +
9A VAL 3.5 27.4 - - - +
10A GLY* 3.1 7.4 + - - +
11A ASP 2.9 17.6 + - - -
14A VAL* 3.6 12.6 - - + -
15A GLY* 1.3 75.6 - - - +
17A THR* 1.3 63.9 + - - +
19A LEU* 3.3 14.8 - - - +
20A LEU* 3.1 25.7 + - - +
57A ASP* 3.9 8.3 - - - +
58A THR* 3.7 15.3 - - - -
59A ALA* 4.1 10.8 - - - +
62A GLU* 2.8 28.2 + - - -
81A CYS* 4.4 4.7 - - + -
4001A SO4 2.8 27.8 + - - +
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Residues in contact with THR 17 (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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16A LYS* 1.3 77.2 - - - +
18A CYS* 1.3 58.1 + - - +
20A LEU* 3.1 6.2 + - - +
21A ILE* 2.9 41.5 + - + +
33A VAL* 5.5 1.3 - - - -
34A PRO 3.4 24.7 - - - +
35A THR* 3.8 18.7 + - - +
36A VAL 4.3 0.2 - - - +
37A PHE* 4.3 7.0 - - + -
57A ASP* 2.7 26.6 + - - +
59A ALA* 3.4 11.1 - - - +
4001A SO4 3.0 17.1 + - - -
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Residues in contact with CYS 18 (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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15A GLY* 3.5 15.6 + - - +
16A LYS 3.3 0.6 - - - -
17A THR* 1.3 81.2 - - - +
19A LEU* 1.3 56.1 + - - +
21A ILE* 3.5 6.2 + - - +
22A SER* 2.8 30.7 + - - -
28A PHE* 3.2 37.2 - - - -
29A PRO* 4.3 5.6 - - - +
33A VAL* 3.9 29.5 - - + +
159A ALA* 3.6 11.9 - - + -
4001A SO4 5.4 0.2 + - - -
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Residues in contact with LEU 19 (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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8A VAL* 5.1 5.6 - - + -
15A GLY 3.0 18.3 + - - +
16A LYS* 3.3 18.6 - - - +
18A CYS* 1.3 73.7 - - - +
20A LEU* 1.3 66.4 + - + +
22A SER* 4.2 1.1 - - - -
23A TYR* 3.0 29.3 + - - +
79A LEU* 5.3 3.1 - - + -
81A CYS* 4.3 17.0 - - - -
113A VAL* 5.0 3.8 - - + -
115A THR* 3.7 21.5 - - - +
157A CYS* 4.5 12.8 - - - -
159A ALA* 3.9 19.0 - - + +
165A LEU* 3.8 13.4 - - + +
168A VAL* 5.8 1.6 - - + -
169A PHE* 3.6 30.7 - - + -
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Residues in contact with LEU 20 (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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8A VAL* 3.9 24.7 - - + -
16A LYS 3.1 17.4 + - - +
17A THR 3.1 7.3 + - - +
19A LEU* 1.3 76.8 - - + +
21A ILE* 1.3 59.2 + - - +
23A TYR* 3.4 3.4 + - + +
24A THR* 2.9 35.7 + - - +
37A PHE* 3.7 21.1 - - + -
55A LEU* 4.2 24.2 - - + -
57A ASP* 3.5 42.4 - - + +
169A PHE* 3.9 26.7 - - + -
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Residues in contact with ILE 21 (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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17A THR* 2.9 29.6 + - + +
18A CYS* 3.8 4.7 - - - +
20A LEU* 1.3 75.3 - - - +
22A SER* 1.3 60.8 + - - +
24A THR* 3.7 5.6 - - - -
25A THR* 2.7 43.8 + - + +
27A LYS* 4.0 20.0 - - - +
29A PRO* 4.3 15.5 - - + -
34A PRO* 3.4 41.3 - - + -
36A VAL 3.8 12.8 - - - +
37A PHE* 4.0 15.7 - - + -
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Residues in contact with SER 22 (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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18A CYS 2.8 19.9 + - - -
19A LEU 3.9 1.6 - - - -
21A ILE* 1.3 78.6 - - - +
23A TYR* 1.3 60.3 + - - +
26A ASN* 3.1 14.7 + - - -
27A LYS 3.5 12.8 + - - -
28A PHE* 4.0 9.9 + - - +
29A PRO* 4.8 0.7 - - - -
159A ALA* 2.9 32.0 + - - -
162A GLN* 3.0 32.8 + - - +
165A LEU* 3.4 8.9 - - - +
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Residues in contact with TYR 23 (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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19A LEU 3.0 19.7 + - - +
20A LEU 3.7 2.9 - - - +
22A SER* 1.3 78.9 - - - +
24A THR* 1.3 73.3 + - + +
25A THR 3.7 0.2 + - - -
26A ASN* 3.8 12.0 + - - +
42A VAL* 4.6 8.1 - - + -
44A VAL* 3.5 31.2 - - + +
53A LEU* 4.1 5.8 - - + +
55A LEU* 4.1 15.9 - - + -
162A GLN* 4.6 1.1 + - - +
165A LEU* 3.5 16.5 - - + +
166A LYS* 4.0 35.4 + - + +
169A PHE* 3.6 57.5 - + + +
170A ASP* 5.1 0.7 + - - -
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Residues in contact with THR 24 (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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20A LEU 2.9 20.3 + - - +
21A ILE* 3.5 5.5 + - - -
23A TYR* 1.3 83.1 - - + +
25A THR* 1.3 67.0 + - - +
26A ASN* 4.5 6.1 + - - -
37A PHE* 3.6 14.8 - - + -
40A TYR* 3.4 44.6 + - + -
42A VAL* 4.9 4.3 - - + +
55A LEU* 3.6 23.8 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.7 37.7 + - + +
24A THR* 1.3 80.9 - - - +
26A ASN* 1.3 71.5 + - - +
27A LYS* 2.8 44.0 + - - +
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Residues in contact with ASN 26 (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 SER 3.1 13.4 + - - -
23A TYR 3.8 9.9 + - - +
24A THR 3.4 6.1 + - - -
25A THR* 1.3 81.2 + - - +
27A LYS* 1.3 62.2 + - - +
162A GLN* 3.8 19.2 - - - +
166A LYS* 4.5 17.3 + - - -
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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