Contacts of the helix formed by residues 17 - 24 (chain A) in PDB entry 5KM2
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 THR 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 4.9 0.3 + - - -
15A GLY* 3.6 0.6 - - - -
16A ASP* 1.3 84.8 - - - +
18A ILE* 1.3 64.8 + - - +
19A PHE 3.4 3.7 + - - -
20A GLY* 3.0 25.1 + - - -
21A LYS* 3.0 9.5 + - - +
59A HIS* 4.3 10.6 + - + -
108A VAL* 4.3 11.2 - - + -
109A TYR* 3.9 29.8 - - + +
110A HIS* 3.7 15.1 + - - +
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Residues in contact with ILE 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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16A ASP 3.8 1.3 + - - +
17A THR* 1.3 73.8 - - - +
19A PHE* 1.3 61.6 + - + +
21A LYS* 3.3 9.7 + - + +
22A ILE* 2.9 37.3 + - + +
27A ILE* 3.6 28.7 - - + -
108A VAL* 5.0 8.8 - - + +
201A C5P 3.6 35.2 - - + +
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Residues in contact with PHE 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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17A THR* 3.1 7.6 + - - +
18A ILE* 1.3 79.5 - - + +
20A GLY* 1.3 65.6 + - - +
22A ILE* 3.3 10.3 + - + +
23A ILE* 3.0 31.1 + - - +
41A PHE* 3.9 18.8 - + - -
53A LEU* 3.6 13.0 - - + -
55A ILE* 3.8 26.1 - - + +
108A VAL* 3.7 22.0 - - + -
110A HIS* 3.8 21.3 - - + -
112A HIS* 3.5 33.7 - + + -
201A C5P 3.3 47.8 - + - -
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Residues in contact with GLY 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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14A GLY 3.7 15.5 - - - -
15A GLY 3.5 22.0 - - - -
17A THR* 3.0 13.4 + - - -
19A PHE* 1.3 74.8 - - - +
21A LYS* 1.3 60.9 + - - +
23A ILE* 3.4 14.3 + - - +
24A ARG* 3.2 27.8 + - - +
110A HIS* 4.5 1.7 + - - -
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Residues in contact with LYS 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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12A ARG* 5.3 3.0 - - - +
16A ASP* 4.1 21.9 + - + +
17A THR 3.0 10.6 + - - +
18A ILE* 3.6 12.3 - - + +
20A GLY* 1.3 75.0 - - - +
22A ILE* 1.3 63.4 + - - +
24A ARG* 3.2 11.1 + - - +
25A LYS 3.2 3.5 + - - -
26A GLU* 2.8 70.2 + - + +
27A ILE* 3.8 35.7 - - + -
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Residues in contact with ILE 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 ILE* 2.9 33.0 + - + +
19A PHE* 3.3 11.2 + - + +
21A LYS* 1.3 74.6 - - - +
23A ILE* 1.3 63.3 + - - +
25A LYS* 3.0 20.1 + - - +
27A ILE* 3.8 29.9 - - + +
28A PRO 4.5 1.6 - - - +
29A ALA* 3.7 26.9 - - + -
31A ILE* 5.4 2.6 - - + +
39A LEU* 3.6 24.5 - - + +
41A PHE* 4.0 31.4 - - + -
201A C5P 4.8 0.9 - - - +
202A GOL 4.2 11.4 - - - +
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Residues in contact with ILE 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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13A PRO 5.4 3.4 - - - +
14A GLY* 5.4 2.7 - - - +
19A PHE 3.0 21.3 + - - +
20A GLY* 3.5 10.8 - - - +
22A ILE* 1.3 77.4 - - - +
24A ARG* 1.3 63.8 + - + +
25A LYS* 3.4 16.3 + - - +
34A GLU* 4.9 4.2 - - - +
39A LEU* 4.4 13.2 - - + -
55A ILE* 3.7 18.8 - - + -
56A PRO 3.6 24.0 - - - +
57A LYS* 3.9 41.3 - - + +
110A HIS* 3.8 16.2 - - + -
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Residues in contact with ARG 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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12A ARG* 3.5 20.1 + - - +
13A PRO* 2.8 60.3 + - + +
14A GLY 3.9 0.2 - - - -
15A GLY 2.9 24.0 + - - +
16A ASP* 3.2 24.2 + - - -
20A GLY 3.2 13.1 + - - +
21A LYS* 3.2 7.2 + - - +
22A ILE 3.2 0.6 - - - -
23A ILE* 1.3 81.4 - - + +
25A LYS* 1.3 72.3 + - - +
26A GLU* 2.9 52.9 + - - +
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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