Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 2K6Q
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 SER 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLN 4.9 0.9 - - - -
10A ARG 3.2 5.6 + - - -
11A ARG* 1.3 68.4 - - - +
13A PHE* 1.3 56.3 + - - +
14A GLU* 3.2 1.3 - - - -
15A GLN* 2.6 74.4 + - - +
16A ARG* 2.7 10.6 + - - -
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Residues in contact with PHE 13 (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 LYS* 4.5 15.2 + - + +
9A GLN 5.1 0.4 + - - -
11A ARG 3.1 7.8 + - - -
12A SER* 1.3 68.0 - - - +
14A GLU* 1.3 56.5 + - + +
16A ARG* 2.5 29.1 + - + -
17A VAL* 2.6 28.1 + - + +
104A ASP* 3.9 17.0 - - - -
105A GLU* 4.9 6.3 - - + -
106A ASP* 3.1 52.9 - - + -
110A TYR* 4.5 3.1 - - - -
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Residues in contact with GLU 14 (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 SER* 3.2 0.6 - - - -
13A PHE* 1.3 83.9 - - + +
15A GLN* 1.3 69.7 + - - +
17A VAL* 3.2 9.1 + - - +
18A GLU* 2.8 30.0 + - - +
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Residues in contact with GLN 15 (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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11A ARG* 5.9 2.2 - - + -
12A SER* 2.6 44.8 + - - +
14A GLU* 1.3 91.0 - - - +
16A ARG* 1.3 55.3 + - - +
18A GLU* 4.0 5.8 - - - +
19A ASP* 3.2 27.7 + - - +
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Residues in contact with ARG 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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7A PHE* 2.5 60.2 + - - +
8A LYS* 5.9 1.1 - - - +
11A ARG* 2.9 42.0 - - + +
12A SER 2.7 10.2 + - - +
13A PHE* 2.5 21.5 + - + +
15A GLN* 1.3 72.7 - - - +
17A VAL* 1.3 60.6 + - + -
19A ASP* 4.2 7.5 + - - -
20A VAL* 3.8 4.9 + - - +
34A ILE* 3.8 21.4 - - - +
50A THR* 5.4 0.8 - - - +
51A LYS* 6.0 0.4 - - - +
108A PHE* 3.2 41.1 - - + +
110A TYR* 3.4 29.1 - - + +
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Residues in contact with VAL 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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13A PHE* 2.6 37.4 + - + +
14A GLU* 3.5 8.3 - - - +
16A ARG* 1.3 74.6 - - - +
18A GLU* 1.3 66.5 + - - +
19A ASP 3.3 0.2 - - - -
20A VAL* 3.1 15.6 + - + +
21A ARG* 3.1 10.0 + - - +
105A GLU 4.9 2.2 - - - +
106A ASP* 3.3 46.7 - - + +
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Residues in contact with GLU 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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14A GLU 2.8 16.9 + - - +
15A GLN* 4.0 7.2 - - - +
17A VAL* 1.3 73.3 - - - +
19A ASP* 1.3 59.0 + - - +
20A VAL 2.9 1.8 - - - -
21A ARG* 2.6 74.0 + - - +
22A LEU* 3.3 8.1 + - + +
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Residues in contact with ASP 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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15A GLN 3.2 16.5 + - - +
16A ARG* 4.2 12.7 + - - +
18A GLU* 1.3 78.1 - - - +
20A VAL* 1.3 60.9 + - - +
22A LEU* 3.5 18.1 + - - +
51A LYS* 3.1 32.9 + - - +
108A PHE* 4.0 8.7 - - + -
335B ASP* 2.7 40.5 - - - +
338B TRP* 3.3 12.9 + - - -
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Residues in contact with VAL 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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16A ARG 3.8 2.5 - - - +
17A VAL 3.1 12.0 + - - +
18A GLU 2.9 0.8 - - - -
19A ASP* 1.3 76.5 - - - +
21A ARG* 1.3 68.2 + - - +
22A LEU 3.0 2.2 - - - -
23A ILE* 2.6 16.5 + - - +
24A ARG* 2.6 29.7 + - + -
32A PRO* 4.2 6.7 - - + -
99A TYR* 5.3 0.7 - - - +
106A ASP 4.3 5.8 - - - +
107A GLY* 3.1 35.7 - - - +
108A PHE* 3.1 37.7 - - + -
338B TRP* 3.8 11.7 - - + -
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Residues in contact with ARG 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 VAL 3.1 7.3 + - - +
18A GLU* 2.6 59.0 + - - +
20A VAL* 1.3 70.8 - - - +
22A LEU* 1.3 65.0 + - + +
24A ARG* 2.8 13.3 + - + +
25A GLU* 2.6 45.6 + - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.3 7.1 + - + +
19A ASP* 3.6 13.7 - - - +
20A VAL 3.0 0.6 - - - -
21A ARG* 1.3 100.3 - - - +
23A ILE* 1.3 52.5 + - + +
25A GLU* 2.9 25.3 + - - +
26A GLN* 2.5 54.0 + - - +
335B ASP* 3.3 37.9 - - + +
336B ASP* 5.2 0.9 - - - +
338B TRP* 5.2 1.6 - - - +
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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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19A ASP 3.8 0.8 + - - -
20A VAL* 2.6 16.9 + - + +
22A LEU* 1.3 77.8 - - + +
24A ARG* 1.3 55.6 + - + +
26A GLN* 4.2 1.1 - - + -
27A HIS* 2.5 60.5 + - + +
30A LYS 5.0 0.9 - - - +
32A PRO* 3.8 22.9 - - + -
53A LEU* 3.3 40.4 - - + -
336B ASP 5.1 1.8 - - - +
337B ASP* 4.7 2.5 - - - -
338B TRP* 3.2 61.2 - - + +
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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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20A VAL* 2.6 33.5 + - + +
21A ARG* 3.0 18.6 - - + +
23A ILE* 1.3 79.5 - - + +
25A GLU* 1.3 57.4 + - - +
26A GLN 3.3 0.9 - - - -
27A HIS 4.5 0.9 - - - -
28A PRO* 3.6 34.5 + - - +
30A LYS 5.9 2.2 - - - -
32A PRO* 5.9 3.8 - - - -
99A TYR* 5.8 3.8 - - - -
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Residues in contact with GLU 25 (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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21A ARG* 2.6 26.5 + - + +
22A LEU* 3.0 35.5 - - - +
24A ARG* 1.3 73.6 - - + +
26A GLN* 1.3 73.9 + - - +
28A PRO* 5.0 2.8 - - - +
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Residues in contact with GLN 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 LEU* 2.5 36.0 + - - +
23A ILE* 5.0 0.2 - - + -
24A ARG 3.3 0.2 - - - -
25A GLU* 1.3 94.8 + - - +
27A HIS* 1.3 74.9 + - + +
28A PRO* 3.1 12.6 - - - +
335B ASP 4.4 0.2 + - - -
336B ASP* 2.7 35.6 + - - +
337B ASP* 2.6 27.2 - - - +
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Residues in contact with HIS 27 (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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23A ILE* 2.5 35.2 + - + +
24A ARG* 4.5 1.2 - - - -
26A GLN* 1.3 90.3 + - + +
28A PRO* 1.4 64.2 - - - +
29A THR* 3.3 2.0 - - - +
30A LYS* 3.4 37.3 + - + +
53A LEU* 2.9 36.6 - - + +
337B ASP* 2.6 35.6 + - + +
340B HIS* 5.8 4.9 - - - -
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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