Contacts of the helix formed by residues 3 - 23 (chain A) in PDB entry 4TKR
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 ASN 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 1.3 63.8 + - + +
5A ARG* 3.3 2.7 - - - +
6A LEU* 3.2 27.0 + - - +
7A ILE* 2.9 37.4 + - - +
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Residues in contact with LYS 4 (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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3A ASN* 1.3 80.6 - - + +
5A ARG* 1.3 58.7 + - + +
7A ILE* 3.7 6.5 - - - +
8A ILE* 2.9 46.5 + - + +
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Residues in contact with ARG 5 (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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3A ASN 3.3 2.4 - - - +
4A LYS* 1.3 78.5 - - + +
6A LEU* 1.3 66.3 + - + +
8A ILE* 4.3 3.1 - - - +
9A LEU* 3.2 34.6 + - + +
136B VAL* 3.2 34.2 + - - +
137B LEU* 3.4 41.4 + - + +
149B ALA* 3.5 19.0 - - - +
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Residues in contact with LEU 6 (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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3A ASN* 3.2 24.3 + - - +
5A ARG* 1.3 79.3 - - + +
7A ILE* 1.3 61.1 + - + +
9A LEU* 3.5 9.1 + - + +
10A LEU* 2.9 43.5 + - + +
75B MET* 5.5 11.7 - - + -
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Residues in contact with ILE 7 (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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3A ASN* 2.9 26.7 + - - +
4A LYS* 3.3 7.4 + - - +
6A LEU* 1.3 78.6 - - + +
8A ILE* 1.3 59.1 + - + +
10A LEU* 3.2 15.2 + - + +
11A GLU* 2.9 50.2 + - + +
49A ARG* 4.2 9.4 - - - +
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Residues in contact with ILE 8 (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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4A LYS* 2.9 30.4 + - + +
5A ARG* 4.3 4.3 - - - +
7A ILE* 1.3 77.0 - - + +
9A LEU* 1.3 62.0 + - - +
11A GLU* 3.4 7.5 + - - +
12A CYS* 3.1 22.9 + - - -
49A ARG* 3.7 52.2 - - + +
52A TRP* 3.6 37.2 - - + -
53A ALA* 4.6 3.1 - - + -
137B LEU* 5.9 2.0 - - + -
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Residues in contact with LEU 9 (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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5A ARG* 3.2 22.2 + - + +
6A LEU* 3.8 9.9 - - + +
8A ILE* 1.3 80.4 - - - +
10A LEU* 1.3 62.3 + - + +
12A CYS* 3.3 6.9 + - - +
13A ALA* 3.1 20.6 + - - +
52A TRP* 4.2 20.4 - - + -
56A PHE* 3.6 35.8 - - + -
75B MET* 5.2 5.2 - - + -
77B SER* 4.0 11.0 - - - +
81B ILE* 4.9 1.3 - - + -
137B LEU* 4.4 13.9 - - + -
138B PHE* 4.0 28.7 - - + -
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Residues in contact with LEU 10 (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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6A LEU* 2.9 32.8 + - + +
7A ILE* 3.6 15.9 - - + +
9A LEU* 1.3 75.0 - - + +
11A GLU* 1.3 60.1 + - + +
13A ALA* 3.0 10.7 + - + +
14A ILE* 2.8 43.6 + - + +
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Residues in contact with GLU 11 (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 ILE* 2.9 31.9 + - + +
8A ILE* 3.7 5.2 - - - +
10A LEU* 1.3 76.7 - - + +
12A CYS* 1.3 62.2 + - - +
14A ILE* 4.4 10.8 - - + -
15A PHE* 3.0 40.8 + - + -
45A ILE* 4.0 9.1 - - + +
48A ARG* 2.8 41.0 + - - -
49A ARG* 2.9 39.6 + - - +
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Residues in contact with CYS 12 (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 ILE* 3.1 22.4 + - - -
9A LEU* 3.3 8.7 - - - +
11A GLU* 1.3 78.5 - - - +
13A ALA* 1.3 55.6 - - - +
15A PHE 3.9 0.2 - - - -
16A ALA* 3.0 29.3 + - - +
45A ILE* 4.4 7.6 - - - -
52A TRP* 4.9 2.0 - - - -
53A ALA* 3.4 42.8 - - - -
56A PHE* 3.5 26.0 - - + -
57A ALA* 3.5 18.8 - - + +
60A LEU* 4.4 0.7 - - - -
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Residues in contact with ALA 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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9A LEU 3.1 11.8 + - - +
10A LEU* 3.0 18.0 + - + +
12A CYS* 1.3 75.5 - - - +
14A ILE* 1.3 59.4 + - + +
16A ALA* 3.4 3.5 + - - +
17A ALA* 3.0 27.5 + - - +
60A LEU* 3.9 18.3 - - + +
64A LEU* 5.5 0.7 - - - +
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Residues in contact with ILE 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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10A LEU* 2.8 34.4 + - + +
11A GLU* 3.8 10.1 - - + +
13A ALA* 1.3 73.9 - - + +
15A PHE* 1.3 64.8 + - + +
17A ALA* 3.0 9.2 + - + +
18A VAL* 2.9 43.2 + - + +
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Residues in contact with PHE 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 GLU* 3.0 35.9 + - + +
12A CYS 4.2 2.2 - - - +
14A ILE* 1.3 82.5 - - + +
16A ALA* 1.3 56.9 + - - +
18A VAL* 4.3 7.9 - - + -
19A ALA* 3.0 27.4 + - - +
41A PRO* 3.3 39.7 - - + +
42A MET* 3.4 4.4 - - + +
44A VAL* 3.5 30.5 - - + -
45A ILE* 3.6 31.6 - - + -
48A ARG* 4.5 12.3 - - - -
182A LEU* 4.8 15.0 - - + -
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Residues in contact with ALA 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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12A CYS 3.0 19.1 + - - +
13A ALA* 3.5 7.2 - - - +
15A PHE* 1.3 76.2 - - - +
17A ALA* 1.3 60.3 + - - +
19A ALA* 3.4 3.7 + - - +
20A MET* 3.0 27.0 + - - +
42A MET* 3.9 9.8 - - - +
57A ALA 3.5 19.3 - - - +
60A LEU* 3.8 18.4 - - + -
61A TRP* 3.9 9.7 - - - +
64A LEU* 4.0 6.4 - - + +
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Residues in contact with ALA 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 ALA 3.0 14.5 + - - +
14A ILE* 3.0 11.2 + - + +
16A ALA* 1.3 74.3 - - - +
18A VAL* 1.3 60.5 + - + +
20A MET* 3.2 4.4 + - - +
21A VAL* 2.9 35.0 + - + +
64A LEU* 4.3 13.4 - - + +
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Residues in contact with VAL 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 ILE* 2.9 33.0 + - + +
15A PHE* 4.0 12.1 - - + +
17A ALA* 1.3 75.3 - - + +
19A ALA* 1.3 56.6 + - - +
21A VAL* 3.2 9.7 + - + +
22A LEU* 3.0 37.4 + - + +
41A PRO* 3.7 19.1 - - + -
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Residues in contact with ALA 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 PHE 3.0 19.7 + - - +
16A ALA 3.6 5.6 - - - +
17A ALA 3.3 0.2 - - - -
18A VAL* 1.3 77.5 - - - +
20A MET* 1.3 61.0 + - - +
22A LEU* 3.3 3.8 + - - +
23A SER* 3.0 26.0 + - - -
38A GLY* 3.3 30.5 - - - +
41A PRO* 3.7 9.6 - - + +
42A MET* 3.9 5.4 - - + -
61A TRP* 3.4 21.3 + - + -
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Residues in contact with MET 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 ALA 3.0 13.9 + - - +
17A ALA* 3.2 9.2 + - - +
19A ALA* 1.3 73.6 - - - +
21A VAL* 1.3 65.8 + - + +
23A SER* 3.3 26.8 + - - -
24A PHE* 3.2 29.5 - - + -
61A TRP* 3.6 5.6 - - + +
64A LEU* 3.8 31.0 - - + -
65A HIS* 3.7 28.0 - - + +
68A THR* 3.5 35.0 - - + +
70A LYS* 3.9 19.5 - - + -
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Residues in contact with VAL 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 ALA* 2.9 22.1 + - + +
18A VAL* 3.2 12.3 + - + +
20A MET* 1.3 76.8 - - - +
22A LEU* 1.3 68.6 + - + +
23A SER 3.1 0.2 - - - -
24A PHE* 3.0 26.1 + - - +
25A ILE* 4.2 4.6 + - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.0 24.0 + - + +
19A ALA 3.3 5.6 + - - +
21A VAL* 1.3 81.5 - - + +
23A SER* 1.3 56.1 + - - +
24A PHE 3.1 1.3 - - - -
25A ILE* 3.0 48.7 + - + +
37A LEU* 3.3 36.4 + - + +
38A GLY 4.2 9.9 - - - +
40A ILE* 4.8 7.0 - - + -
41A PRO* 3.7 26.0 - - + -
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Residues in contact with SER 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 ALA 3.0 15.0 + - - -
20A MET* 3.3 28.0 - - - -
21A VAL 3.1 0.6 - - - -
22A LEU* 1.3 76.1 - - - +
24A PHE* 1.3 59.2 + - - +
25A ILE 3.1 7.4 + - - +
26A PRO* 4.9 1.6 - - - +
37A LEU 6.2 0.4 - - - +
38A GLY* 4.9 1.5 - - - +
61A TRP* 3.2 13.3 + - - -
65A HIS* 4.7 0.2 - - - -
70A LYS* 3.8 18.9 + - - -
301A TPP 2.6 33.5 + - - -
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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