Contacts of the strand formed by residues 3 - 20 (chain F) in PDB entry 1TKK
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 ILE 3 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F LYS* 1.3 71.5 - - - +
4F ILE* 1.3 61.3 + - - +
5F ARG 4.3 1.3 - - - +
6F ILE* 3.9 29.8 - - + -
36F ILE* 4.0 11.9 - - + -
37F THR 4.2 0.4 - - - -
38F TYR* 3.5 24.2 - - + -
74F LEU* 3.5 39.3 - - + +
75F LEU* 3.8 6.7 - - + -
76F GLY* 3.0 24.6 + - - -
77F LYS* 2.9 22.1 + - + +
79F LEU* 4.7 5.6 - - + -
85F ILE* 4.7 1.6 - - + -
107F LEU* 3.6 28.5 - - + -
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Residues in contact with ILE 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LYS* 3.4 8.2 + - + +
3F ILE* 1.3 77.4 - - - +
5F ARG* 1.3 64.2 + - + +
37F THR* 3.1 29.6 + - + +
38F TYR 3.6 17.9 - - - +
39F ASP* 3.7 28.7 - - + +
75F LEU* 3.7 11.7 - - - +
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Residues in contact with ARG 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE 3.7 0.8 - - - -
4F ILE* 1.3 84.2 - - + +
6F ILE* 1.3 71.9 + - - +
7F GLU* 3.3 43.4 + - + +
35F ARG 4.5 0.4 - - - -
36F ILE* 3.5 3.6 - - - +
37F THR* 3.0 44.1 + - + +
75F LEU* 3.8 5.1 - - - +
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Residues in contact with ILE 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 3.9 15.3 - - + -
5F ARG* 1.3 84.4 - - - +
7F GLU* 1.3 65.5 + - - +
8F THR* 5.5 0.2 - - + -
34F VAL* 4.3 17.9 - - + -
35F ARG 3.4 7.6 - - - +
36F ILE* 4.2 16.4 - - + -
66F ILE* 4.5 17.7 - - + -
67F HIS* 4.2 5.4 - - - -
70F LEU 5.3 0.4 - - - -
71F LYS* 3.6 44.2 + - + +
74F LEU* 3.8 32.5 - - + -
75F LEU* 4.1 7.5 - - + +
103F VAL* 5.6 6.1 - - + -
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Residues in contact with GLU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 3.3 50.3 + - + +
6F ILE* 1.3 77.3 - - - +
8F THR* 1.3 71.3 + - - +
34F VAL* 3.5 2.8 - - - +
35F ARG* 2.9 71.8 + - + +
37F THR* 4.3 10.0 + - - -
67F HIS* 4.6 3.4 - - - -
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Residues in contact with THR 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F GLU* 1.3 81.8 - - - +
9F SER* 1.3 60.7 + - - +
32F VAL* 4.0 11.4 - - + -
33F ILE 3.2 8.5 - - - -
34F VAL* 4.1 14.1 - - + -
35F ARG* 6.3 0.7 - - - -
63F GLU* 3.1 21.0 + - + +
66F ILE* 3.8 26.0 - - + -
67F HIS* 2.5 35.8 + - + +
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Residues in contact with SER 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F THR* 1.3 75.0 - - - +
10F ARG* 1.3 69.4 + - - +
11F ILE* 5.0 3.6 - - - +
32F VAL* 3.5 8.5 - - - +
33F ILE* 3.0 44.8 + - - +
35F ARG* 5.5 9.6 + - - -
63F GLU* 4.5 3.4 - - - -
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Residues in contact with ARG 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F SER* 1.3 82.9 + - - +
11F ILE* 1.3 68.9 + - - +
30F GLU* 5.9 0.4 + - - -
31F SER 3.5 4.9 - - - +
32F VAL* 5.1 1.3 - - + -
59F MET* 3.3 41.9 - - + +
60F ASP* 3.0 43.6 + - - +
63F GLU* 3.1 33.6 + - - +
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Residues in contact with ILE 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F SER* 5.0 4.5 - - - +
10F ARG* 1.3 80.1 - - - +
12F ALA* 1.3 62.4 + - - +
13F VAL* 3.8 19.7 - - + -
29F ALA* 4.6 5.6 - - + +
30F GLU* 3.4 8.9 - - - +
31F SER* 3.0 44.7 + - - +
33F ILE* 3.6 21.5 - - + -
59F MET* 4.5 2.8 - - - +
300F THR* 3.5 32.3 - - + -
332F VAL* 4.3 15.3 - - + -
333F PHE* 5.8 1.3 - - + -
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Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 1.3 78.8 - - - +
13F VAL* 1.3 62.1 + - - +
14F PRO* 4.0 6.2 - - - +
28F THR* 4.7 5.8 - - - +
29F ALA 3.4 7.2 - - - -
30F GLU* 4.1 17.9 - - + +
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Residues in contact with VAL 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 3.8 24.2 - - + -
12F ALA* 1.3 78.4 - - - +
14F PRO* 1.3 79.5 - - + +
15F LEU* 4.0 0.2 - - - +
28F THR* 4.3 3.0 + - - -
29F ALA* 2.9 34.1 + - + +
328F LEU* 4.0 17.8 - - + +
329F LYS* 5.1 0.4 - - + -
330F THR* 3.6 39.9 - - - +
332F VAL* 3.7 25.1 - - + -
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Residues in contact with PRO 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA 4.0 6.1 - - - +
13F VAL* 1.3 93.7 - - + +
15F LEU* 1.3 59.0 + - - +
27F TYR 4.1 7.6 - - - +
28F THR* 4.1 8.5 - - - -
328F LEU* 3.7 4.2 - - - -
329F LYS* 3.0 49.3 + - + +
330F THR* 6.1 0.4 - - - +
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F PRO* 1.3 74.4 - - - +
16F THR* 1.3 59.7 + - - +
17F LYS* 3.5 19.5 - - - +
19F PHE* 3.6 31.2 - - + -
26F VAL* 3.8 14.6 - - + +
27F TYR* 3.1 17.2 + - - +
28F THR* 3.7 8.3 - - - +
29F ALA* 3.3 32.8 - - + +
298F ILE* 4.5 5.4 - - + -
327F MET* 3.5 25.6 - - + +
328F LEU* 3.7 19.1 - - + -
329F LYS* 2.8 19.0 + - - -
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Residues in contact with THR 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 1.3 72.1 - - - +
17F LYS* 1.3 61.2 + - + +
18F PRO* 4.9 0.7 - - - +
326F LEU 4.8 2.6 + - - -
327F MET* 3.0 18.7 + - - -
328F LEU 3.9 2.3 + - - -
329F LYS* 3.7 34.5 + - + +
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Residues in contact with LYS 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 3.5 19.9 - - - +
16F THR* 1.3 80.0 - - + +
18F PRO* 1.3 85.2 + - + +
19F PHE* 3.4 3.1 + - - -
137F SER* 5.6 1.6 - - - -
139F ASN* 3.9 9.5 - - - +
143F GLU* 2.7 31.3 + - - +
147F ASP* 2.7 40.8 + - - +
151F TYR* 4.8 8.5 - - - +
327F MET* 4.6 4.4 + - - +
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Residues in contact with PRO 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 5.0 1.1 - - + -
16F THR 4.9 0.7 - - - +
17F LYS* 1.3 104.0 + - + +
19F PHE* 1.3 61.0 + - - +
20F LYS* 3.8 28.7 + - - +
25F THR* 4.4 3.4 - - + -
26F VAL 3.5 13.0 - - - +
27F TYR* 4.0 31.0 - - + -
137F SER* 3.6 11.6 + - - -
139F ASN* 5.1 0.5 + - - -
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Residues in contact with PHE 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 3.6 22.0 - - + -
17F LYS 3.4 1.8 + - - +
18F PRO* 1.3 72.6 - - - +
20F LYS* 1.3 59.8 + - - +
21F THR* 3.6 20.6 - - + -
24F ARG* 5.5 1.1 - - + -
25F THR* 3.3 4.0 - - - -
26F VAL* 2.8 44.1 + - + +
135F THR* 3.8 19.1 - - + -
137F SER* 3.5 11.9 - - - -
162F LYS* 4.2 0.9 - - + -
298F ILE* 3.6 28.7 - - + -
327F MET* 3.5 35.4 - - + -
2480F ALA* 3.6 24.0 - - + -
2481F GLU* 3.4 23.8 - - - -
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Residues in contact with LYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO* 3.9 28.7 - - - +
19F PHE* 1.3 79.4 - - - +
21F THR* 1.3 62.3 + - - +
24F ARG 3.6 4.9 - - - -
25F THR* 3.7 21.3 - - + +
27F TYR* 5.5 3.4 - - - -
137F SER* 3.1 15.5 + - - -
138F VAL* 3.0 49.5 + - + +
139F ASN* 2.7 26.8 + - - +
143F GLU* 5.1 1.8 + - - -
162F LYS* 3.7 6.6 - - - +
165F LYS* 4.8 9.6 - - - +
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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