Contacts of the strand formed by residues 3 - 20 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D LYS* 1.3 70.9 - - - +
4D ILE* 1.3 63.7 + - - +
5D ARG 4.4 0.7 - - - +
6D ILE* 4.2 9.4 - - + -
36D ILE* 3.9 18.4 - - + -
37D THR 4.1 2.9 - - - -
38D TYR* 3.4 24.0 - - + -
74D LEU* 3.6 42.6 - - + +
75D LEU* 3.8 12.8 - - + -
76D GLY* 2.9 27.7 + - - -
77D LYS 2.8 15.9 + - - +
79D LEU* 4.6 2.9 - - + -
85D ILE* 4.5 9.9 - - + -
107D LEU* 3.6 31.2 - - + -
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 3.7 12.1 - - + +
3D ILE* 1.3 78.2 - - - +
5D ARG* 1.3 70.1 + - + +
37D THR* 2.9 27.9 + - + +
38D TYR 3.8 14.4 - - - +
39D ASP* 3.6 32.5 - - + +
75D LEU* 4.0 11.5 - - - +
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Residues in contact with ARG 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.8 1.4 - - - +
4D ILE* 1.3 86.8 - - + +
6D ILE* 1.3 68.9 + - - +
7D GLU* 2.9 43.9 + - + +
35D ARG 3.9 0.9 - - - +
36D ILE* 3.4 4.2 - - - +
37D THR* 2.9 53.2 + - - +
75D LEU* 3.9 5.8 - - - +
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 4.2 7.9 - - + -
5D ARG* 1.3 81.0 - - - +
7D GLU* 1.3 64.7 + - - +
8D THR* 5.0 0.4 - - + -
34D VAL* 4.3 17.7 - - + -
35D ARG 3.7 2.5 - - - -
36D ILE* 4.0 18.4 - - + -
66D ILE* 3.9 28.3 - - + -
67D HIS* 3.9 14.8 - - + -
70D LEU* 6.3 0.4 - - + -
71D LYS* 3.8 37.4 + - + +
74D LEU* 3.7 40.4 - - + -
75D LEU* 4.3 5.6 - - + +
103D VAL* 5.4 3.4 - - + -
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Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 2.9 47.6 + - + +
6D ILE* 1.3 75.7 - - - +
8D THR* 1.3 70.4 + - - +
34D VAL* 3.4 3.3 - - - +
35D ARG* 3.0 78.4 + - - +
37D THR* 4.2 9.0 + - - +
43D VAL* 5.9 0.2 - - - +
67D HIS* 4.8 2.5 - - - -
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Residues in contact with THR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLU* 1.3 81.7 - - - +
9D SER* 1.3 62.1 + - - +
32D VAL* 4.1 7.6 - - + -
33D ILE 3.1 10.3 - - - +
34D VAL* 4.2 6.1 - - + -
35D ARG* 5.1 3.4 + - - +
63D GLU* 3.1 23.1 + - + +
66D ILE* 3.9 33.4 - - + -
67D HIS* 2.6 36.2 + - + +
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Residues in contact with SER 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 1.3 76.0 - - - +
10D ARG* 1.3 71.0 + - - +
11D ILE* 5.7 0.3 - - - +
32D VAL* 3.3 6.8 - - - +
33D ILE* 2.8 45.4 + - - +
35D ARG* 4.4 17.1 + - - -
63D GLU* 4.5 3.6 - - - -
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 1.3 83.3 - - - +
11D ILE* 1.3 71.8 + - - +
31D SER 3.3 7.2 - - - +
32D VAL* 4.9 2.0 - - + -
59D MET* 3.8 44.1 - - + +
60D ASP* 2.8 37.2 + - - +
63D GLU* 2.8 33.7 + - - +
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Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 5.7 0.7 - - - +
10D ARG* 1.3 81.1 - - - +
12D ALA* 1.3 64.3 + - - +
13D VAL* 4.5 5.4 - - + -
29D ALA 4.9 1.6 - - - +
30D GLU* 3.3 7.3 - - - +
31D SER* 3.1 33.7 + - - +
33D ILE* 3.3 28.5 - - + -
59D MET* 5.2 0.2 - - - +
300D THR* 3.6 31.4 - - + +
332D VAL* 3.8 24.5 - - + -
333D PHE* 4.2 8.3 - - + -
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 1.3 76.1 - - - +
13D VAL* 1.3 62.3 + - - +
14D PRO* 3.5 9.9 - - - +
28D THR* 4.7 6.3 - - - +
29D ALA 3.6 6.1 - - - -
30D GLU* 3.8 23.8 - - + +
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Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 4.5 11.2 - - + -
12D ALA* 1.3 75.0 - - - +
14D PRO* 1.3 78.9 - - + +
28D THR* 3.8 2.0 - - - -
29D ALA* 2.9 36.4 + - + +
300D THR* 4.6 7.2 - - + -
328D LEU* 3.8 14.8 - - + +
330D THR* 3.4 38.8 - - - +
332D VAL* 3.7 35.0 - - + -
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Residues in contact with PRO 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA 3.5 8.7 - - - +
13D VAL* 1.3 91.5 - - + +
15D LEU* 1.3 62.8 + - - +
27D TYR 4.4 0.7 - - - +
28D THR* 4.3 12.3 - - + -
328D LEU* 3.6 2.1 - - - -
329D LYS* 2.9 52.2 + - + +
330D THR* 5.8 1.8 - - - +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO* 1.3 75.9 - - - +
16D THR* 1.3 66.8 + - - +
17D LYS* 3.0 21.5 + - - +
19D PHE* 3.8 19.7 - - + +
26D VAL* 3.5 26.0 - - + +
27D TYR 3.2 19.9 + - - +
28D THR* 3.7 8.3 - - - +
29D ALA* 3.2 43.3 - - + +
298D ILE* 4.4 5.4 - - + -
327D MET* 3.5 24.7 - - + +
328D LEU* 3.7 9.9 - - + -
329D LYS* 5.1 2.4 + - - -
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO 3.9 2.8 + - - -
15D LEU* 1.3 70.5 - - - +
17D LYS* 1.3 65.9 + - + +
326D LEU 5.2 1.3 + - - -
327D MET 3.1 12.4 + - - -
328D LEU 3.8 15.9 + - - -
329D LYS* 3.9 29.5 + - - +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.4 22.8 - - - +
16D THR* 1.3 85.1 + - + +
18D PRO* 1.3 84.6 + - + +
19D PHE 3.5 0.7 + - - -
137D SER* 5.1 4.0 - - - -
139D ASN* 4.3 14.5 - - - +
143D GLU* 4.9 7.6 + - - -
147D ASP* 2.9 40.2 + - - -
151D TYR* 4.4 10.7 + - - +
327D MET* 4.6 3.9 + - - +
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Residues in contact with PRO 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 1.3 101.2 + - + +
19D PHE* 1.3 60.3 + - - +
20D LYS* 3.7 13.4 + - + +
25D THR* 4.2 9.2 - - + -
26D VAL 3.5 9.2 - - - +
27D TYR* 3.8 37.2 - - + -
137D SER* 3.6 13.3 + - - -
139D ASN* 5.2 1.4 + - - -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.8 19.0 - - + +
17D LYS 3.5 3.4 + - - -
18D PRO* 1.3 71.7 - - - +
20D LYS* 1.3 57.7 + - - +
21D THR* 3.2 31.2 - - + -
24D ARG* 5.3 1.3 - - + -
25D THR* 3.4 4.7 - - - +
26D VAL* 2.9 43.8 + - + +
135D THR* 3.9 16.6 - - + -
137D SER* 3.5 11.9 - - - -
162D LYS* 4.0 2.5 - - + -
298D ILE* 3.8 16.2 - - + -
327D MET* 3.5 35.4 - - + -
2476D ALA* 3.5 32.5 - - + -
2477D GLU* 3.7 20.9 - - + -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PRO* 4.0 17.2 - - + +
19D PHE* 1.3 79.1 - - - +
21D THR* 1.3 67.8 + - - +
24D ARG 3.8 4.3 - - - -
25D THR* 3.6 28.5 - - + +
27D TYR* 5.9 0.6 + - + -
137D SER* 3.2 14.0 + - - -
138D VAL* 3.0 54.5 + - + +
139D ASN* 3.3 21.0 + - - +
162D LYS* 3.7 5.4 - - - +
165D LYS* 4.5 16.1 - - - +
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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