Contacts of the strand formed by residues 25 - 38 (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 THR 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D PRO* 4.2 2.7 - - + -
19D PHE 3.4 10.8 - - - +
20D LYS* 3.6 29.3 - - + +
24D ARG* 1.3 79.5 + - - +
26D VAL* 1.3 67.8 + - - +
27D TYR* 3.5 46.1 + - + +
165D LYS* 4.2 11.8 + - - -
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Residues in contact with VAL 26 (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* 3.5 14.1 - - + +
18D PRO* 3.5 4.9 - - - +
19D PHE* 2.9 51.9 + - + +
24D ARG* 3.4 47.6 - - + +
25D THR* 1.3 77.5 - - - +
27D TYR* 1.3 63.9 + - - +
28D THR 3.7 24.2 - - - +
29D ALA* 4.8 0.2 - - - -
298D ILE* 4.2 15.7 - - + -
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Residues in contact with TYR 27 (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* 4.4 0.3 - - - +
15D LEU* 3.2 29.1 + - - +
18D PRO* 3.8 28.9 - - + -
20D LYS* 5.7 0.9 + - + +
25D THR* 3.5 36.0 - - + +
26D VAL* 1.3 73.7 - - - +
28D THR* 1.3 74.1 + - + +
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Residues in contact with THR 28 (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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12D ALA* 4.7 6.1 - - - +
13D VAL 3.8 9.9 - - - -
14D PRO* 4.3 9.9 - - + -
15D LEU* 3.7 6.5 - - - +
26D VAL* 3.7 9.5 - - - +
27D TYR* 1.3 91.2 - - + +
29D ALA* 1.3 60.5 + - - +
30D GLU* 3.5 22.3 + - - +
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Residues in contact with ALA 29 (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* 3.9 3.5 - - - +
12D ALA* 3.6 1.2 - - - -
13D VAL* 2.9 33.8 + - + +
15D LEU* 3.2 10.5 - - + +
26D VAL* 4.8 0.9 - - - -
28D THR* 1.3 69.0 - - - +
30D GLU* 1.3 62.8 + - - +
31D SER* 5.2 0.6 - - - -
298D ILE* 3.5 35.7 - - + +
299D GLU 5.7 0.4 - - - -
300D THR* 5.5 5.8 - - + +
328D LEU* 3.7 18.8 - - + -
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Residues in contact with GLU 30 (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 3.3 5.7 - - - +
12D ALA* 3.8 24.8 - - + +
28D THR* 3.5 17.6 + - - +
29D ALA* 1.3 75.4 - - - +
31D SER* 1.3 62.8 + - - +
49D PRO* 3.2 23.0 - - - +
50D PRO* 3.2 16.1 - - + +
59D MET* 3.3 33.6 - - + +
298D ILE 4.9 0.9 - - - +
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Residues in contact with SER 31 (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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10D ARG* 3.3 5.9 - - - +
11D ILE* 3.1 46.6 + - - -
29D ALA 5.2 0.2 - - - -
30D GLU* 1.3 77.1 + - - +
32D VAL* 1.3 62.1 + - - +
33D ILE* 3.6 2.6 - - - +
47D GLU* 2.5 42.7 + - - +
48D ALA 3.8 4.5 - - - -
49D PRO* 3.5 12.3 - - - +
59D MET* 4.0 5.0 - - - -
298D ILE 4.9 0.7 + - - -
299D GLU* 5.0 0.2 - - - -
300D THR* 4.9 1.6 - - - -
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Residues in contact with VAL 32 (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* 4.1 18.2 - - + -
9D SER 3.3 8.5 - - - +
10D ARG* 4.9 1.6 - - + -
31D SER* 1.3 74.7 - - - +
33D ILE* 1.3 63.2 + - - +
34D VAL* 4.2 2.7 + - + +
47D GLU* 3.3 6.9 - - - +
48D ALA* 2.8 41.8 + - + +
59D MET* 4.0 32.3 - - + +
62D ILE* 4.1 20.6 - - + -
63D GLU* 3.9 34.1 - - + -
66D ILE* 4.5 3.8 - - + -
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Residues in contact with ILE 33 (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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7D GLU 3.7 0.3 - - - +
8D THR* 3.1 6.1 - - - -
9D SER* 2.8 49.2 + - - +
10D ARG 4.1 0.4 - - - -
11D ILE* 3.3 41.5 - - + +
31D SER* 3.6 16.6 - - - +
32D VAL* 1.3 75.6 - - - +
34D VAL* 1.3 65.0 + - - +
35D ARG* 4.1 4.8 + - + -
45D TRP* 3.9 23.3 - - + -
46D GLY 3.4 11.2 - - - +
47D GLU* 5.2 2.2 - - + -
302D LEU* 3.9 13.9 - - + -
333D PHE* 3.9 18.4 - - + -
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Residues in contact with VAL 34 (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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6D ILE* 4.3 11.9 - - + -
7D GLU 3.4 8.1 - - - +
8D THR* 4.2 4.3 - - + -
32D VAL* 4.6 3.6 - - + +
33D ILE* 1.3 76.8 - - - +
35D ARG* 1.3 66.4 + - - +
36D ILE* 4.0 25.1 - - + -
45D TRP* 3.3 6.1 - - - -
46D GLY* 2.8 41.4 + - - +
66D ILE* 3.7 23.1 - - + -
102D ALA* 3.7 32.3 - - + +
103D VAL* 4.6 6.5 - - + +
106D ALA* 4.3 6.1 - - + -
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Residues in contact with ARG 35 (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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5D ARG 3.9 0.9 - - - +
6D ILE* 3.7 1.6 - - - -
7D GLU* 3.0 77.7 + - - +
8D THR 5.1 1.6 + - - -
9D SER* 4.4 21.2 + - - -
33D ILE* 4.1 4.7 + - + +
34D VAL* 1.3 73.4 - - - +
36D ILE* 1.3 60.9 + - - +
37D THR* 4.2 1.2 + - - +
43D VAL* 3.6 16.2 - - + -
44D GLY 3.1 4.3 - - - -
45D TRP* 3.6 50.0 - - + -
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Residues in contact with ILE 36 (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* 3.9 19.1 - - + -
5D ARG 3.4 8.5 - - - +
6D ILE* 4.0 17.3 - - + -
34D VAL* 4.0 7.9 - - + -
35D ARG* 1.3 74.4 - - - +
37D THR* 1.3 65.6 + - - +
38D TYR* 3.6 32.4 - - + +
43D VAL* 3.2 6.3 - - - -
44D GLY 2.9 29.8 + - - -
74D LEU* 4.5 7.4 - - + -
103D VAL* 3.9 26.9 - - + +
106D ALA* 3.3 29.6 - - + -
107D LEU* 4.1 9.0 - - + +
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Residues in contact with THR 37 (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* 3.9 1.4 - - - -
4D ILE* 2.9 37.6 + - + +
5D ARG* 2.9 40.3 + - - +
7D GLU* 4.2 14.4 + - - -
35D ARG 5.0 0.9 + - - -
36D ILE* 1.3 75.1 - - - +
38D TYR* 1.3 70.1 + - - +
41D GLY* 4.8 7.2 - - - +
42D ALA 3.5 8.5 - - - +
43D VAL* 4.1 16.5 - - + +
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Residues in contact with TYR 38 (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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1D MET* 3.6 31.9 - - + -
2D LYS 3.1 19.1 - - - +
3D ILE* 3.4 26.5 - - + -
4D ILE* 3.8 9.6 - - - +
36D ILE* 3.6 26.7 - - + +
37D THR* 1.3 76.9 - - - +
39D ASP* 1.3 58.6 + - - +
40D SER* 3.1 7.6 - - - +
41D GLY* 2.9 21.1 + - - -
42D ALA* 3.0 26.9 + - + +
44D GLY 3.8 9.2 - - - -
79D LEU* 3.9 15.9 - - + -
106D ALA 2.7 22.3 + - - -
107D LEU* 3.3 16.3 + - - +
110D GLY* 3.7 21.4 - - - -
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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