Contacts of the strand formed by residues 25 - 38 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B PRO* 4.6 3.1 - - + -
19B PHE 3.3 11.4 - - - +
20B LYS* 3.8 27.5 - - + +
24B ARG* 1.3 78.6 + - - +
26B VAL* 1.3 69.0 + - - +
27B TYR* 3.9 39.9 + - + +
165B LYS* 4.3 9.4 + - - -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.6 14.0 - - + +
18B PRO* 3.6 3.8 - - - +
19B PHE* 2.9 47.0 + - + -
24B ARG* 3.4 46.2 - - + +
25B THR* 1.3 78.1 - - - +
27B TYR* 1.3 60.7 + - - +
28B THR 3.3 30.5 - - - +
29B ALA* 4.6 1.1 - - - +
298B ILE* 4.5 15.0 - - + -
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 3.9 2.9 - - - +
15B LEU* 3.0 27.5 + - - +
18B PRO* 4.1 31.4 - - + -
20B LYS* 6.4 0.2 - - - -
25B THR* 3.9 27.0 - - + +
26B VAL* 1.3 73.9 - - - +
28B THR* 1.3 68.8 + - + +
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 4.5 4.5 - - - +
13B VAL 3.9 16.2 + - - -
14B PRO* 3.8 15.9 - - - -
15B LEU* 4.0 2.0 - - - +
26B VAL* 3.3 16.2 - - - +
27B TYR* 1.3 89.8 - - + +
29B ALA* 1.3 64.3 + - - +
30B GLU* 3.5 19.6 + - + +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.9 7.7 - - + +
12B ALA* 3.5 2.6 - - - -
13B VAL* 2.9 38.1 + - - +
15B LEU* 3.7 5.5 - - + +
26B VAL* 4.8 0.9 - - - -
28B THR* 1.3 69.6 + - - +
30B GLU* 1.3 64.4 + - - +
298B ILE* 3.9 20.6 - - + +
299B GLU* 5.6 1.6 - - - +
300B THR* 5.7 2.5 - - + -
328B LEU* 3.6 31.2 - - + -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE 3.4 7.4 - - - +
12B ALA* 4.6 10.7 - - + +
28B THR* 3.5 21.3 + - - +
29B ALA* 1.3 78.9 - - - +
31B SER* 1.3 67.8 + - - +
49B PRO* 3.5 6.9 - - - +
50B PRO* 3.4 29.5 - - + +
59B MET* 3.6 29.2 - - + +
298B ILE 4.7 1.4 - - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.5 4.5 - - - -
11B ILE* 3.0 40.3 + - - -
30B GLU* 1.3 78.0 + - - +
32B VAL* 1.3 60.0 + - - +
33B ILE* 3.5 14.4 - - - +
47B GLU* 2.6 34.1 + - - +
48B ALA 3.8 4.5 - - - -
49B PRO* 3.5 16.5 - - - +
59B MET* 3.8 9.8 - - - +
298B ILE 4.7 1.2 + - - -
299B GLU* 4.9 0.2 - - - -
300B THR* 5.0 0.4 - - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 4.0 10.1 - - + -
9B SER 3.5 10.3 - - - +
10B ARG* 4.8 1.3 - - + -
31B SER* 1.3 72.3 - - - +
33B ILE* 1.3 72.4 + - - +
34B VAL* 4.3 2.8 + - + +
47B GLU* 3.3 5.5 - - - -
48B ALA* 3.0 36.7 + - + +
59B MET* 3.9 36.1 - - + +
62B ILE* 3.8 28.3 - - + -
63B GLU* 3.8 25.8 - - + -
66B ILE* 4.2 4.7 - - + -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 3.2 8.8 - - - -
9B SER* 3.0 43.9 + - - +
11B ILE* 3.6 30.5 - - + +
31B SER* 3.5 20.6 - - - +
32B VAL* 1.3 81.3 - - - +
34B VAL* 1.3 64.7 + - - +
35B ARG* 4.4 5.4 + - + +
45B TRP* 3.9 33.0 - - + -
46B GLY 3.4 9.2 - - - +
47B GLU* 4.8 5.4 - - + -
302B LEU* 4.4 2.0 - - + -
333B PHE* 3.6 26.0 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 11.0 - - + -
7B GLU 3.5 8.7 - - - +
8B THR* 4.0 4.7 - - + -
32B VAL* 4.4 4.5 - - + +
33B ILE* 1.3 80.3 - - - +
35B ARG* 1.3 66.2 + - - +
36B ILE* 4.2 21.3 - - + -
44B GLY 3.5 0.5 - - - +
45B TRP* 3.3 8.5 - - - +
46B GLY 2.8 34.9 + - - +
66B ILE* 3.8 27.8 - - + -
102B ALA* 3.9 24.7 - - + +
103B VAL* 4.8 9.0 - - + +
106B ALA* 4.5 6.7 - - + -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG 3.7 0.9 - - - +
6B ILE* 3.6 1.4 - - - -
7B GLU* 3.0 80.5 + - + +
8B THR 4.5 11.9 + - - -
9B SER* 4.6 13.3 + - - -
33B ILE* 4.4 6.8 + - + +
34B VAL* 1.3 72.5 - - - +
36B ILE* 1.3 62.8 - - - +
37B THR* 3.8 4.7 + - - +
43B VAL* 3.7 18.2 - - + -
44B GLY 3.3 3.6 - - - -
45B TRP* 3.4 46.9 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 3.7 28.0 - - + -
5B ARG 3.4 4.3 - - - +
6B ILE* 4.2 18.8 - - + -
34B VAL* 4.0 8.0 - - + -
35B ARG* 1.3 72.6 - - - +
37B THR* 1.3 62.2 + - - +
38B TYR* 3.4 33.6 - - + +
43B VAL* 3.3 3.2 - - - -
44B GLY 2.8 33.1 + - - -
74B LEU* 4.6 6.1 - - + -
103B VAL* 3.9 25.1 - - + +
106B ALA* 3.5 28.9 - - + -
107B LEU* 4.1 7.9 - - - +
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 4.1 2.1 - - - -
4B ILE* 3.2 29.6 + - + +
5B ARG* 2.9 32.0 + - + +
7B GLU* 3.9 16.3 + - - -
35B ARG* 3.8 4.7 + - - +
36B ILE* 1.3 73.2 - - - +
38B TYR* 1.3 71.6 + - - +
41B GLY* 4.6 9.0 - - - +
42B ALA 3.6 7.0 - - - +
43B VAL* 4.3 19.7 - - + +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.0 22.0 - - + -
2B LYS 3.2 23.3 - - - +
3B ILE* 3.5 21.5 - - + -
4B ILE* 3.7 10.6 - - - +
36B ILE* 3.4 28.0 - - + +
37B THR* 1.3 78.9 - - - +
39B ASP* 1.3 59.4 + - - +
40B SER* 3.2 6.7 - - - +
41B GLY* 3.2 17.5 + - - -
42B ALA* 2.8 33.8 + - + +
44B GLY 3.9 8.5 - - - -
79B LEU* 3.5 23.5 - - + +
106B ALA 2.9 21.3 + - - -
107B LEU* 3.4 17.5 + - - +
110B GLY* 3.8 20.0 - - - -
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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