Contacts of the strand formed by residues 3 - 20 (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 ILE 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 1.3 71.0 - - - +
4B ILE* 1.3 66.4 + - - +
5B ARG 4.1 2.7 - - - +
6B ILE* 4.2 7.4 - - + -
36B ILE* 3.7 20.4 - - + -
37B THR 4.2 0.7 - - - -
38B TYR* 3.5 25.4 - - + -
74B LEU* 3.6 41.5 - - + +
75B LEU* 3.9 17.9 - - + -
76B GLY* 2.9 28.6 + - - -
77B LYS 2.9 14.7 + - - +
79B LEU* 4.5 4.9 - - + -
85B ILE* 4.8 7.0 - - + -
107B LEU* 3.7 27.4 - - + -
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Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 4.1 11.7 - - + +
3B ILE* 1.3 79.3 - - - +
5B ARG* 1.3 69.9 + - + +
37B THR* 3.2 20.5 + - + +
38B TYR 3.7 18.8 - - - +
39B ASP* 4.0 24.2 - - + +
75B LEU* 4.1 15.1 - - - +
76B GLY* 5.0 1.1 - - - +
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Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.9 0.6 - - - +
4B ILE* 1.3 87.6 - - + +
6B ILE* 1.3 66.8 + - - +
7B GLU* 2.8 46.8 + - + +
35B ARG 4.4 0.4 - - - -
36B ILE* 3.4 5.5 - - - +
37B THR* 2.9 47.8 + - - +
75B LEU* 3.9 6.8 - - - +
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.2 5.4 - - + -
5B ARG* 1.3 82.5 - - - +
7B GLU* 1.3 70.2 + - - +
8B THR* 5.0 0.2 - - + -
34B VAL* 4.4 11.9 - - + -
35B ARG 3.6 2.7 - - - -
36B ILE* 4.2 14.4 - - + -
66B ILE* 3.8 28.9 - - + +
67B HIS* 3.6 15.3 - - + -
70B LEU* 6.2 0.4 - - + -
71B LYS* 3.9 35.8 + - + +
74B LEU* 3.9 39.3 - - + -
75B LEU* 4.0 11.8 - - + +
103B VAL* 5.4 3.6 - - + -
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 2.8 53.7 + - + +
6B ILE* 1.3 77.5 - - - +
8B THR* 1.3 70.1 + - - +
34B VAL* 3.5 2.9 - - - +
35B ARG* 3.0 73.3 + - - +
37B THR* 3.9 12.1 + - - -
67B HIS* 4.5 2.9 - - - -
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 1.3 80.6 - - - +
9B SER* 1.3 63.7 + - - +
32B VAL* 4.0 3.8 - - + -
33B ILE 3.2 12.1 - - - +
34B VAL* 4.0 10.8 - - + -
35B ARG* 4.5 7.1 + - - +
63B GLU* 2.8 29.7 + - + +
66B ILE* 3.9 30.7 - - + -
67B HIS* 2.7 32.9 + - + +
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 1.3 74.4 - - - +
10B ARG* 1.3 74.1 + - - +
11B ILE* 5.0 2.9 - - - +
32B VAL* 3.5 7.3 - - - +
33B ILE* 3.0 40.6 + - - +
35B ARG* 4.6 14.0 + - - +
63B GLU* 4.6 3.3 - - - +
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Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 1.3 85.1 + - - +
11B ILE* 1.3 71.1 + - - +
31B SER 3.5 8.1 - - - +
32B VAL* 4.8 1.8 - - + +
59B MET* 3.7 50.2 + - + +
60B ASP* 3.0 27.9 + - - +
63B GLU* 2.7 31.5 + - - +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 5.0 3.1 - - - +
10B ARG* 1.3 83.9 - - - +
12B ALA* 1.3 62.9 + - - +
13B VAL* 3.8 21.1 - - + -
29B ALA 3.9 10.8 - - - +
30B GLU* 3.4 3.5 - - - +
31B SER* 3.0 37.3 + - - +
33B ILE* 3.6 35.4 - - + -
59B MET* 5.2 1.0 - - - +
300B THR* 3.6 28.3 - - + -
328B LEU* 5.5 0.2 - - + -
332B VAL* 4.2 16.8 - - + -
333B PHE* 5.2 2.2 - - + -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 1.3 75.7 - - - +
13B VAL* 1.3 68.1 + - - +
14B PRO* 4.5 3.0 - - - +
28B THR* 4.5 9.0 - - - +
29B ALA 3.5 6.3 - - - +
30B GLU* 4.6 12.3 - - + +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.8 15.3 - - + -
12B ALA* 1.3 81.2 - - - +
14B PRO* 1.3 77.6 - - + +
15B LEU* 4.1 0.9 - - - +
28B THR* 4.0 3.5 + - - -
29B ALA* 2.9 36.7 + - - +
328B LEU* 3.9 22.3 - - + +
330B THR* 3.8 34.3 - - - +
332B VAL* 3.6 29.8 - - + -
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Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 4.5 2.0 - - - +
13B VAL* 1.3 90.4 - - + +
15B LEU* 1.3 64.3 + - - +
27B TYR 4.4 3.8 - - - +
28B THR* 3.8 16.1 - - - -
328B LEU* 3.9 0.5 - - - -
329B LYS* 3.0 55.3 + - + +
330B THR* 5.7 1.3 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 1.3 76.6 - - - +
16B THR* 1.3 65.3 + - - +
17B LYS 3.6 18.9 - - - +
18B PRO* 4.8 0.6 - - + +
19B PHE* 3.6 23.6 - - + -
26B VAL* 3.6 26.2 - - + +
27B TYR 3.0 17.9 + - - +
28B THR 4.1 3.6 - - - -
29B ALA* 3.7 22.9 - - + +
298B ILE* 4.5 7.6 - - + -
327B MET* 3.6 24.2 - - + +
328B LEU* 3.5 26.5 - - + -
329B LYS* 3.6 10.7 + - - -
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO 3.8 1.2 + - - -
15B LEU* 1.3 73.4 - - - +
17B LYS* 1.3 63.4 + - + +
18B PRO* 4.7 1.2 - - - +
151B TYR* 5.8 4.5 - - + +
326B LEU 5.3 1.7 + - - -
327B MET* 2.9 17.1 + - - -
328B LEU 3.9 13.5 + - - -
329B LYS* 4.0 22.3 + - - +
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Residues in contact with LYS 17 (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 17.8 - - - +
16B THR* 1.3 83.2 - - + +
18B PRO* 1.3 85.3 + - + +
19B PHE* 3.4 2.1 + - - -
20B LYS* 5.7 2.4 - - - +
137B SER* 6.0 0.8 - - - -
139B ASN* 3.8 10.9 - - - +
143B GLU* 2.8 29.2 + - - -
147B ASP* 3.1 31.2 + - - +
151B TYR* 3.6 27.4 - - + +
327B MET* 4.5 4.5 + - - +
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Residues in contact with PRO 18 (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* 4.7 2.2 - - + -
16B THR 4.7 1.3 - - - +
17B LYS* 1.3 105.4 + - + +
19B PHE* 1.3 60.7 + - - +
20B LYS* 4.0 27.4 + - + +
25B THR* 4.6 2.2 - - + -
26B VAL 3.6 12.3 - - - +
27B TYR* 4.1 29.6 - - + -
137B SER* 3.6 10.9 + - - -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.6 21.0 - - + +
17B LYS 3.4 2.6 + - - -
18B PRO* 1.3 71.9 - - - +
20B LYS* 1.3 60.6 + - - +
21B THR* 3.4 30.1 - - + -
24B ARG* 5.4 1.8 - - + -
25B THR* 3.3 4.7 - - - +
26B VAL* 2.9 43.8 + - + +
135B THR* 3.7 26.5 - - + -
137B SER* 3.4 12.8 - - - -
162B LYS* 3.8 2.5 - - + -
298B ILE* 3.5 21.5 - - + -
327B MET* 3.7 27.6 - - + -
2472B ALA* 3.6 26.5 - - + -
2473B GLU* 3.6 17.5 - - - -
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Residues in contact with LYS 20 (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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17B LYS* 5.7 2.0 - - - +
18B PRO* 4.1 24.6 - - - +
19B PHE* 1.3 82.5 - - - +
21B THR* 1.3 64.1 + - - +
24B ARG 3.6 4.7 - - - -
25B THR* 3.8 24.7 - - + +
137B SER* 3.1 16.2 + - - -
138B VAL* 3.2 42.4 + - + +
139B ASN* 3.2 28.5 + - - +
143B GLU* 6.0 0.2 - - - -
162B LYS* 3.7 3.3 - - - +
165B LYS* 4.4 13.9 - - - +
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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
------------------------------------------------------------
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