Contacts of the strand formed by residues 3 - 20 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET 4.4 0.2 - - - -
2H LYS* 1.3 69.6 - - - +
4H ILE* 1.3 67.6 + - - +
5H ARG 4.3 2.0 - - - +
6H ILE* 4.2 17.3 - - + -
36H ILE* 4.1 17.7 - - + -
37H THR 4.1 0.7 - - - -
38H TYR* 3.5 26.2 - - + -
74H LEU* 3.5 49.1 - - + +
75H LEU* 4.2 4.5 - - + -
76H GLY* 2.9 25.5 + - - -
77H LYS 3.0 13.0 + - - +
79H LEU* 4.4 2.7 - - + -
85H ILE* 4.4 10.1 - - + -
107H LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LYS* 4.0 21.3 - - + +
3H ILE* 1.3 80.4 - - - +
5H ARG* 1.3 69.5 + - + +
37H THR* 3.1 24.3 + - + +
38H TYR 3.6 22.4 - - - +
39H ASP* 3.8 11.4 - - + +
75H LEU* 3.6 16.2 - - - +
76H GLY* 4.8 2.7 - - - +
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Residues in contact with ARG 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE 4.0 0.2 - - - -
4H ILE* 1.3 85.1 - - + +
6H ILE* 1.3 68.1 + - - +
7H GLU* 3.4 45.3 + - + +
35H ARG 3.7 1.0 - - - +
36H ILE* 3.3 6.9 - - - +
37H THR* 3.0 42.6 + - - +
75H LEU* 3.9 6.0 - - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.2 12.3 - - + -
5H ARG* 1.3 81.6 - - - +
7H GLU* 1.3 65.3 + - - +
34H VAL* 4.2 17.7 - - + -
35H ARG 3.5 2.5 - - - -
36H ILE* 4.1 16.6 - - + -
66H ILE* 3.9 27.1 - - + -
67H HIS* 3.9 6.7 - - + -
70H LEU* 5.1 0.4 - - + -
71H LYS* 3.5 46.5 - - + +
74H LEU* 4.0 35.2 - - + -
75H LEU* 4.3 5.6 - - + +
103H VAL* 5.4 6.7 - - + -
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Residues in contact with GLU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG* 3.4 50.1 + - - +
6H ILE* 1.3 76.0 - - - +
8H THR* 1.3 66.4 + - - +
33H ILE 3.7 0.2 - - - +
34H VAL* 3.3 6.2 - - - +
35H ARG* 2.9 79.6 + - - +
37H THR* 4.7 8.8 + - - -
67H HIS* 4.5 3.6 - - - -
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Residues in contact with THR 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLU* 1.3 83.3 - - - +
9H SER* 1.3 64.9 + - - +
32H VAL* 4.1 6.5 - - + -
33H ILE 3.1 6.5 - - - -
34H VAL* 3.7 23.3 - - + -
35H ARG* 5.0 3.5 + - - -
63H GLU* 2.8 28.3 + - + +
66H ILE* 4.0 20.9 - - + -
67H HIS* 2.6 32.5 + - + +
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Residues in contact with SER 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H THR* 1.3 76.5 - - - +
10H ARG* 1.3 66.0 + - - +
11H ILE* 5.5 1.7 - - - +
32H VAL* 3.5 4.0 - - - +
33H ILE* 2.7 50.3 + - - +
35H ARG* 4.8 13.4 + - - -
63H GLU* 4.5 4.7 - - - -
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Residues in contact with ARG 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 1.3 81.0 - - - +
11H ILE* 1.3 72.9 + - - +
31H SER 3.4 5.8 - - - +
32H VAL* 4.8 2.7 - - + +
59H MET* 3.6 57.2 + - + +
60H ASP* 2.8 30.1 + - - +
63H GLU* 3.2 32.6 + - - +
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Residues in contact with ILE 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 5.5 2.5 - - - +
10H ARG* 1.3 82.8 - - - +
12H ALA* 1.3 64.0 + - - +
13H VAL* 3.9 19.1 - - + -
29H ALA* 4.0 9.2 - - + +
30H GLU* 3.5 5.4 - - - +
31H SER* 3.0 44.1 + - - +
33H ILE* 3.3 35.2 - - + -
59H MET* 5.2 1.0 - - - +
300H THR* 3.4 28.5 - - + -
332H VAL* 4.5 14.4 - - + -
333H PHE* 5.5 0.4 - - + -
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Residues in contact with ALA 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ILE* 1.3 76.7 - - - +
13H VAL* 1.3 64.8 + - - +
14H PRO* 4.0 7.0 - - - +
28H THR* 4.4 10.3 - - - +
29H ALA 3.3 7.6 - - - +
30H GLU* 4.6 13.9 - - + +
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Residues in contact with VAL 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ILE* 3.9 15.9 - - + -
12H ALA* 1.3 79.1 - - - +
14H PRO* 1.3 78.5 - - + +
15H LEU* 3.9 0.5 - - - +
28H THR* 4.3 1.5 + - - -
29H ALA* 3.0 31.9 + - - +
328H LEU* 3.7 29.8 - - + +
329H LYS* 4.6 1.1 - - + -
330H THR* 3.7 24.9 - - - +
332H VAL* 3.3 30.5 - - + -
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Residues in contact with PRO 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ALA 4.0 5.8 - - - +
13H VAL* 1.3 90.3 - - + +
15H LEU* 1.3 66.6 + - - +
27H TYR 3.8 9.6 - - - +
28H THR* 4.0 10.7 - - - +
328H LEU* 3.8 0.5 - - - -
329H LYS* 3.0 46.6 + - + +
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PRO* 1.3 79.2 - - - +
16H THR* 1.3 63.8 - - - +
17H LYS* 3.3 15.9 - - - +
19H PHE* 3.7 26.9 - - + +
26H VAL* 3.3 30.5 - - + +
27H TYR 2.9 16.5 + - - +
28H THR 3.9 3.6 - - - -
29H ALA* 3.3 29.6 - - + +
298H ILE* 4.5 6.5 - - + -
327H MET* 3.4 23.1 - - + +
328H LEU* 3.5 20.9 - - + +
329H LYS* 4.8 2.2 - - - +
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Residues in contact with THR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PRO 4.0 1.2 + - - -
15H LEU* 1.3 73.5 - - - +
17H LYS* 1.3 62.7 + - + +
18H PRO* 4.8 1.0 - - - +
326H LEU 5.1 1.7 + - - -
327H MET* 3.1 16.8 + - - -
328H LEU 3.9 12.3 + - - -
329H LYS* 4.1 15.9 - - - +
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Residues in contact with LYS 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 3.3 20.0 - - - +
16H THR* 1.3 83.8 - - + +
18H PRO* 1.3 86.9 + - + +
19H PHE* 3.4 1.4 + - - -
20H LYS* 5.4 2.6 - - - +
137H SER* 5.4 1.4 - - - -
139H ASN* 3.8 15.8 - - - +
143H GLU* 3.0 28.1 + - - -
147H ASP* 3.4 33.5 + - - +
151H TYR* 4.8 8.5 - - - +
327H MET* 4.8 3.7 + - - +
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Residues in contact with PRO 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 4.6 1.3 - - + -
16H THR 4.8 0.9 - - - +
17H LYS* 1.3 103.2 + - + +
19H PHE* 1.3 62.6 + - - +
20H LYS* 3.7 19.8 + - - +
25H THR* 4.0 10.8 - - + -
26H VAL 3.5 14.1 - - - +
27H TYR* 3.9 33.7 - - + -
137H SER* 3.4 11.1 + - - -
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Residues in contact with PHE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.7 19.7 - - + +
17H LYS 3.4 3.2 + - - +
18H PRO* 1.3 71.2 - - - +
20H LYS* 1.3 59.0 + - - +
21H THR* 3.3 30.1 - - + -
24H ARG* 5.3 1.3 - - + -
25H THR* 3.3 5.5 - - - +
26H VAL* 3.0 39.1 + - + +
135H THR* 3.7 24.7 - - + -
137H SER* 3.3 15.3 - - - -
162H LYS* 3.9 2.5 - - + -
298H ILE* 3.6 16.6 - - + -
327H MET* 3.7 29.8 - - + -
2484H ALA* 3.5 30.1 - - + -
2485H GLU* 3.8 21.8 - - + -
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Residues in contact with LYS 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H LYS* 5.4 1.9 - - - +
18H PRO* 3.7 29.3 - - - +
19H PHE* 1.3 79.7 - - - +
21H THR* 1.3 65.5 + - - +
24H ARG 3.6 3.8 - - - -
25H THR* 3.5 22.7 - - + +
27H TYR* 5.8 2.2 - - - -
137H SER* 2.9 16.0 + - - -
138H VAL* 3.0 47.9 + - + +
139H ASN* 2.7 27.1 + - - +
143H GLU* 5.0 3.0 + - - -
162H LYS* 3.8 3.6 - - - +
165H LYS* 4.9 10.5 - - - +
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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