Contacts of the helix formed by residues 50 - 68 (chain B) in PDB entry 4TKR
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 GLY 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE 3.6 0.6 + - - -
46B ALA* 3.0 21.0 + - - +
48B ARG 3.9 0.2 - - - -
49B ARG* 1.3 80.5 - - - +
51B PHE* 1.3 65.7 + - - +
52B TRP* 3.6 1.8 - - - -
53B ALA 3.6 0.8 + - - -
54B ALA* 3.2 24.6 + - - +
94B GLY* 4.3 1.6 - - - -
97B SER* 3.7 15.4 - - - -
101B ARG* 5.3 2.2 - - - -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.9 19.3 - + - -
129A PHE* 3.7 28.5 - + + -
130A TRP* 3.8 20.4 - + - -
50B GLY* 1.3 69.9 - - - -
52B TRP* 1.3 69.5 + - - +
54B ALA 3.2 9.7 + - - -
55B GLY 3.2 9.4 + - - -
91B ALA* 3.1 49.2 - - + +
92B PHE* 3.8 28.7 - + - -
94B GLY 3.8 12.7 + - - +
95B VAL* 4.1 16.8 - - + -
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Residues in contact with TRP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.7 4.3 - - + -
129A PHE* 4.1 9.4 - + + -
130A TRP* 3.4 30.0 - + + -
133A VAL* 3.8 37.7 - - + +
137A LEU* 3.7 33.4 - - + -
8B ILE* 3.6 40.1 - - + +
9B LEU* 4.2 18.6 - - + -
12B CYS* 4.9 0.7 - - - -
49B ARG 4.7 10.9 + - - -
51B PHE* 1.3 80.8 - - + +
53B ALA* 1.3 69.3 + - + +
55B GLY 3.4 0.3 + - - -
56B PHE* 3.0 34.3 + + + +
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.4 4.7 - - + -
12B CYS* 3.5 21.4 - - - -
45B ILE* 4.6 4.3 - - + +
49B ARG* 3.5 34.8 - - + +
50B GLY 3.6 4.2 + - - +
51B PHE 3.2 0.6 - - - -
52B TRP* 1.3 92.9 - - + +
54B ALA* 1.3 61.3 + - - +
56B PHE* 4.5 0.2 - - - -
57B ALA* 2.8 33.5 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 4.7 3.5 - - - +
45B ILE* 4.8 4.9 - - - -
46B ALA* 3.7 25.0 - - + +
50B GLY 3.2 18.4 + - - +
51B PHE 3.2 5.1 + - - +
53B ALA* 1.3 77.5 - - - +
55B GLY* 1.3 57.1 + - - +
57B ALA* 4.1 3.9 - - - +
58B GLY* 2.8 27.2 + - - -
90B ILE* 3.5 28.1 - - + +
91B ALA* 3.7 7.0 - - - +
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.9 10.6 - - - +
130A TRP* 4.1 5.2 - - - -
51B PHE 3.2 7.9 + - - -
52B TRP 3.4 2.9 + - - -
53B ALA 3.3 0.2 - - - -
54B ALA* 1.3 77.2 - - - +
56B PHE* 1.3 57.6 + - - +
58B GLY* 3.9 0.3 - - - -
59B LEU* 2.9 30.7 + - - +
88B SER* 3.6 13.8 - - - -
91B ALA* 3.5 20.8 - - - +
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.9 32.1 - - - -
80A ILE* 4.2 17.9 - - + -
81A ILE* 3.5 31.9 - - + -
85A LEU* 4.0 11.5 - - + +
130A TRP* 5.2 0.2 - - + -
9B LEU* 3.8 27.4 - - + -
12B CYS* 3.5 28.7 - - + -
52B TRP* 3.0 25.7 + + + +
53B ALA 3.8 2.9 - - - +
55B GLY* 1.3 74.3 - - - +
57B ALA* 1.3 58.8 + - - +
59B LEU* 3.4 2.9 + - - +
60B LEU* 3.0 61.5 + - + +
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Residues in contact with ALA 57 (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 CYS* 3.5 35.7 - - + +
16B ALA* 3.4 9.6 - - - +
42B MET* 3.9 15.9 - - + +
45B ILE* 4.2 12.1 - - + -
53B ALA 2.8 18.6 + - - +
54B ALA 4.1 2.5 - - - +
56B PHE* 1.3 74.1 - - - +
58B GLY* 1.3 60.1 - - - +
60B LEU* 3.3 3.6 + - - -
61B TRP* 2.9 25.5 + - - +
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Residues in contact with GLY 58 (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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42B MET* 3.6 16.7 - - - -
54B ALA 2.8 18.0 + - - -
57B ALA* 1.3 77.4 - - - +
59B LEU* 1.3 56.1 + - - +
61B TRP* 3.1 5.1 + - - +
62B GLY 2.8 23.6 + - - -
87B PHE* 3.2 27.0 - - - +
90B ILE* 4.0 6.3 - - - -
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Residues in contact with LEU 59 (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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80A ILE* 3.5 31.0 - - + +
84A ILE* 3.5 22.9 - - + -
85A LEU* 3.6 20.2 - - + -
55B GLY 2.9 19.1 + - - +
56B PHE* 3.8 4.7 - - - +
58B GLY* 1.3 71.1 - - - +
60B LEU* 1.3 60.9 + - - +
62B GLY 3.2 0.8 + - - +
63B LEU* 2.8 47.2 + - + +
83B TYR 4.6 1.1 - - - +
84B ILE* 3.7 31.0 - - + +
87B PHE* 3.5 6.5 + - - -
88B SER* 3.5 17.7 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.9 12.3 - - + -
12B CYS 4.3 2.5 - - - +
13B ALA* 3.9 30.7 - - + +
16B ALA* 3.7 8.3 - - + -
56B PHE* 3.0 58.8 + - + +
57B ALA 3.5 7.4 - - - +
58B GLY 3.3 0.2 - - - -
59B LEU* 1.3 75.4 - - - +
61B TRP* 1.3 58.0 + - - +
63B LEU* 3.3 12.8 + - + +
64B LEU* 3.0 37.6 + - + +
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.8 15.4 - - + +
19B ALA* 3.4 14.4 + - + -
20B MET* 3.6 22.3 - - - +
23B SER* 3.0 29.0 + - - -
36B SER* 3.2 24.9 - - - -
38B GLY* 3.5 23.6 - - - -
39B MET* 3.8 7.9 - - - -
42B MET* 3.5 31.0 - - + -
57B ALA 2.9 13.7 + - - +
58B GLY* 3.1 8.7 + - - +
60B LEU* 1.3 75.8 - - - +
62B GLY* 1.3 54.4 + - - +
64B LEU* 3.4 11.4 + - - +
65B HIS* 2.7 32.7 + + - -
87B PHE* 3.5 26.2 - + - -
90B ILE* 3.8 6.1 - - + -
127B ARG* 3.6 14.4 - - - -
301B TPP 3.8 7.2 - - - -
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Residues in contact with GLY 62 (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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58B GLY 2.8 10.9 + - - -
59B LEU 3.2 3.1 + - - -
61B TRP* 1.3 77.2 - - - +
63B LEU* 1.3 59.4 + - - +
65B HIS* 3.3 24.7 + - - +
66B PHE* 4.0 2.1 - - - -
83B TYR* 3.3 31.5 - - - +
87B PHE* 3.6 19.0 - - - -
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Residues in contact with LEU 63 (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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80A ILE* 3.8 32.3 - - + -
84A ILE* 4.9 6.5 - - + -
59B LEU* 2.8 38.1 + - + +
60B LEU* 3.8 11.7 - - + +
62B GLY* 1.3 68.2 - - - +
64B LEU* 1.3 63.2 + - + +
65B HIS 3.1 4.9 - - - -
66B PHE* 3.1 32.1 + - + +
67B LEU* 3.6 14.7 - - + +
84B ILE* 4.1 30.5 - - + -
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Residues in contact with LEU 64 (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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13B ALA 5.7 0.2 - - - +
16B ALA* 3.7 30.5 - - + +
17B ALA* 4.2 8.1 - - + -
20B MET* 3.6 22.0 - - + -
60B LEU* 3.0 25.8 + - + +
61B TRP* 3.6 7.4 - - - +
62B GLY 3.3 0.6 - - - -
63B LEU* 1.3 77.6 - - + +
65B HIS* 1.3 51.7 + - - +
67B LEU* 3.8 24.2 - - + +
68B THR* 2.6 44.9 + - + +
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Residues in contact with HIS 65 (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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20B MET* 4.0 13.0 - - + +
23B SER* 4.1 2.0 + - - -
61B TRP* 2.7 49.4 + + - -
62B GLY* 3.3 13.8 + - - +
63B LEU 3.1 0.4 - - - -
64B LEU* 1.3 78.3 - - - +
66B PHE* 1.3 55.9 + - - +
68B THR* 3.8 4.9 - - - -
69B GLY* 3.1 4.0 + - - -
70B LYS* 2.7 42.6 + - + -
71B ALA* 3.1 13.5 + - + +
83B TYR* 3.5 31.8 - + + -
87B PHE* 3.5 20.1 - + - -
301B TPP 2.5 28.2 + - - -
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Residues in contact with PHE 66 (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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62B GLY 4.0 6.3 - - - -
63B LEU* 3.1 24.1 + - + +
65B HIS* 1.3 76.9 - - - +
67B LEU* 1.3 69.8 + - + +
69B GLY* 3.2 12.6 + - - -
71B ALA* 4.1 10.1 - - + -
73B ILE* 3.9 29.6 - - + -
79B ALA* 3.8 24.2 - - + -
83B TYR* 3.8 29.2 - - + -
84B ILE* 4.3 19.5 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.6 19.5 - - + +
64B LEU* 3.4 26.3 + - + +
66B PHE* 1.3 86.2 - - + +
68B THR* 1.3 61.2 + - + +
69B GLY 3.3 0.8 + - - -
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Residues in contact with THR 68 (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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20B MET* 3.4 33.3 - - + +
24B PHE* 4.0 26.2 - - + -
64B LEU* 2.6 28.5 + - + +
65B HIS 3.8 2.9 + - - -
67B LEU* 1.3 80.4 - - + +
69B GLY* 1.3 62.6 + - - +
70B LYS* 3.3 3.5 + - - +
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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
------------------------------------------------------------
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