Contacts of the helix formed by residues 72 - 86 (chain B) in PDB entry 1T2K
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 ASP 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B LYS 4.3 4.0 - - - +
71B PRO* 1.3 75.3 - - - +
73B LEU* 1.3 68.3 + - - +
74B PRO* 3.4 10.3 - - - +
75B THR* 2.6 40.2 + - + -
76B TRP* 3.1 33.5 + - - +
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Residues in contact with LEU 73 (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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47B GLN* 6.2 0.2 - - - -
48B GLN* 3.5 38.4 - - + +
51B PHE* 3.1 47.5 - - + -
71B PRO* 4.2 5.2 - - + -
72B ASP* 1.3 79.5 - - - +
74B PRO* 1.3 79.0 - - + +
76B TRP* 3.0 32.1 + - + +
77B LYS* 3.0 13.9 + - - +
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Residues in contact with PRO 74 (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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41B GLY* 6.5 0.7 - - - -
51B PHE* 4.4 3.4 - - + -
72B ASP* 3.1 8.0 - - - +
73B LEU* 1.3 99.6 - - + +
75B THR* 1.3 58.5 + - - +
77B LYS* 3.4 3.3 + - - +
78B ARG* 2.9 30.0 + - - +
17E A 3.7 37.2 - - + +
18E C 3.7 19.6 + - - +
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Residues in contact with THR 75 (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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72B ASP* 2.6 39.2 + - + +
74B PRO* 1.3 76.1 - - - +
76B TRP* 1.3 70.5 + - + +
78B ARG* 3.1 24.1 + - - +
79B ASN* 2.9 46.4 + - - +
11F T 4.2 9.0 - - - +
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Residues in contact with TRP 76 (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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48B GLN* 3.8 0.7 - - - -
51B PHE* 4.4 1.8 - - + -
54B PHE* 3.2 28.9 - - + +
55B GLN* 3.1 56.1 - - + -
57B TRP* 5.5 1.6 - - - -
58B ALA* 3.5 18.8 - - + +
63B ALA* 6.0 1.3 - - + +
64B TYR* 3.3 39.7 - + + +
71B PRO* 3.6 18.4 - - + -
72B ASP* 3.1 33.3 + - + +
73B LEU* 3.0 34.6 + - + +
75B THR* 1.3 81.4 - - + +
77B LYS* 1.3 62.7 + - - +
79B ASN* 4.1 3.8 - - - +
80B PHE* 3.1 24.1 + - - +
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Residues in contact with LYS 77 (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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38B TRP* 2.9 50.7 + - + +
39B LYS 3.2 26.1 + - - -
40B HIS* 4.7 0.6 - - - +
51B PHE* 3.8 13.4 - - + -
54B PHE* 3.5 32.7 - - + +
73B LEU 3.0 10.5 + - - +
74B PRO 3.7 7.4 - - - +
76B TRP* 1.3 76.3 - - - +
78B ARG* 1.3 66.0 + - - +
80B PHE* 3.3 2.3 + - - +
81B ARG* 3.0 22.7 + - - +
18E C 3.2 36.2 + - - +
19E T 4.2 9.0 - - - +
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Residues in contact with ARG 78 (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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74B PRO 2.9 18.1 + - - +
75B THR* 3.1 30.3 + - - +
77B LYS* 1.3 79.5 - - - +
79B ASN* 1.3 84.8 + - - +
81B ARG* 3.2 18.5 + - - +
82B SER* 2.9 36.1 + - - +
18E C 6.6 0.2 - - - -
19E T 4.1 24.9 - - + +
20E G 5.2 0.7 - - - -
11F T 3.6 23.6 + - + +
12F T 3.2 42.3 + - + +
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TRP* 5.3 7.0 - - + -
75B THR* 2.9 28.1 + - - +
76B TRP* 4.2 4.3 - - - +
78B ARG* 1.3 104.4 + - - +
80B PHE* 1.3 64.0 + - - +
82B SER* 3.3 5.3 + - - -
83B ALA* 2.9 25.7 + - - +
10F T 2.7 62.3 + - - +
11F T 3.0 7.8 + - - +
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Residues in contact with PHE 80 (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 ILE* 4.4 12.3 - - + -
11B TRP* 5.2 3.4 - + - -
12B LEU* 4.2 20.4 - - + -
36B ILE* 4.6 14.1 - - + -
38B TRP* 5.4 4.3 - + - -
53B ILE* 3.6 27.1 - - + -
54B PHE* 3.1 41.3 - + + -
57B TRP* 4.8 17.9 - + + -
76B TRP 3.1 18.8 + - - +
77B LYS 3.7 3.6 - - - +
78B ARG 3.2 0.2 - - - -
79B ASN* 1.3 79.3 - - - +
81B ARG* 1.3 64.2 + - - +
83B ALA* 3.2 4.1 + - - +
84B LEU* 3.2 52.4 + - + +
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Residues in contact with ARG 81 (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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38B TRP* 3.8 26.6 - - + -
77B LYS 3.0 14.9 + - - +
78B ARG* 3.7 19.3 + - - +
80B PHE* 1.3 78.4 - - - +
82B SER* 1.3 70.2 + - - +
84B LEU* 3.3 3.0 + - - +
85B ASN* 2.9 38.8 + - - +
105B LYS* 5.2 3.6 - - - +
107B TYR* 4.5 10.3 + - - +
18E C 4.7 0.2 - - - +
19E T 2.7 78.4 + - - +
20E G 2.8 45.6 + - - -
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Residues in contact with SER 82 (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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78B ARG* 2.9 25.1 + - - +
79B ASN 3.8 2.9 - - - -
81B ARG* 1.3 91.0 + - - +
83B ALA* 1.3 63.8 + - - +
85B ASN* 3.1 15.8 + - - +
86B ARG* 3.1 26.4 + - - +
20E G 5.6 0.2 + - - -
21E A 4.6 6.6 + - - -
10F T 4.0 10.5 - - - -
11F T 3.9 29.3 + - - +
12F T 4.9 0.3 + - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.5 15.3 - - + -
57B TRP* 5.3 1.8 - - - +
79B ASN 2.9 17.9 + - - +
80B PHE* 3.7 5.4 - - - +
82B SER* 1.3 77.2 - - - +
84B LEU* 1.3 64.6 + - - +
86B ARG* 3.6 10.2 + - - +
87B LYS* 3.7 18.7 - - - +
9F C 4.2 34.1 - - - +
10F T 3.8 13.4 - - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.5 27.6 - - + -
9B LEU* 4.8 7.2 - - + -
12B LEU* 4.9 5.6 - - + -
34B PHE* 4.6 7.9 - - + -
36B ILE* 5.9 0.2 - - + -
38B TRP* 6.0 0.2 - - + -
80B PHE* 3.2 38.8 + - + +
81B ARG* 3.7 7.0 - - - +
83B ALA* 1.3 78.1 - - - +
85B ASN* 1.3 67.1 + - - +
87B LYS* 3.2 20.5 + - + +
90B LEU* 3.4 31.2 - - + +
107B TYR* 3.5 46.9 - - + +
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Residues in contact with ASN 85 (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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81B ARG* 2.9 31.1 + - - +
82B SER* 3.1 7.6 + - - +
84B LEU* 1.3 78.1 - - - +
86B ARG* 1.3 73.1 + - - +
87B LYS 3.2 4.3 + - - -
88B GLU 4.7 1.4 + - - -
90B LEU 5.3 2.6 - - - +
92B LEU* 5.4 10.4 - - - +
107B TYR* 6.0 2.0 - - - -
20E G 2.8 46.7 + - - +
21E A 5.7 0.3 + - - -
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 6.0 0.2 - - - +
82B SER* 3.1 30.8 + - - +
83B ALA 4.0 6.5 - - - +
84B LEU 3.3 0.4 - - - -
85B ASN* 1.3 91.8 - - - +
87B LYS* 1.3 65.9 + - + +
88B GLU* 3.5 5.3 + - - +
20E G 5.4 2.2 + - - +
21E A 4.0 17.2 + - - +
22E A 3.6 29.4 + - - +
23E A 5.0 2.4 - - - +
9F C 4.1 27.7 - - + +
10F T 3.5 26.1 + - - +
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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