Contacts of the helix formed by residues 46 - 65 (chain B) in PDB entry 3K0T
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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL 4.1 1.0 + - - -
45B GLU* 1.3 78.3 + - - +
47B ILE* 1.3 60.7 + - - -
48B GLU* 3.5 4.9 - - - -
49B ALA 3.3 2.7 + - - -
50B GLN* 2.9 31.3 + - - +
116B GLN* 3.9 8.6 - - - +
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Residues in contact with ILE 47 (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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46B GLY* 1.3 68.4 - - - -
48B GLU* 1.3 81.2 + - + +
50B GLN* 3.1 1.7 + - + -
51B ILE* 2.9 58.0 + - + +
79B LEU* 4.8 1.6 - - + -
84B HIS* 3.6 52.7 - - + +
87B LYS* 5.2 4.7 - - + -
116B GLN* 3.6 35.8 - - + +
117B VAL* 4.5 10.5 - - + -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY* 3.5 2.3 - - - -
47B ILE* 1.3 90.5 + - - +
49B ALA* 1.3 62.4 + - - +
51B ILE* 3.4 2.7 + - - +
52B THR* 2.9 30.6 + - - +
87B LYS* 3.8 37.6 + - + +
91B ILE* 3.9 14.0 - - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.5 15.6 - - + +
45B GLU 3.3 24.7 - - - +
46B GLY* 3.3 1.4 + - - -
47B ILE 3.3 0.2 - - - -
48B GLU* 1.3 79.6 - - - +
50B GLN* 1.3 58.1 + - - +
52B THR* 3.5 6.3 + - - -
53B GLN* 2.8 30.7 + - - +
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Residues in contact with GLN 50 (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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35B PRO* 3.4 27.4 - - + +
43B LEU* 4.3 17.2 - - - +
44B VAL* 3.1 28.3 + - + +
45B GLU* 4.8 3.4 + - - +
46B GLY 2.9 22.8 + - - +
47B ILE* 3.1 6.3 + - + +
49B ALA* 1.3 73.3 - - - +
51B ILE* 1.3 64.5 + - - +
53B GLN* 3.2 2.8 + - - +
54B VAL* 3.0 27.2 + - - +
114B GLY 5.2 1.4 + - - -
115B ALA* 4.9 0.4 - - - +
116B GLN* 3.0 49.7 + - - +
117B VAL* 4.0 7.1 + - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 2.9 43.2 + - + +
48B GLU 3.8 3.6 - - - +
50B GLN* 1.3 74.7 - - - +
52B THR* 1.3 64.4 + - - +
54B VAL* 3.2 5.7 + - - +
55B PHE* 3.1 45.0 + - + -
84B HIS 4.5 0.7 - - - +
87B LYS* 3.9 18.4 - - + -
88B VAL* 3.5 41.3 - - + +
91B ILE* 3.7 17.9 - - + -
117B VAL* 4.0 11.9 - - + -
119B MSE 4.0 8.5 - - + -
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Residues in contact with THR 52 (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 GLU* 2.9 19.5 + - - +
49B ALA* 3.7 7.0 - - - -
51B ILE* 1.3 76.3 - - - +
53B GLN* 1.3 57.2 + - - +
55B PHE* 3.2 4.8 + - - +
56B GLU* 2.9 34.4 + - + +
91B ILE* 4.0 22.2 - - - +
95B TYR* 3.3 22.0 - - + +
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Residues in contact with GLN 53 (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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35B PRO* 3.8 15.3 - - + +
36B LEU 3.4 23.5 + - - +
37B ASP* 4.3 7.8 - - - +
38B PRO* 3.6 11.9 - - - +
44B VAL* 3.8 22.5 - - + +
49B ALA 2.8 20.8 + - - +
50B GLN 3.2 4.7 + - - +
52B THR* 1.3 73.3 - - - +
54B VAL* 1.3 58.5 + - - +
56B GLU* 3.2 14.0 + - - +
57B ASN* 2.8 58.7 + - - +
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Residues in contact with VAL 54 (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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33B GLN* 3.6 20.2 - - + +
34B ILE 3.6 30.3 - - - -
35B PRO* 3.6 9.6 - - + -
50B GLN 3.0 18.7 + - - +
51B ILE 3.2 7.6 + - - +
53B GLN* 1.3 74.9 - - - +
55B PHE* 1.3 56.9 + - - +
57B ASN* 3.2 4.7 + - - +
58B LEU* 2.9 34.6 + - + +
117B VAL* 4.0 13.5 - - + +
119B MSE 3.7 36.3 - - + +
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Residues in contact with PHE 55 (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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51B ILE* 3.1 39.8 + - + -
52B THR 3.7 5.8 - - - +
54B VAL* 1.3 77.1 - - - +
56B GLU* 1.3 57.6 + - - +
58B LEU* 3.4 6.2 + - + -
59B LYS* 2.8 26.6 + - - +
69B PHE* 3.1 28.6 - + - -
75B LEU* 4.3 7.0 - - + -
88B VAL* 4.4 3.8 - - + -
91B ILE* 3.8 15.5 - - + -
92B MSE 3.7 40.2 - - + -
95B TYR* 3.7 25.6 - + + -
96B PHE* 3.7 18.4 - + - -
119B MSE 3.4 31.9 - - + -
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Residues in contact with GLU 56 (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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52B THR* 2.9 28.2 + - + +
53B GLN* 3.6 18.6 - - - +
55B PHE* 1.3 75.4 - - - +
57B ASN* 1.3 59.2 + - - +
59B LYS* 3.2 15.5 + - - +
60B SER* 3.0 32.4 + - - -
95B TYR* 2.6 31.7 + - - +
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Residues in contact with ASN 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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10B LYS 5.1 0.2 - - - +
11B ALA* 4.0 1.3 - - - +
12B PRO* 3.5 26.6 - - + +
33B GLN* 3.3 21.2 + - + +
34B ILE 3.0 26.5 + - - -
36B LEU 3.2 18.6 + - - +
38B PRO* 3.7 6.4 - - - +
53B GLN* 2.8 37.7 + - - +
54B VAL 3.6 4.3 - - - +
56B GLU* 1.3 77.2 - - - +
58B LEU* 1.3 62.9 + - - +
60B SER* 3.2 8.8 + - - +
61B VAL* 3.1 25.6 + - - +
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Residues in contact with LEU 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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30B MSE 3.2 31.4 - - + +
31B SER 4.0 9.2 - - - +
33B GLN* 3.7 22.4 - - + -
54B VAL* 2.9 23.4 + - + +
55B PHE* 3.8 11.4 - - + +
57B ASN* 1.3 76.7 - - - +
59B LYS* 1.3 57.0 + - - +
61B VAL* 3.3 0.8 + - - -
62B ALA* 2.8 27.5 + - - +
69B PHE* 3.7 11.8 - - + -
72B ILE* 5.5 1.1 - - + -
75B LEU* 4.2 19.7 - - + -
119B MSE 3.9 37.0 - - + +
120B ASP* 4.5 7.4 - - - +
121B ALA* 4.7 4.0 - - + +
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Residues in contact with LYS 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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55B PHE 2.8 18.1 + - - +
56B GLU* 3.4 18.0 + - - +
57B ASN 3.1 0.2 - - - -
58B LEU* 1.3 74.7 - - - +
60B SER* 1.3 66.2 + - - +
62B ALA* 3.2 1.6 + - + +
63B GLN* 2.9 57.5 + - + +
68B SER* 6.5 0.7 - - - -
69B PHE* 3.4 23.5 - - + +
95B TYR* 4.5 24.5 - - + -
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Residues in contact with SER 60 (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 SER* 3.4 26.0 + - - -
10B LYS* 3.7 18.6 + - - +
11B ALA* 3.8 13.2 - - - -
56B GLU 3.0 14.5 + - - -
57B ASN* 3.2 9.0 + - - -
59B LYS* 1.3 75.9 - - - +
61B VAL* 1.3 56.7 + - - +
63B GLN* 3.3 12.5 + - - +
64B ALA 2.9 24.3 + - - -
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Residues in contact with VAL 61 (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* 3.7 4.4 - - + +
8B SER* 4.2 5.6 - - - -
11B ALA* 3.6 11.7 - - + -
20B GLN* 3.6 32.8 - - + +
21B ALA* 3.6 27.8 - - + -
30B MSE 3.5 22.7 - - + -
33B GLN* 3.8 19.1 - - + +
57B ASN 3.1 14.2 + - - +
58B LEU* 3.8 1.6 - - - +
60B SER* 1.3 75.1 - - - +
62B ALA* 1.3 58.3 + - - +
64B ALA* 3.2 4.3 + - - +
65B ALA* 2.9 26.7 + - + +
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Residues in contact with ALA 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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30B MSE 3.5 7.4 - - + +
58B LEU 2.8 17.2 + - - +
59B LYS* 3.6 9.0 - - - +
61B VAL* 1.3 75.8 - - - +
63B GLN* 1.3 59.8 - - - +
65B ALA* 3.1 10.2 + - - +
67B GLY* 2.9 26.8 + - - +
68B SER* 4.2 16.8 - - - -
69B PHE* 4.4 7.4 - - + -
123B LEU* 3.7 27.1 - - + +
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Residues in contact with GLN 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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59B LYS* 2.9 52.6 + - + +
60B SER* 3.7 11.7 + - - +
62B ALA* 1.3 73.3 - - + +
64B ALA* 1.3 61.2 + - - +
66B GLY* 2.9 19.8 + - - -
67B GLY 3.5 14.4 - - - +
68B SER* 5.3 5.6 - - - -
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Residues in contact with ALA 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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6B ILE* 3.8 14.2 - - + +
7B THR 3.7 17.5 - - - +
8B SER* 3.6 31.9 - - - +
60B SER 2.9 6.1 + - - -
61B VAL 3.5 8.5 - - - +
63B GLN* 1.3 76.1 - - - +
65B ALA* 1.3 57.7 - - - +
66B GLY* 3.1 3.7 + - - -
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Residues in contact with ALA 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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6B ILE* 3.7 18.8 - - + +
23B LYS* 4.2 13.7 - - - +
28B VAL* 3.9 35.0 - - + -
30B MSE 6.2 0.2 - - + -
61B VAL 2.9 12.8 + - - +
62B ALA* 3.1 14.0 + - - +
64B ALA* 1.3 76.6 - - - +
66B GLY* 1.3 61.0 + - - +
67B GLY 3.3 1.1 - - - +
123B LEU* 4.7 3.6 - - + -
125B ILE* 3.7 11.3 - - - +
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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