Contacts of the helix formed by residues 45 - 61 (chain B) in PDB entry 6B3I
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 THR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B ARG* 1.3 76.3 - - - +
46B SER* 1.3 60.1 + - - +
47B ASP* 3.7 6.8 + - - +
48B GLU* 3.0 37.5 + - - +
49B ARG* 2.8 29.6 + - - +
277B GLU* 3.3 19.1 - - - +
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Residues in contact with SER 46 (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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45B THR* 1.3 71.6 - - - +
47B ASP* 1.3 58.2 + - - +
49B ARG* 3.2 27.4 + - - +
50B GLN* 2.9 34.8 + - - +
85B ASP 4.4 3.8 + - - -
86B HIS* 4.6 6.2 - - - -
87B PRO* 3.7 29.0 - - - +
277B GLU* 2.7 25.3 + - - -
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Residues in contact with ASP 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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45B THR* 3.3 6.7 + - - +
46B SER* 1.3 78.5 - - - +
48B GLU* 1.3 65.3 + - + +
50B GLN* 3.3 10.2 + - - +
51B GLN* 3.0 51.0 + - - +
277B GLU* 5.2 0.8 + - - -
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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
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14A PHE* 3.4 55.9 - - + +
43B GLY 4.5 1.0 - - - +
44B ARG* 3.4 17.3 - - + -
45B THR* 3.0 41.1 + - - +
47B ASP* 1.3 81.0 - - - +
49B ARG* 1.3 58.2 + - - +
51B GLN* 3.2 5.6 + - - +
52B ILE* 2.9 34.6 + - - +
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Residues in contact with ARG 49 (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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40B ILE* 4.6 4.0 - - + +
41B LEU* 3.3 38.3 + - + +
44B ARG* 3.3 22.8 + - + -
45B THR 2.8 13.8 + - - +
46B SER* 3.2 47.9 + - - +
48B GLU* 1.3 76.1 - - - +
50B GLN* 1.3 61.5 + - - +
52B ILE* 3.7 9.9 - - + +
53B LYS* 2.9 29.3 + - - +
83B LEU* 2.4 62.5 + - - +
84B LEU* 4.6 12.2 - - + +
85B ASP 4.6 1.4 + - - -
276B ALA* 5.6 6.1 - - - +
277B GLU* 4.0 6.7 + - - +
314B LEU* 6.1 0.2 - - - +
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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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46B SER* 2.9 22.7 + - - +
47B ASP* 3.6 11.9 - - - +
48B GLU 3.2 0.2 - - - -
49B ARG* 1.3 75.8 - - - +
51B GLN* 1.3 64.6 + - + +
53B LYS* 3.4 22.7 + - - +
54B GLN* 3.0 26.0 + - - +
83B LEU 4.8 2.0 + - - -
84B LEU* 2.9 33.5 + - - +
85B ASP 3.9 12.7 + - - -
86B HIS* 3.6 37.2 - - + +
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Residues in contact with GLN 51 (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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14A PHE* 3.3 24.3 - - + -
16A VAL* 3.6 16.6 - - + +
47B ASP* 3.0 36.6 + - - +
48B GLU* 3.2 8.4 + - - +
50B GLN* 1.3 77.1 - - + +
52B ILE* 1.3 56.8 + - - +
54B GLN* 3.4 7.4 + - - +
55B LYS* 2.9 31.5 + - - +
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Residues in contact with ILE 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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14A PHE* 4.0 17.7 - - + -
16A VAL* 4.0 11.2 - - + -
19A ASP* 3.6 31.9 - - + +
20A ALA* 4.1 17.2 - - - +
23A LEU* 3.8 27.4 - - + -
40B ILE* 4.0 8.3 - - + -
44B ARG* 4.0 17.0 - - + -
48B GLU 2.9 21.4 + - - +
49B ARG* 3.7 8.7 - - + +
50B GLN 3.3 0.2 - - - -
51B GLN* 1.3 74.9 - - - +
53B LYS* 1.3 58.5 + - - +
55B LYS* 3.7 1.8 - - - +
56B TYR* 2.9 29.4 + - + +
64B LEU* 4.9 3.1 - - + -
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Residues in contact with LYS 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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49B ARG 2.9 17.2 + - - +
50B GLN* 3.4 26.1 + - - +
52B ILE* 1.3 78.1 - - - +
54B GLN* 1.3 60.8 + - - +
56B TYR* 3.6 3.3 + - - +
57B LYS* 3.5 21.0 + - - +
63B GLU* 5.4 5.6 - - - +
64B LEU* 4.2 31.8 + - + +
65B GLU* 3.6 34.7 + - + +
84B LEU* 2.6 36.5 + - + +
85B ASP* 4.7 3.2 + - - +
89B GLU* 5.4 3.2 + - - -
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Residues in contact with GLN 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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50B GLN 3.0 16.5 + - - +
51B GLN* 3.9 6.5 - - - +
53B LYS* 1.3 75.7 - - - +
55B LYS* 1.3 65.1 + - - +
56B TYR 3.4 0.2 + - - -
57B LYS* 3.4 5.4 + - - +
58B ALA* 3.2 22.2 + - + +
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Residues in contact with LYS 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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16A VAL* 3.6 29.1 - - + +
17A ASP* 3.2 38.6 + - - +
20A ALA* 4.5 6.5 - - + -
51B GLN 2.9 17.7 + - - +
52B ILE* 3.8 2.7 - - - +
54B GLN* 1.3 77.4 - - - +
56B TYR* 1.3 57.6 + - - +
58B ALA* 3.4 8.0 + - + +
59B THR* 3.0 43.1 + - - +
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Residues in contact with TYR 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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20A ALA* 3.7 20.8 - - + +
23A LEU* 4.3 5.8 - - + -
24A ASN* 3.2 52.4 + - + -
27A CYS* 4.1 12.0 - - - +
28A LYS* 4.4 2.8 + - - -
52B ILE* 2.9 17.7 + - + +
53B LYS 3.8 6.1 - - - +
54B GLN 3.2 0.4 - - - -
55B LYS* 1.3 77.4 - - - +
57B LYS* 1.3 56.5 + - - +
60B TYR* 2.9 47.7 + + + +
62B LYS* 3.4 20.8 - - + +
64B LEU* 3.8 44.0 - - + -
67B VAL* 4.2 17.9 - - + +
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Residues in contact with LYS 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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53B LYS 3.5 11.3 + - - +
54B GLN* 3.4 6.3 + - - +
55B LYS 3.4 0.2 - - - -
56B TYR* 1.3 79.8 - - - +
58B ALA* 1.3 58.9 + - - +
61B GLY* 3.0 49.2 + - - -
62B LYS* 3.2 27.2 + - - +
63B GLU* 3.4 35.8 - - - +
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Residues in contact with ALA 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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54B GLN* 3.2 18.2 + - + +
55B LYS* 3.8 10.5 - - + +
57B LYS* 1.3 82.3 - - - +
59B THR* 1.3 63.3 + - - +
61B GLY* 4.3 1.9 + - - -
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Residues in contact with THR 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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17A ASP* 4.6 6.5 + - - +
20A ALA* 6.0 0.6 - - - +
55B LYS* 3.0 28.9 + - - +
58B ALA* 1.3 80.7 - - - +
60B TYR* 1.3 94.1 + - + +
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Residues in contact with TYR 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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17A ASP 5.0 0.3 + - - -
20A ALA* 3.8 23.8 - - + -
21A LYS* 3.1 31.2 + - - +
24A ASN* 3.5 39.4 - - + +
56B TYR* 2.9 39.3 + + + +
59B THR* 1.3 103.0 - - + +
61B GLY* 1.3 63.6 + - - +
62B LYS* 3.1 20.6 + - + +
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Residues in contact with GLY 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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57B LYS* 3.0 34.0 + - - -
58B ALA 4.3 1.9 + - - -
59B THR 3.6 2.0 + - - -
60B TYR* 1.3 76.1 - - - +
62B LYS* 1.3 63.6 + - - +
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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