Contacts of the helix formed by residues 56 - 69 (chain B) in PDB entry 2X6L
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 GLU 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TYR* 5.8 0.3 - - - +
16B THR 5.0 7.7 - - - +
17B ALA* 6.1 0.2 - - - -
53B ASP* 3.6 40.1 - - + +
54B PRO 3.1 1.8 - - - -
55B SER* 1.3 81.4 - - - +
57B SER* 1.3 69.2 + - - +
58B TRP* 3.1 32.1 + - + -
59B VAL* 3.1 11.2 + - + +
60B GLN* 3.1 16.4 + - - +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER 4.0 1.8 + - - -
56B GLU* 1.3 73.8 - - - +
58B TRP* 1.3 65.3 + - - +
60B GLN* 3.1 9.7 + - - +
61B GLU* 3.0 41.1 + - - +
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Residues in contact with TRP 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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16B THR* 4.2 13.0 - - + -
18B ARG 3.7 15.7 - - - -
19B LYS* 3.6 48.7 - - + +
20B LEU* 3.6 31.4 - - + -
42B PHE* 3.8 28.0 - + - -
52B ALA* 4.4 3.4 - - + -
53B ASP 5.9 0.2 - - - -
56B GLU* 3.1 29.4 + - + -
57B SER* 1.3 79.6 - - - +
59B VAL* 1.3 76.2 + - + +
61B GLU* 3.4 9.1 + - - +
62B TYR* 3.1 58.5 + + + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.7 31.0 - - + -
42B PHE* 3.9 15.2 - - + -
52B ALA* 4.0 9.0 - - + -
53B ASP 3.1 31.4 - - - +
54B PRO* 4.1 5.6 - - + -
56B GLU* 3.1 8.0 + - + +
58B TRP* 1.3 109.2 - - + +
60B GLN* 1.3 61.4 + - - +
62B TYR* 3.2 4.0 + - - +
63B VAL* 2.9 28.2 + - + +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO 3.3 21.0 - - - +
55B SER* 4.0 10.9 - - - +
56B GLU 3.1 17.3 - - - +
57B SER* 3.5 8.0 + - - +
59B VAL* 1.3 75.9 - - - +
61B GLU* 1.3 61.0 + - + +
63B VAL* 3.7 6.7 - - - +
64B TYR* 2.8 51.6 + - + -
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.0 33.4 + - - +
58B TRP* 3.4 11.0 - - - +
59B VAL 3.2 0.2 - - - -
60B GLN* 1.3 79.0 - - - +
62B TYR* 1.3 65.3 + - + +
65B ASP* 3.1 23.6 + - - +
1070B GOL 2.5 66.1 + - - +
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Residues in contact with TYR 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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19B LYS* 3.3 20.9 - - - -
20B LEU 2.6 29.3 + - - -
22B ARG* 3.1 50.9 + - + +
25B VAL* 4.2 22.0 - - + -
42B PHE* 3.7 15.3 - + + -
58B TRP* 3.1 38.9 + + + +
59B VAL 3.7 7.0 - - - +
61B GLU* 1.3 80.4 - - + +
63B VAL* 1.3 62.4 + - - +
65B ASP* 3.7 5.9 - - + +
66B LEU* 2.9 39.9 + - + +
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Residues in contact with VAL 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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28B TYR* 3.8 43.4 - - + -
30B GLU* 4.9 4.7 - - - +
40B VAL* 3.9 25.8 - - + -
42B PHE* 4.4 3.4 - - + -
59B VAL* 2.9 20.0 + - + +
60B GLN* 3.3 8.3 + - - +
62B TYR* 1.3 78.2 - - - +
64B TYR* 1.3 66.3 + - + +
65B ASP 3.1 0.3 + - - -
66B LEU* 3.9 0.9 - - - +
67B GLU* 3.0 23.7 + - - +
24E PHE* 3.9 22.7 - - + -
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Residues in contact with TYR 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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60B GLN* 2.8 46.4 + - + +
63B VAL* 1.3 74.1 - - + +
65B ASP* 1.3 57.2 + - - +
68B LEU* 3.0 42.5 + - + +
1070B GOL 3.5 31.2 - - - -
21E PRO* 3.6 21.4 - - + +
23E ASN* 3.5 28.8 + - - -
24E PHE* 3.7 29.6 - + - -
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Residues in contact with ASP 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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22B ARG* 3.1 34.8 + - - +
61B GLU 3.1 19.3 + - - +
62B TYR* 3.8 6.7 - - - +
63B VAL 3.1 0.4 - - - -
64B TYR* 1.3 75.3 - - - +
66B LEU* 1.3 61.5 + - - +
69B ASN* 2.5 61.5 + - - +
1070B GOL 4.2 10.4 + - - +
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Residues in contact with LEU 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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22B ARG* 3.5 28.0 - - - +
25B VAL* 4.0 14.6 - - + +
26B VAL 4.0 24.9 - - - +
27B ASP* 3.8 26.0 - - - +
28B TYR* 3.8 25.4 - - + -
42B PHE* 4.2 5.6 - - + -
62B TYR* 2.9 20.4 + - + +
65B ASP* 1.3 77.2 - - - +
67B GLU* 1.3 62.9 + - - +
69B ASN 3.7 9.0 - - - +
46E ARG* 3.3 30.4 + - - +
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Residues in contact with GLU 67 (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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28B TYR* 2.5 29.2 + - - +
63B VAL 3.0 17.6 + - - +
64B TYR 3.9 3.1 - - - +
66B LEU* 1.3 80.2 - - - +
68B LEU* 1.3 65.7 + - + +
69B ASN 4.3 1.9 - - - +
24E PHE* 3.6 40.1 - - + -
44E THR* 3.3 21.2 + - - +
45E LYS* 3.5 19.0 + - + +
46E ARG* 3.0 52.0 + - - +
48E LYS* 4.3 2.4 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.0 30.2 + - + +
67B GLU* 1.3 93.0 - - + +
69B ASN* 1.3 69.7 + - - +
23E ASN* 3.2 48.2 - - + +
24E PHE* 3.9 4.9 - - + -
45E LYS* 3.2 39.4 + - + +
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Residues in contact with ASN 69 (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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65B ASP* 2.5 47.8 + - - +
66B LEU* 3.7 14.3 - - - +
67B GLU 4.3 1.6 - - - +
68B LEU* 1.3 88.9 - - - +
1070B GOL 5.8 0.6 + - - -
46E ARG* 5.3 1.9 + - - -
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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