Contacts of the helix formed by residues 56 - 69 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C TYR* 5.3 0.5 - - - +
16C THR 4.0 15.8 - - - +
53C ASP* 3.1 40.1 + - + +
54C PRO 3.5 5.2 - - - +
55C SER* 1.3 83.8 - - - +
57C SER* 1.3 63.3 + - - +
58C TRP* 3.4 29.4 + - + +
59C VAL* 3.7 9.4 - - + +
60C GLN* 3.3 20.3 + - - +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C SER 3.9 1.0 + - - -
56C GLU* 1.3 73.1 - - - +
58C TRP* 1.3 63.6 + - - +
60C GLN* 3.6 4.7 + - - +
61C GLU* 2.9 31.8 + - - +
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Residues in contact with TRP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR* 3.9 24.5 - - + -
18C ARG 5.1 0.4 - - - -
19C LYS* 3.7 42.7 - - + +
20C LEU* 4.1 17.0 - - + -
42C PHE* 3.5 28.9 - + - -
52C ALA* 4.1 5.8 - - + -
56C GLU* 3.5 31.9 + - + -
57C SER* 1.3 80.4 + - - +
59C VAL* 1.3 81.2 + - + +
61C GLU* 4.0 11.7 - - - +
62C TYR* 2.8 67.6 + + + -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.7 31.6 - - + -
42C PHE* 3.5 8.7 - - + -
52C ALA* 3.5 22.9 - - + -
53C ASP 3.1 29.8 - - - +
54C PRO* 4.0 7.0 - - + +
56C GLU* 3.7 9.4 - - + +
58C TRP* 1.3 106.2 - - + +
60C GLN* 1.3 59.2 + - - +
62C TYR* 3.1 2.9 + - - +
63C VAL* 2.9 30.5 + - + +
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 5.5 2.0 + - - -
40C VAL* 4.7 6.1 - - - +
54C PRO* 2.9 42.9 + - - +
55C SER 5.3 0.4 - - - -
56C GLU 3.3 10.1 + - - +
57C SER* 4.0 5.4 - - - +
58C TRP 3.3 0.2 - - - -
59C VAL* 1.3 81.2 - - - +
61C GLU* 1.3 65.0 + - - +
63C VAL* 4.3 11.7 - - - +
64C TYR* 2.8 54.3 + - + -
24D PHE* 6.0 0.2 - - - -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 5.0 5.4 + - - -
57C SER* 2.9 22.1 + - - +
58C TRP* 3.5 10.6 - - - +
59C VAL 3.2 0.2 - - - -
60C GLN* 1.3 76.5 - - - +
62C TYR* 1.3 81.0 + - + +
64C TYR* 3.4 6.8 + - - +
65C ASP* 3.1 22.5 + - + +
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Residues in contact with TYR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.1 23.6 + - - -
20C LEU 2.6 31.0 + - - -
22C ARG* 3.1 49.8 + - + +
25C VAL* 4.3 17.3 - - + -
42C PHE* 3.6 17.3 - + + -
58C TRP* 2.8 45.0 + + + +
59C VAL 3.4 8.3 - - - +
61C GLU* 1.3 93.0 - - + +
63C VAL* 1.3 64.9 + - - +
65C ASP* 3.2 6.5 + - - +
66C LEU* 3.0 31.4 + - + +
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 3.7 33.0 - - + +
30C GLU* 5.6 2.5 - - - +
40C VAL* 4.0 36.8 - - + -
42C PHE* 4.1 3.3 - - + -
59C VAL* 2.9 21.6 + - + +
60C GLN* 3.8 18.2 - - - +
61C GLU 3.4 0.2 - - - -
62C TYR* 1.3 75.6 - - - +
64C TYR* 1.3 62.3 + - + +
66C LEU* 3.4 7.2 + - - +
67C GLU* 3.0 22.9 + - - +
24D PHE* 3.9 17.3 - - + -
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Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 2.8 52.2 + - + +
61C GLU* 3.7 6.7 - - - +
62C TYR 3.2 0.2 - - - -
63C VAL* 1.3 74.0 - - - +
65C ASP* 1.3 67.2 + - - +
67C GLU 3.3 0.3 + - - -
68C LEU* 3.0 44.3 + - + +
21D PRO* 3.7 21.8 - - + +
23D ASN* 5.5 5.6 - - - -
24D PHE* 3.8 33.7 - + - -
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 2.8 35.3 + - - +
61C GLU* 3.1 17.4 + - + +
62C TYR* 3.7 4.5 - - - +
64C TYR* 1.3 76.6 - - - +
66C LEU* 1.3 58.0 + - - +
69C ASN* 2.5 68.2 + - - +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 3.4 26.7 - - - +
25C VAL* 3.9 19.3 - - + +
26C VAL 4.0 25.8 - - - +
27C ASP* 4.0 4.0 - - - -
28C TYR* 3.5 42.0 - - + -
42C PHE* 4.2 7.0 - - + -
62C TYR* 3.0 21.6 + - + +
63C VAL 3.7 3.6 - - - +
65C ASP* 1.3 78.3 - - - +
67C GLU* 1.3 61.2 + - - +
69C ASN 3.7 10.7 - - - +
46D ARG* 3.1 23.8 - - - +
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 2.7 26.4 + - + +
63C VAL 3.0 17.2 + - - +
65C ASP 3.3 0.2 - - - -
66C LEU* 1.3 80.0 - - - +
68C LEU* 1.3 60.0 + - - +
69C ASN 4.6 1.4 - - - +
24D PHE* 3.5 45.7 - - + -
44D THR* 3.2 16.1 + - - +
45D LYS* 2.9 39.4 + - + +
46D ARG* 2.8 48.6 + - - +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C TYR* 3.0 36.4 + - + +
67C GLU* 1.3 85.3 - - - +
69C ASN* 1.3 70.8 + - - +
23D ASN* 3.2 45.1 - - + +
24D PHE* 4.1 11.4 - - + -
45D LYS* 3.7 18.6 - - + +
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Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASP* 2.5 47.6 + - - +
66C LEU* 3.7 12.7 - - - +
67C GLU 4.6 1.9 - - - +
68C LEU* 1.3 91.7 - - - +
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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