Contacts of the helix formed by residues 51 - 65 (chain E) in PDB entry 5XVO
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 ASN 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E ARG* 4.0 15.9 - - + +
6E MET* 4.3 7.3 - - - +
49E LEU* 4.3 5.0 - - - +
50E LEU* 1.3 89.5 - - - +
52E ASP* 1.3 64.3 + - - +
53E THR* 2.9 13.4 + - - +
54E ALA* 2.6 37.5 + - - +
55E ASN* 3.3 17.2 + - - +
17R A 2.9 31.0 + - - +
18R T 3.7 30.2 - - + +
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Residues in contact with ASP 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ARG* 3.4 22.6 + - - +
6E MET* 4.2 17.0 - - + +
51E ASN* 1.3 72.6 - - - +
53E THR* 1.3 79.7 + - - +
55E ASN* 3.4 11.1 - - + +
56E LYS* 3.0 44.5 + - + +
27Q A 4.1 9.6 - - + +
28Q C 3.2 34.6 + - - -
29Q A 5.0 0.7 + - - -
18R T 3.9 2.6 - - - +
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Residues in contact with THR 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ASN* 2.9 12.3 + - - -
52E ASP* 1.3 85.4 + - - +
54E ALA* 1.3 60.3 - - - +
56E LYS* 3.4 9.4 + - - +
57E ALA* 3.2 20.4 + - + +
29Q A 4.2 2.1 + - - -
16R C 3.5 39.5 - - + +
17R A 3.0 38.8 + - + +
18R T 3.4 9.7 + - - -
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Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 4.2 11.5 - - + +
50E LEU* 4.3 12.3 - - + +
51E ASN* 2.6 31.2 + - - +
53E THR* 1.3 73.0 - - - +
55E ASN* 1.3 59.3 + - - +
57E ALA* 3.4 8.2 + - - +
58E MET* 3.0 28.2 + - - +
61E ARG* 4.7 2.1 + - - -
16R C 5.6 6.1 - - - +
17R A 5.2 4.0 + - - +
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Residues in contact with ASN 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E MET* 4.2 12.6 - - - -
8E LEU* 4.0 1.7 - - - +
49E LEU* 3.4 28.1 - - + +
51E ASN 3.3 9.6 + - - +
52E ASP* 3.2 14.7 + - - +
54E ALA* 1.3 77.2 - - - +
56E LYS* 1.3 70.8 + - - +
58E MET* 3.1 2.8 + - - +
59E LEU* 2.9 38.2 + - - +
76E ASN* 3.1 40.3 + - - +
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASP* 3.0 39.9 + - - +
53E THR* 3.4 9.2 + - - +
55E ASN* 1.3 80.3 - - - +
57E ALA* 1.3 58.2 + - - +
59E LEU* 3.4 10.0 + - - +
60E ALA* 3.0 27.5 + - - +
27Q A 4.5 9.9 + - - +
28Q C 4.4 30.0 + - - -
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Residues in contact with ALA 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E THR* 3.2 11.2 + - + +
54E ALA* 3.5 12.6 - - - +
55E ASN 3.1 0.4 - - - -
56E LYS* 1.3 80.8 - - - +
58E MET* 1.3 57.2 + - - +
60E ALA* 3.3 8.1 + - - +
61E ARG* 3.1 40.7 + - - +
15R T 4.6 16.0 + - - +
16R C 5.1 8.3 - - - +
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Residues in contact with MET 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 4.0 21.8 - - + -
31E PHE* 3.8 24.2 - - + -
35E GLU* 3.4 34.1 - - + +
37E PHE* 3.8 22.9 - - + -
47E LYS* 4.8 12.1 - - + -
49E LEU* 4.4 14.1 - - + -
54E ALA 3.0 16.7 + - - +
55E ASN 3.1 4.2 + - - +
57E ALA* 1.3 73.4 - - - +
59E LEU* 1.3 60.0 + - - +
61E ARG* 3.1 16.8 + - + +
62E LEU* 2.8 37.6 + - + +
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.8 33.0 - - + -
55E ASN* 2.9 25.5 + - - +
56E LYS* 3.6 11.9 - - - +
58E MET* 1.3 75.9 - - - +
60E ALA* 1.3 63.1 + - - +
62E LEU* 3.1 8.9 + - + +
63E LYS* 3.1 44.1 + - - +
74E LEU* 4.6 14.8 - - + -
76E ASN* 4.6 8.5 - - - +
86F ILE* 3.7 28.9 - - + -
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LYS 3.0 14.0 + - - +
57E ALA* 3.3 13.5 - - - +
58E MET 3.1 0.4 - - - -
59E LEU* 1.3 76.7 - - - +
61E ARG* 1.3 62.0 + - - +
63E LYS* 3.3 11.2 + - - +
64E GLN* 3.2 27.4 + - - +
15R T 6.2 0.2 - - - +
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.8 8.5 - - + -
35E GLU* 2.2 46.6 + - - -
47E LYS* 6.2 0.4 - - - +
54E ALA 4.7 2.0 + - - -
57E ALA* 3.1 36.1 + - - +
58E MET* 3.1 33.5 + - + +
60E ALA* 1.3 76.3 - - - +
62E LEU* 1.3 62.1 + - - +
64E GLN* 3.2 16.8 + - - +
65E ASN* 2.7 34.0 + - - +
15R T 3.7 27.2 + - - +
16R C 5.1 6.5 + - - -
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 4.3 18.2 - - + -
10E LEU* 4.1 17.7 - - + -
28E PHE* 4.1 15.7 - - + -
31E PHE* 3.7 22.0 - - + -
32E LEU* 4.4 3.8 - - + -
37E PHE* 4.4 5.2 - - + -
58E MET* 2.8 27.9 + - + +
59E LEU* 3.1 11.0 + - - +
61E ARG* 1.3 79.3 - - - +
63E LYS* 1.3 57.3 + - - +
65E ASN 3.2 2.6 + - - -
66E ASN* 2.9 26.9 + - - -
74E LEU* 3.9 31.0 - - + -
88F LEU* 3.9 19.6 - - + +
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E LEU* 3.1 33.2 + - - +
60E ALA* 3.3 9.3 + - - +
62E LEU* 1.3 76.1 - - - +
64E GLN* 1.3 62.0 + - + +
65E ASN 3.4 0.5 + - - -
66E ASN* 3.4 18.5 + - - +
86F ILE* 5.5 12.1 - - - +
88F LEU* 4.2 18.8 - - + -
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Residues in contact with GLN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ALA* 3.2 15.9 + - - +
61E ARG* 3.5 25.2 - - - +
62E LEU 3.1 0.4 - - - -
63E LYS* 1.3 79.9 - - + +
65E ASN* 1.3 64.9 + - - +
66E ASN 3.4 1.4 + - - +
14R G 2.8 31.6 + - - -
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LYS* 5.7 7.8 + - - +
28E PHE* 3.7 10.7 - - - +
31E PHE* 3.5 47.2 - - + +
61E ARG* 2.7 30.8 + - - +
62E LEU 3.2 3.3 + - - +
64E GLN* 1.3 88.1 + - - +
66E ASN* 1.3 68.7 + - - +
67E PRO* 3.1 9.7 - - - +
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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