Contacts of the strand formed by residues 50 - 57 (chain E) in PDB entry 1XPU
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 PHE 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MET 3.6 4.4 + - - -
2E ASN* 3.4 41.5 - - + +
3E LEU* 3.5 14.5 + - - +
47E GLU 4.8 9.9 - - - -
48E ASP* 3.4 21.7 + - - -
49E ILE* 1.3 83.6 - - - +
51E GLY* 1.3 61.3 + - - +
99E GLY* 3.6 9.6 - - - +
100E LYS* 5.1 8.7 - - + -
101E ILE* 3.5 14.6 - - - +
117E ASN* 4.0 26.0 - - - -
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Residues in contact with GLY 51 (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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2E ASN* 4.9 1.6 - - - -
3E LEU* 3.9 18.6 - - - -
50E PHE* 1.3 78.9 - - - +
52E ASP* 1.3 63.8 + - - +
65E LEU* 6.0 0.7 - - - -
79E ILE* 4.6 2.0 - - - -
98E SER* 3.7 0.9 - - - -
99E GLY 2.9 34.1 + - - +
101E ILE* 4.0 13.9 - - - -
113E LEU* 5.8 0.6 - - - +
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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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2E ASN* 4.7 0.2 - - - +
3E LEU* 4.5 5.1 - - - +
4E THR* 3.2 40.4 + - - +
51E GLY* 1.3 76.8 - - - +
53E GLY* 1.3 61.7 + - - +
65E LEU* 4.7 3.2 - - - +
66E ARG 5.2 0.2 - - - -
67E SER* 5.1 7.3 - - - -
79E ILE* 3.7 20.6 - - - +
96E THR* 5.6 4.9 - - + +
97E ILE 3.0 17.0 - - - +
98E SER* 3.8 15.8 + - - +
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Residues in contact with GLY 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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52E ASP* 1.3 80.6 + - - +
54E VAL* 1.3 64.8 + - - -
65E LEU* 3.4 15.9 - - - +
66E ARG 3.4 14.4 - - - -
67E SER* 4.9 2.5 - - - -
96E THR* 3.4 7.7 - - - +
97E ILE 3.0 30.1 + - - -
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Residues in contact with VAL 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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53E GLY* 1.3 75.4 - - - +
55E LEU* 1.3 67.2 + - - +
56E GLU* 3.6 0.7 + - - +
64E PHE 3.5 0.9 - - - +
65E LEU* 4.0 0.4 - - - -
66E ARG* 2.7 37.4 + - - +
68E ALA* 5.7 1.1 - - + +
72E TYR* 3.5 31.2 - - + +
94E GLY* 3.6 30.7 - - - +
95E ASP 3.7 3.4 - - - -
96E THR* 4.4 4.5 - - + +
226E GLU* 5.6 0.2 - - - +
245E MET* 4.2 16.6 - - + +
249E LYS* 3.5 37.0 - - + +
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Residues in contact with LEU 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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54E VAL* 1.3 73.2 - - - +
56E GLU* 1.3 61.6 + - - +
57E ILE* 3.7 23.8 - - + -
63E GLY* 4.1 2.5 - - - -
64E PHE 3.4 22.4 - - - +
65E LEU* 3.7 9.3 - - + +
81E VAL* 3.7 31.0 - - + -
86E ILE* 3.8 5.2 - - + -
91E LEU* 3.6 27.6 - - + -
92E ARG 3.4 21.1 - - - +
93E THR* 3.3 3.6 - - - -
94E GLY 2.9 24.3 + - - -
95E ASP* 2.9 20.6 + - + +
97E ILE* 4.3 7.4 - - + -
245E MET* 4.0 5.1 - - - +
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Residues in contact with GLU 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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55E LEU* 1.3 72.7 - - - +
57E ILE* 1.3 66.7 + - - +
58E LEU* 3.4 13.3 + - + +
63E GLY* 3.2 2.0 - - - -
64E PHE 2.8 30.1 + - - +
66E ARG* 2.5 48.6 + - + +
93E THR* 4.5 4.3 - - + -
241E GLN* 3.2 22.6 + - - +
245E MET* 3.2 37.9 - - + +
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Residues in contact with ILE 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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55E LEU* 3.7 18.8 - - + -
56E GLU* 1.3 72.3 - - - +
58E LEU* 1.3 74.6 + - - +
61E GLY* 3.9 19.1 - - - +
62E PHE 3.8 7.4 - - - +
63E GLY* 3.7 4.7 - - - -
86E ILE* 3.8 22.7 - - + -
91E LEU 3.4 26.9 - - - +
92E ARG* 3.7 17.5 - - - -
93E THR* 3.4 22.4 - - + +
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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