Contacts of the strand formed by residues 50 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET 4.3 1.0 + - - +
2C ASN* 3.6 23.1 + - + +
3C LEU* 3.0 29.3 + - - +
39C LEU* 5.9 0.3 - - - +
47C GLU* 3.2 43.3 - - + -
48C ASP* 3.2 14.1 + - - -
49C ILE* 1.3 73.1 - - - +
51C GLY* 1.3 62.2 + - - +
99C GLY* 3.3 9.9 - - - +
100C LYS* 3.4 39.0 - - + -
101C ILE* 4.3 1.6 - - - -
117C ASN* 4.6 6.5 - - - -
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Residues in contact with GLY 51 (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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2C ASN* 5.1 1.3 + - - -
3C LEU* 4.2 11.4 - - - -
50C PHE* 1.3 74.7 - - - +
52C ASP* 1.3 63.5 + - - +
65C LEU* 5.2 2.2 - - - -
79C ILE* 4.2 6.1 - - - -
97C ILE 4.9 0.2 - - - -
98C SER* 4.0 1.1 - - - -
99C GLY 2.8 31.0 + - - +
101C ILE* 3.6 27.5 - - - +
113C LEU* 6.5 0.7 - - - -
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Residues in contact with ASP 52 (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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2C ASN* 5.1 4.3 - - - +
3C LEU* 4.5 6.0 - - - +
4C THR* 3.0 34.1 + - - +
7C LYS* 6.0 0.9 - - - +
51C GLY* 1.3 75.7 - - - +
53C GLY* 1.3 71.4 + - - +
65C LEU* 4.1 3.6 - - - +
67C SER* 4.7 10.9 - - - -
79C ILE* 3.4 23.1 - - - +
96C THR* 3.9 14.6 - - - +
97C ILE 3.2 16.6 - - - +
98C SER* 3.7 14.2 + - - +
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Residues in contact with GLY 53 (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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52C ASP* 1.3 86.9 + - - +
54C VAL* 1.3 64.3 + - - -
65C LEU* 3.5 19.8 - - - +
66C ARG 3.4 11.4 - - - -
67C SER* 4.5 4.3 - - - -
96C THR* 3.7 3.7 - - - -
97C ILE 3.1 26.6 + - - -
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Residues in contact with VAL 54 (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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53C GLY* 1.3 73.4 - - - -
55C LEU* 1.3 67.7 + - - +
56C GLU* 3.6 1.4 + - - +
64C PHE 3.3 1.4 - - - +
65C LEU* 4.1 0.4 - - - -
66C ARG* 2.6 38.0 + - - +
68C ALA* 5.8 0.7 - - + +
72C TYR* 3.6 25.8 - - + +
94C GLY* 3.5 32.5 - - - +
95C ASP 3.3 3.1 - - - -
96C THR* 3.6 10.1 - - + +
226C GLU* 5.4 0.4 - - - +
245C MET* 4.5 11.9 - - + +
249C LYS* 3.6 36.1 - - + +
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Residues in contact with LEU 55 (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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54C VAL* 1.3 74.7 - - - +
56C GLU* 1.3 62.0 + - - +
57C ILE* 3.9 20.0 - - + -
63C GLY* 4.0 9.2 - - - -
64C PHE 3.0 30.3 - - - +
65C LEU* 3.8 3.9 - - + +
81C VAL* 3.9 23.3 - - + -
86C ILE* 4.6 2.9 - - + -
91C LEU* 3.8 27.4 - - + -
92C ARG 3.6 21.8 - - - +
93C THR* 3.2 2.1 + - - -
94C GLY* 2.8 28.6 + - - -
95C ASP* 2.7 18.5 + - + +
97C ILE* 3.9 17.7 - - + -
245C MET* 4.2 2.1 - - - +
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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