Contacts of the strand formed by residues 55 - 60 (chain C) in PDB entry 1PR1
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 ARG 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ALA* 4.5 1.2 - - - +
14C ASP* 2.8 37.4 + - - -
15C VAL* 3.6 20.9 - - - +
51C THR* 3.1 3.6 - - - -
52C TYR* 2.8 40.1 + - + +
53C LYS 3.1 4.5 + - - +
54C GLY* 1.3 75.2 - - - +
56C LYS* 1.3 99.2 + - - +
57C ILE* 3.4 6.9 + - + +
232C VAL* 3.7 11.6 - - - +
233C LEU* 3.6 18.8 - - + -
236C ASP* 2.9 42.7 + - - +
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Residues in contact with LYS 56 (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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10C GLY* 2.9 28.6 + - - -
12C PHE 3.9 5.4 + - - -
13C ALA* 3.4 20.8 - - + +
49C THR* 3.8 23.3 - - + -
50C GLY 3.5 10.5 - - - +
51C THR* 3.9 9.1 - - + +
54C GLY 3.6 4.4 + - - -
55C ARG* 1.3 106.0 + - - +
57C ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 3.3 7.2 - - - -
15C VAL* 3.7 12.1 - - + +
17C LEU* 3.7 21.3 - - + -
33C LEU* 3.3 28.5 - - + +
49C THR* 3.5 1.2 - - - -
50C GLY 2.8 34.9 + - - +
52C TYR* 4.0 9.6 - - + +
55C ARG* 3.7 18.2 - - - +
56C LYS* 1.3 77.0 - - - +
58C SER* 1.3 74.4 + - - +
229C LEU* 3.2 29.8 - - + -
232C VAL* 4.7 14.4 - - + -
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Residues in contact with SER 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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12C PHE* 3.4 19.8 - - - -
13C ALA 2.8 26.9 + - - -
15C VAL 3.3 5.1 + - - -
16C VAL* 3.5 13.4 - - - -
17C LEU* 3.0 22.9 + - - +
33C LEU* 4.6 1.3 - - - -
48C PHE 3.0 12.6 - - - -
49C THR* 2.8 19.2 + - - -
57C ILE* 1.3 83.4 - - - +
59C VAL* 1.3 64.4 + - - +
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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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16C VAL* 4.2 0.7 - - - -
17C LEU* 3.2 19.5 - - + +
19C PRO* 4.2 3.6 - - + -
25C ALA* 3.6 37.5 - - + +
28C ILE* 3.8 27.1 - - + -
29C ALA* 4.0 11.7 - - + +
33C LEU* 4.2 10.1 - - + -
47C GLY* 3.4 1.0 - - - -
48C PHE* 2.8 56.3 + - + +
58C SER* 1.3 77.3 - - - +
60C MET* 1.3 62.3 + - - +
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Residues in contact with MET 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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5C ILE* 4.0 13.2 - - + -
12C PHE* 3.8 30.7 - - + -
16C VAL* 4.1 9.3 - - + +
17C LEU 3.1 5.9 + - - -
18C MET* 3.0 40.2 - - + +
19C PRO* 4.0 4.5 - - - -
25C ALA* 4.0 2.5 - - - -
40C ASN* 3.8 18.2 - - - +
45C MET* 3.9 4.0 - - + +
46C LEU 3.2 19.7 - - - +
47C GLY* 3.5 9.2 - - - -
59C VAL* 1.3 77.5 - - - +
61C GLY* 1.3 68.3 + - - +
72C TYR* 3.4 42.0 - - + -
76C LEU* 4.7 4.0 - - + -
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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