Contacts of the strand formed by residues 55 - 60 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 2.4 43.4 + - - -
15A VAL* 3.7 18.8 - - - +
51A THR* 2.8 5.9 - - - -
52A TYR 2.7 40.5 + - - +
53A LYS 3.1 3.0 + - - +
54A GLY* 1.3 76.3 - - - +
56A LYS* 1.3 90.1 + - - +
57A ILE* 3.4 7.6 + - + +
83A LYS* 5.3 0.6 - - - +
84A LYS* 6.1 1.4 - - - +
232A VAL* 3.6 12.4 - - + +
233A LEU* 3.6 20.6 - - + -
236A ASP* 2.8 41.4 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 3.0 28.1 + - - -
12A PHE 3.5 10.1 + - - -
13A ALA* 3.5 25.3 - - + +
14A ASP* 5.2 2.2 - - - +
15A VAL* 4.9 0.3 - - - +
37A ARG* 4.5 6.9 - - - +
49A THR* 3.8 18.8 - - + -
50A GLY 3.3 10.5 - - - +
51A THR* 3.8 8.3 - - + -
54A GLY 3.6 3.4 + - - +
55A ARG* 1.3 99.8 + - - +
57A ILE* 1.3 68.7 + - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.5 5.6 - - - -
15A VAL* 4.1 14.1 - - + +
17A LEU* 4.5 9.0 - - + +
33A LEU* 3.6 25.2 - - + +
49A THR* 3.4 1.1 - - - -
50A GLY 2.8 40.3 + - - +
52A TYR* 3.9 17.3 - - + -
55A ARG* 3.4 13.2 + - + +
56A LYS* 1.3 85.2 - - - +
58A SER* 1.3 76.8 + - - +
59A VAL* 4.8 1.1 - - + -
229A LEU* 3.5 34.3 - - + +
232A VAL* 4.6 21.5 - - + -
233A LEU* 5.8 0.4 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.4 21.8 - - - -
13A ALA 2.8 24.6 + - - -
15A VAL 3.3 9.9 + - - -
16A VAL* 3.5 7.3 - - - -
17A LEU 2.9 25.2 + - - -
48A PHE 2.9 10.8 - - - -
49A THR* 2.7 23.0 + - - -
57A ILE* 1.3 76.5 - - - +
59A VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 5.1 0.2 - - - -
16A VAL* 4.8 1.1 - - - -
17A LEU* 3.3 18.4 - - + +
19A PRO* 4.1 3.6 - - + -
25A ALA* 3.7 32.8 - - - +
28A ILE* 3.8 37.0 - - + -
29A ALA* 4.8 1.6 - - - +
33A LEU* 3.5 26.9 - - + -
46A LEU 3.9 0.5 - - - +
47A GLY* 3.1 1.6 - - - -
48A PHE* 2.7 41.2 + - + +
57A ILE* 4.8 2.2 - - + -
58A SER* 1.3 80.9 - - - +
60A MET* 1.3 66.8 + - - +
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Residues in contact with MET 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.9 25.1 - - + -
12A PHE* 4.0 19.7 - - + -
16A VAL* 4.6 3.0 - - + +
17A LEU 3.2 6.1 + - - -
18A MET* 3.3 45.2 - - + +
19A PRO* 3.8 4.7 - - - -
25A ALA* 3.9 2.7 - - - -
40A ASN* 3.5 24.9 - - - +
45A MET* 3.8 10.1 - - + +
46A LEU 3.2 21.8 - - - +
47A GLY* 3.6 5.4 - - - -
59A VAL* 1.3 79.5 - - - +
61A GLY* 1.3 69.7 + - - +
72A TYR* 4.2 9.4 - - + -
76A LEU* 4.0 17.9 - - + -
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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