Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 1RPU
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 VAL 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 4.0 34.5 - - + +
11A ARG* 4.6 4.7 - - - +
14A ALA* 3.3 26.5 - - + -
64A GLY* 3.5 1.6 - - - -
65A PHE* 3.1 34.3 + - + +
66A GLY 3.3 1.6 - - - -
67A LYS* 1.3 80.1 - - + +
69A VAL* 1.3 59.1 + - - +
70A PHE* 3.6 22.6 - - + -
102A PHE* 4.2 21.1 - - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 4.2 5.4 + - - +
14A ALA* 3.5 22.5 - - - +
15A ASN* 3.9 5.5 + - - -
62A SER* 4.3 7.0 - - - +
63A TRP 3.5 7.9 - - - +
64A GLY* 4.1 10.3 - - - -
66A GLY 4.4 6.1 - - - +
67A LYS 3.2 10.8 + - - +
68A VAL* 1.3 76.1 - - - +
70A PHE* 1.3 74.4 + - - +
71A LYS* 4.2 22.5 - - + +
10C C 3.8 41.1 - - - +
11C A 5.2 2.2 - - - +
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Residues in contact with PHE 70 (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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14A ALA* 3.6 31.6 - - + -
17A GLU* 3.7 22.2 - - + +
26A ILE* 4.1 5.4 - - + -
27A THR 3.7 14.6 - - - -
28A SER* 4.2 3.4 - - - -
29A PRO* 3.5 31.6 - - + -
30A PHE* 3.8 18.3 - - + -
62A SER* 3.0 6.9 - - - -
63A TRP 2.7 38.4 + - - +
65A PHE* 3.9 13.7 - + - -
68A VAL* 3.6 24.9 - - + -
69A VAL* 1.3 72.4 - - - +
71A LYS* 1.3 63.7 + - - +
102A PHE* 3.7 28.3 - + - -
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Residues in contact with LYS 71 (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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14A ALA 5.1 0.8 + - - -
17A GLU* 5.1 0.2 + - - -
18A ARG* 3.6 35.6 - - + +
30A PHE* 3.9 1.6 - - - -
60A LYS* 3.6 34.1 - - - +
61A GLU 3.4 7.2 - - - +
62A SER* 3.6 8.5 - - - -
69A VAL* 4.2 15.9 - - + +
70A PHE* 1.3 80.8 - - - +
72A ARG* 1.3 86.6 + - - +
11C A 3.9 30.4 + - - -
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Residues in contact with ARG 72 (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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17A GLU* 2.8 44.8 + - - -
18A ARG* 3.9 11.5 - - - +
28A SER* 4.1 0.6 + - - -
30A PHE* 3.3 47.4 + - + +
32A LEU 2.8 24.5 + - - +
33A PRO* 4.3 5.6 - - - +
34A ASP* 3.4 32.7 - - - +
59A PHE* 4.1 0.3 - - - +
60A LYS* 3.3 5.4 - - - +
61A GLU* 2.8 45.4 + - + +
71A LYS* 1.3 106.0 + - - +
73A TYR* 1.3 59.8 + - - +
74A LEU* 4.0 12.5 + - + -
89A SER* 5.0 1.6 - - - +
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Residues in contact with TYR 73 (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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18A ARG* 3.4 21.1 - - - +
34A ASP* 3.0 6.7 + - - -
35A GLU* 2.8 41.4 + - - -
36A SER* 3.6 13.5 - - - +
37A PRO* 4.0 8.3 - - + -
42A TRP* 5.8 0.3 - - - -
57A LEU* 3.3 13.8 + - + +
58A GLY* 3.0 29.4 + - - -
59A PHE* 3.3 18.8 - - - -
60A LYS* 4.2 11.0 - - + -
72A ARG* 1.3 73.7 - - - +
74A LEU* 1.3 71.3 + - - +
75A ARG* 4.0 19.7 - - - -
1D C 3.2 50.3 + - - -
2D G 5.1 0.4 - - - -
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Residues in contact with LEU 74 (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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32A LEU* 4.7 12.8 - - + +
33A PRO 3.6 25.4 - - - +
34A ASP* 4.8 1.3 - - - -
35A GLU* 3.6 17.5 - - - +
58A GLY* 3.1 1.0 - - - -
59A PHE* 3.0 53.4 + - + -
61A GLU* 3.4 13.2 - - - +
72A ARG* 4.5 9.4 - - + -
73A TYR* 1.3 84.2 - - - +
75A ARG* 1.3 67.0 + - - +
76A TYR 3.5 0.2 + - - -
85A ARG* 5.1 2.0 - - - +
86A VAL* 4.5 11.9 - - + -
89A SER* 3.1 36.1 - - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 2.5 48.0 + - + +
36A SER 4.2 1.2 + - - -
37A PRO* 3.4 14.8 - - - +
41A GLU* 2.6 41.7 + - - -
57A LEU* 3.5 38.2 - - + +
58A GLY* 4.0 0.2 - - - -
73A TYR* 4.0 6.5 - - - -
74A LEU* 1.3 73.6 - - - +
76A TYR* 1.3 59.0 + - - +
77A ASP 4.4 0.2 - - - -
82A SER* 4.3 0.7 + - - -
85A ARG* 2.8 25.5 + - - +
86A VAL* 3.6 4.9 - - - +
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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