Contacts of the strand formed by residues 58 - 65 (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 GLY 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 3.4 6.1 - - - +
57A LEU* 1.3 78.7 - - - +
59A PHE* 1.3 61.5 + - - -
73A TYR* 3.0 19.0 + - - -
74A LEU 3.1 15.0 - - - -
75A ARG* 4.0 0.4 - - - -
76A TYR* 3.7 11.9 - - - -
116A PHE* 3.6 20.0 - - - -
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Residues in contact with PHE 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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58A GLY* 1.3 74.4 - - - +
60A LYS* 1.3 66.2 + - - +
61A GLU* 3.3 36.1 - - + -
73A TYR* 3.3 10.2 - - - -
74A LEU* 3.0 44.4 + - + -
76A TYR* 3.9 13.7 - + + -
86A VAL* 3.7 37.2 - - + -
114A ILE* 3.6 23.8 - - + -
115A ARG 3.4 16.6 - - - +
116A PHE* 3.8 15.5 - - + -
141A LYS* 3.9 16.2 - - - -
145A LEU* 3.9 17.3 - - + -
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Residues in contact with LYS 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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18A ARG* 3.8 12.3 - - - +
59A PHE* 1.3 78.4 - - - +
61A GLU* 1.3 66.6 + - - +
62A SER* 6.0 0.4 - - - -
71A LYS* 3.6 40.6 - - - +
72A ARG 3.3 13.7 - - - +
73A TYR* 4.2 12.1 - - + +
113A SER 4.0 0.2 - - - +
114A ILE* 3.4 3.8 - - - +
115A ARG* 3.0 40.2 + - + +
1D C 5.8 2.9 - - - -
2D G 3.2 31.8 + - - +
3D U 4.7 7.3 + - - -
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Residues in contact with GLU 61 (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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30A PHE* 3.8 18.6 - - + -
59A PHE* 3.3 20.9 - - + -
60A LYS* 1.3 78.3 - - - +
62A SER* 1.3 64.8 + - - +
71A LYS* 3.4 2.1 - - - +
72A ARG* 2.8 38.2 + - + +
74A LEU* 3.4 6.9 - - - +
89A SER* 2.7 26.3 + - - -
90A TRP* 3.1 7.3 + - - -
112A TYR* 2.7 33.7 + - + +
113A SER 3.1 12.8 - - - +
114A ILE* 4.2 1.8 - - + -
141A LYS* 2.9 19.9 + - - -
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Residues in contact with SER 62 (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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30A PHE* 4.2 2.7 - - - -
60A LYS* 6.0 0.4 - - - -
61A GLU* 1.3 77.8 - - - +
63A TRP* 1.3 61.5 + - - +
69A VAL* 4.3 6.9 - - - +
70A PHE 3.0 17.3 - - - -
71A LYS* 3.6 16.8 - - - +
111A THR* 3.7 2.6 - - - +
112A TYR* 3.2 8.2 - - - -
113A SER* 2.9 41.3 + - - -
10C C 4.7 1.0 + - - -
11C A 3.3 21.7 + - - -
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Residues in contact with TRP 63 (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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29A PRO* 4.2 13.7 - - + -
30A PHE* 3.9 27.5 - + + -
62A SER* 1.3 71.2 - - - +
64A GLY* 1.3 57.8 + - - +
65A PHE* 4.2 20.9 - + + -
69A VAL* 3.5 2.8 - - - -
70A PHE* 2.7 36.3 + - - +
90A TRP* 3.4 46.0 - + - -
95A VAL* 3.8 25.0 - - + +
110A CYS* 5.5 0.4 - - + -
111A THR* 3.2 26.9 - - - -
112A TYR* 3.2 42.8 - + + -
130A LEU* 4.2 13.9 - - + -
133A LEU* 4.4 10.5 - - + -
134A CYS* 3.9 20.6 - - - -
137A ALA* 4.0 6.5 - - + -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 1.3 75.9 - - - +
65A PHE* 1.3 65.0 + - - -
66A GLY 3.5 4.0 - - - -
68A VAL 3.5 7.9 - - - -
69A VAL* 4.0 16.2 - - - -
109A GLY 4.6 0.2 - - - -
110A CYS* 3.1 8.0 - - - +
111A THR* 2.7 41.7 + - - -
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Residues in contact with PHE 65 (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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29A PRO* 3.3 35.0 - - + -
63A TRP* 4.2 18.2 - + + -
64A GLY* 1.3 73.2 - - - -
66A GLY* 1.3 61.4 + - - +
67A LYS 3.3 2.6 + - - -
68A VAL* 3.1 23.5 + - + +
70A PHE* 3.9 19.5 - + - -
95A VAL* 3.8 32.3 - - + -
98A ALA* 4.6 4.3 - - + -
99A ALA* 3.6 32.5 - - + -
102A PHE* 4.5 20.5 - + + +
103A LEU* 4.5 12.9 - - + +
108A VAL* 4.6 6.3 - - - +
110A CYS* 4.2 17.0 - - + -
130A LEU* 4.4 8.3 - - + -
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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