Contacts of the strand formed by residues 97 - 103 (chain E) in PDB entry 1RBO
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 TYR 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E PHE 3.3 0.7 - - - +
41E ARG* 3.4 2.8 - - - -
42E VAL* 2.8 45.8 + - + +
44E PRO* 4.2 11.7 - - + -
50E PRO* 3.8 38.3 - - + +
87E ILE* 4.0 24.9 - - + -
88E GLU 3.3 7.0 - - - +
89E PRO* 3.8 29.8 - - + -
90E VAL* 4.0 4.0 - - - +
95E ASN* 3.4 37.3 + - - -
96E GLN* 1.3 78.3 - - - +
98E ILE* 1.3 63.5 + - - +
99E CYS* 3.7 9.3 + - - -
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Residues in contact with ILE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA* 4.4 8.5 - - + -
40E PHE 3.2 4.9 - - - +
41E ARG* 4.0 29.6 - - + +
86E HIS 3.9 0.7 - - - +
87E ILE* 3.4 3.8 - - - -
88E GLU* 2.7 49.7 + - + +
90E VAL* 3.8 22.9 - - + +
97E TYR* 1.3 71.1 - - - +
99E CYS* 1.3 59.6 + - - +
100E TYR* 3.5 33.9 - - + +
136E GLU* 4.9 2.2 - - + -
358E ARG* 4.4 8.3 - - - +
363E TYR* 4.0 32.5 - - + +
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Residues in contact with CYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA 3.5 2.1 - - - +
39E ALA* 3.7 0.2 - - - -
40E PHE* 2.8 39.4 + - + +
42E VAL* 3.6 31.4 - - + -
50E PRO* 4.4 4.3 - - - -
54E GLY* 4.0 20.6 - - - -
57E VAL* 6.4 0.7 - - + -
84E CYS* 4.1 12.6 - - - -
86E HIS 3.5 3.8 - - - -
87E ILE* 4.0 24.0 - - - -
97E TYR* 4.3 6.1 - - - -
98E ILE* 1.3 76.6 - - - +
100E TYR* 1.3 61.9 + - - +
101E VAL* 3.9 5.0 + - + -
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Residues in contact with TYR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA 3.3 5.4 - - - +
39E ALA* 4.2 10.3 - - + -
84E CYS* 3.3 5.9 - - - -
85E TYR* 3.0 53.2 + + + +
86E HIS* 2.9 46.0 + - + +
88E GLU* 3.6 10.7 + - - -
98E ILE* 3.5 24.9 - - + +
99E CYS* 1.3 74.8 - - - +
101E VAL* 1.3 59.4 + - - +
358E ARG* 3.3 26.7 + - - -
363E TYR* 3.7 17.1 + + + +
364E PHE* 3.7 34.5 - + - -
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE 3.8 0.9 - - - +
37E LEU* 3.4 4.0 - - - -
38E ALA* 2.8 38.0 + - - +
40E PHE* 4.0 23.3 - - + -
54E GLY 4.5 5.2 - - - +
57E VAL* 4.6 2.9 - - + -
58E ALA* 3.7 30.3 - - + -
83E ARG 3.2 14.1 - - - +
84E CYS* 4.3 9.0 - - + -
85E TYR* 3.7 3.6 - - - -
99E CYS* 4.5 6.3 - - + +
100E TYR* 1.3 78.6 - - - +
102E ALA* 1.3 63.1 + - - +
103E TYR* 3.6 33.9 - - + +
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Residues in contact with ALA 102 (chain E).
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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29E TYR* 3.7 30.5 - - + -
35E ASP* 3.9 5.6 - - - +
36E ILE 3.6 4.5 - - - -
37E LEU* 3.8 19.1 - - + -
81E LYS 4.2 0.5 - - - +
82E GLY* 3.2 6.1 - - - -
83E ARG* 2.9 34.2 + - + +
85E TYR* 3.7 10.3 - - + -
101E VAL* 1.3 73.2 - - - +
103E TYR* 1.3 60.5 + - - +
104E PRO* 4.1 2.6 - - - +
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Residues in contact with TYR 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ASP* 3.3 5.4 - - - -
36E ILE* 2.8 50.0 + - + +
38E ALA* 3.9 20.2 - - + -
40E PHE* 3.7 17.7 - - - -
57E VAL 4.5 0.3 + - - -
58E ALA 4.6 0.9 - - - -
61E SER* 2.6 45.8 + - - -
62E SER* 4.3 7.4 - - - -
82E GLY* 4.3 0.9 - - - -
101E VAL* 3.6 27.9 - - + +
102E ALA* 1.3 77.0 - - - +
104E PRO* 1.3 68.7 - - + +
107E LEU* 4.1 16.2 - - + -
108E PHE* 3.6 25.8 - + + -
119E SER* 5.9 0.2 - - - -
120E ILE* 4.0 25.4 - - + +
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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