Contacts of the strand formed by residues 36 - 43 (chain L) 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 ILE 36 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L THR 4.1 4.9 - - - +
35L ASP* 1.3 73.3 - - - +
37L LEU* 1.3 61.1 + - - +
102L ALA* 3.6 1.6 - - - -
103L TYR* 2.8 39.9 + - + +
105L LEU* 4.4 10.5 - - + -
108L PHE* 3.5 39.9 - - + -
116L MET* 5.2 5.8 - - - -
120L ILE* 3.9 26.9 - - + -
138L LEU* 4.1 15.9 - - + -
139L ARG 3.4 9.6 - - - +
140L ILE* 5.0 2.5 - - + -
141L PRO* 3.7 26.9 - - + -
144L TYR* 4.7 13.9 - - + -
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Residues in contact with LEU 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L THR* 3.7 33.7 - - + +
35L ASP* 3.8 14.6 - - + -
36L ILE* 1.3 73.9 - - - +
38L ALA* 1.3 61.7 + - - +
85L TYR* 3.8 15.9 - - - +
101L VAL 3.4 2.0 - - - +
102L ALA* 3.8 18.8 - - + -
138L LEU* 3.1 9.4 - - - +
139L ARG* 2.8 67.8 + - + +
364L PHE* 3.7 30.8 - - + -
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Residues in contact with ALA 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L LEU* 1.3 75.8 - - - +
39L ALA* 1.3 60.6 + - - +
40L PHE* 3.8 26.5 - - + -
99L CYS 3.5 1.4 - - - +
100L TYR* 3.3 5.9 - - - -
101L VAL* 2.8 34.8 + - + +
103L TYR* 3.9 16.2 - - + -
120L ILE* 4.5 1.1 - - + -
135L LEU* 3.9 4.7 - - + -
137L ASP 3.6 3.6 - - - -
138L LEU* 3.7 17.7 - - + -
364L PHE* 3.8 4.0 - - - -
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Residues in contact with ALA 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ALA* 1.3 71.2 - - - +
40L PHE* 1.3 60.4 + - - +
98L ILE* 4.4 4.0 - - + -
99L CYS 3.7 4.7 - - - -
100L TYR* 4.2 7.9 - - + -
135L LEU* 3.7 3.4 - - - +
136L GLU* 2.9 29.5 + - + +
137L ASP 3.1 12.7 + - - +
363L TYR* 3.8 33.4 - - + -
364L PHE* 3.8 19.7 - - + -
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ALA* 3.8 19.1 - - + -
39L ALA* 1.3 72.8 - - - +
41L ARG* 1.3 58.5 + - - +
42L VAL* 3.4 17.5 + - + +
57L VAL* 3.7 24.2 - - + -
97L TYR 3.3 1.9 - - - +
98L ILE* 3.2 6.4 - - - -
99L CYS* 2.8 43.2 + - + +
101L VAL* 4.0 16.4 - - + -
103L TYR* 3.7 14.6 - - - -
120L ILE* 3.6 35.7 - - + -
124L VAL* 4.5 0.2 - - + -
125L PHE* 4.2 18.8 - + - -
133L LEU* 3.8 25.1 - - + -
134L ARG 3.4 8.3 - - - -
135L LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ALA 4.2 0.6 + - - -
40L PHE* 1.3 68.1 - - - +
42L VAL* 1.3 59.3 + - - +
43L SER* 4.1 0.9 + - - -
90L VAL* 3.8 17.8 - - - +
96L GLN* 2.9 48.3 + - + +
97L TYR 3.4 4.0 - - - -
98L ILE* 4.0 15.9 - - + +
133L LEU* 3.4 5.3 - - - -
134L ARG* 2.7 41.6 + - + +
136L GLU* 2.8 38.6 + - + +
305L LYS* 3.2 53.4 + - - +
306L ASN* 4.6 5.7 - - - +
363L TYR* 3.7 13.1 + - - -
474L THR 5.1 1.0 + - - -
475L VAL* 4.5 6.9 + - - +
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Residues in contact with VAL 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L PHE* 3.7 15.7 - - + +
41L ARG* 1.3 71.9 - - - +
43L SER* 1.3 63.9 + - - +
44L PRO* 3.6 8.9 - - + +
53L ALA* 4.1 17.0 - - + -
54L GLY* 5.3 0.7 - - - -
57L VAL* 4.9 7.0 - - + -
96L GLN* 3.4 3.7 - - - +
97L TYR* 2.8 41.6 + - + +
99L CYS* 3.6 28.9 - - + -
130L LEU* 3.8 27.6 - - + -
133L LEU* 3.7 22.7 - - + -
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Residues in contact with SER 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG 5.0 0.9 + - - -
42L VAL* 1.3 74.7 + - - +
44L PRO* 1.3 67.4 - - - +
94L GLU 5.8 0.4 - - - -
95L ASN 3.8 7.2 - - - -
96L GLN* 3.4 27.5 + - - +
130L LEU* 3.7 1.0 - - - -
131L ARG* 2.7 35.0 + - - +
132L ALA* 3.1 34.6 + - - +
306L ASN* 4.9 2.9 + - - +
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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