Contacts of the strand formed by residues 132 - 139 (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 ALA 132 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41L ARG 4.6 0.2 - - - -
42L VAL* 4.1 0.7 - - - -
43L SER* 3.1 40.1 + - - +
125L PHE 5.9 0.7 - - - -
130L LEU* 3.5 6.8 - - - +
131L ARG* 1.3 84.3 - - + +
133L LEU* 1.3 65.5 + - - +
306L ASN* 3.4 35.9 - - + +
307L HIS* 3.6 13.7 - - - +
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Residues in contact with LEU 133 (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* 3.8 23.1 - - + -
41L ARG 3.4 8.7 - - - +
42L VAL* 3.7 33.4 - - + -
57L VAL* 4.3 9.0 - - + -
124L VAL* 3.6 44.6 - - + +
125L PHE* 3.0 36.8 - - + +
130L LEU* 4.1 13.2 - - + -
132L ALA* 1.3 77.9 - - - +
134L ARG* 1.3 61.3 + - - +
306L ASN 3.6 2.2 + - - -
307L HIS* 3.2 8.1 + - + -
308L GLY 3.0 18.5 + - - -
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Residues in contact with ARG 134 (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* 3.4 7.1 - - - -
41L ARG* 2.7 44.6 + - + +
125L PHE* 4.4 0.4 - - - -
133L LEU* 1.3 76.0 - - - +
135L LEU* 1.3 63.0 + - - +
136L GLU* 3.0 36.9 + - - -
302L ASP 3.1 25.7 + - - -
304L GLN 3.3 19.0 + - - -
305L LYS* 3.3 25.6 + - - +
306L ASN 3.9 11.9 - - - +
307L HIS 4.0 0.9 - - - -
308L GLY 3.2 24.0 - - - +
309L MET 4.0 2.8 - - - +
310L HIS* 3.4 25.9 - - - +
473L ASP* 3.0 29.5 + - - -
474L THR 5.3 1.0 + - - -
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Residues in contact with LEU 135 (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* 3.9 20.9 - - + -
39L ALA 3.7 9.6 - - - +
40L PHE* 4.0 21.3 - - + -
117L PHE* 5.2 2.0 - - + -
120L ILE* 4.1 11.4 - - + -
121L VAL* 3.9 20.2 - - + -
125L PHE* 4.0 9.5 - - + -
134L ARG* 1.3 71.6 - - - +
136L GLU* 1.3 59.2 + - - +
137L ASP 3.6 19.7 - - - +
138L LEU* 4.1 8.5 - - + -
308L GLY 3.0 9.9 + - - +
309L MET* 3.4 8.8 - - + -
310L HIS 2.8 27.7 + - - -
313L VAL* 3.9 31.5 - - + +
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Residues in contact with GLU 136 (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* 2.9 15.8 + - + +
41L ARG* 2.8 54.2 + - + +
98L ILE* 4.9 2.5 - - + -
134L ARG* 3.0 31.6 + - - +
135L LEU* 1.3 75.3 - - - +
137L ASP* 1.3 60.5 + - - +
310L HIS* 3.7 6.1 - - - +
312L ARG* 2.7 53.6 + - - +
313L VAL* 3.6 3.9 - - - +
363L TYR* 3.8 29.8 - - + +
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Residues in contact with ASP 137 (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* 3.6 2.9 - - - -
39L ALA* 3.1 24.9 + - + -
135L LEU* 3.6 6.7 - - - +
136L GLU* 1.3 80.3 - - - +
138L LEU* 1.3 77.4 + - - +
312L ARG* 3.9 14.3 - - - +
313L VAL* 3.6 8.8 - - - +
316L LYS* 3.0 27.6 + - - +
348L LEU* 5.4 0.7 - - - +
362L ILE* 3.9 7.3 - - - +
363L TYR* 3.0 44.9 + - + -
364L PHE* 3.4 18.7 + - + +
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Residues in contact with LEU 138 (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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36L ILE* 4.1 5.4 - - + -
37L LEU 3.1 16.4 - - - +
38L ALA* 3.7 21.3 - - + -
116L MET* 4.1 31.0 - - + -
117L PHE* 4.3 6.1 - - + -
120L ILE* 3.7 27.6 - - + -
135L LEU* 4.1 10.8 - - + -
137L ASP* 1.3 81.8 + - - +
139L ARG* 1.3 55.6 + - - +
140L ILE* 3.6 13.1 + - + -
313L VAL* 4.0 23.6 - - + +
316L LYS* 2.6 39.4 + - + +
364L PHE* 3.9 2.9 - - - -
366L GLN* 3.5 1.9 - - - +
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Residues in contact with ARG 139 (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* 5.1 2.4 + - - -
32L LEU 3.0 25.3 + - - -
33L ASP* 4.0 19.3 + - - +
35L ASP 2.7 31.1 + - - +
36L ILE* 3.4 8.7 - - - +
37L LEU* 2.8 59.3 + - + +
138L LEU* 1.3 71.2 - - - +
140L ILE* 1.3 72.2 + - - +
141L PRO* 3.9 6.9 - - - -
364L PHE* 3.6 25.6 - - + -
365L THR 3.5 24.1 + - - +
366L GLN* 3.7 4.9 - - - +
367L SER 6.3 0.2 - - - +
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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