Contacts of the strand formed by residues 132 - 139 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41H ARG 4.6 0.4 - - - -
42H VAL* 4.1 0.7 - - - -
43H SER* 3.1 38.6 + - - +
125H PHE 5.9 0.7 - - - -
130H LEU* 3.5 7.5 - - - +
131H ARG* 1.3 84.8 - - + +
133H LEU* 1.3 64.4 - - - +
306H ASN* 3.4 37.5 - - + +
307H HIS* 3.6 13.2 - - - +
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.8 23.1 - - + -
41H ARG 3.4 9.2 - - - +
42H VAL* 3.7 33.4 - - + -
57H VAL* 4.3 9.0 - - + -
124H VAL* 3.6 44.0 - - + +
125H PHE* 3.0 38.4 - - + +
130H LEU* 4.1 12.8 - - + -
132H ALA* 1.3 76.9 - - - +
134H ARG* 1.3 60.6 + - - +
306H ASN 3.8 1.3 - - - -
307H HIS* 3.2 7.9 + - + +
308H GLY 3.0 18.5 + - - -
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Residues in contact with ARG 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.4 6.7 - - - -
41H ARG* 2.7 45.7 + - + +
125H PHE* 4.0 0.4 - - - -
133H LEU* 1.3 76.4 - - - +
135H LEU* 1.3 62.8 + - - +
136H GLU* 3.0 36.2 + - - -
302H ASP* 3.1 26.5 + - - +
304H GLN 3.3 19.5 + - - -
305H LYS* 3.3 26.2 + - - +
306H ASN 3.9 11.7 - - - +
307H HIS 4.0 1.1 - - - -
308H GLY 3.2 24.5 - - - +
309H MET 4.0 2.4 - - - +
310H HIS* 3.4 24.9 - - - +
473H ASP* 3.0 30.3 + - - -
474H THR 5.3 1.2 + - - -
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Residues in contact with LEU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 3.9 20.2 - - + -
39H ALA 3.7 9.4 - - - +
40H PHE* 4.0 21.1 - - + -
117H PHE* 5.2 2.0 - - + -
120H ILE* 4.1 11.9 - - + -
121H VAL* 3.9 20.0 - - + -
125H PHE* 4.0 9.9 - - + -
134H ARG* 1.3 72.4 - - - +
136H GLU* 1.3 59.7 + - - +
137H ASP 3.6 20.2 - - - +
138H LEU* 4.1 8.3 - - + -
308H GLY 3.0 9.3 + - - +
309H MET* 3.4 9.3 - - + -
310H HIS 2.8 27.4 + - - -
313H VAL* 3.9 31.7 - - + +
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Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ALA* 2.9 16.4 + - + +
41H ARG* 2.8 53.1 + - + +
98H ILE* 4.9 2.7 - - + -
134H ARG* 3.0 32.0 + - - +
135H LEU* 1.3 74.0 - - - +
137H ASP* 1.3 61.2 + - - +
310H HIS* 3.7 5.6 - - - +
312H ARG* 2.7 53.8 + - - +
313H VAL* 3.6 4.8 - - - +
363H TYR* 3.8 30.8 - - + +
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Residues in contact with ASP 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 3.6 2.9 - - - -
39H ALA* 3.1 24.7 + - + -
135H LEU* 3.6 7.8 - - - +
136H GLU* 1.3 78.9 - - - +
138H LEU* 1.3 77.9 + - - +
312H ARG* 3.9 14.9 - - - +
313H VAL* 3.6 8.0 - - - +
316H LYS* 3.0 27.9 + - - +
348H LEU* 5.4 0.7 - - - +
362H ILE* 3.9 7.1 - - - +
363H TYR* 3.0 44.1 + - + -
364H PHE* 3.4 19.6 + - + +
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ILE* 4.1 5.4 - - + -
37H LEU 3.1 18.2 - - - +
38H ALA* 3.7 20.4 - - + -
116H MET* 4.1 31.6 - - + -
117H PHE* 4.3 6.3 - - + -
120H ILE* 3.7 27.8 - - + -
135H LEU* 4.1 10.5 - - + -
137H ASP* 1.3 82.7 + - - +
139H ARG* 1.3 56.7 + - - +
140H ILE* 3.6 13.5 + - + +
313H VAL* 4.0 24.7 - - + +
316H LYS* 2.6 38.8 + - + +
364H PHE* 3.9 2.9 - - - -
366H GLN* 3.5 1.7 - - - +
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Residues in contact with ARG 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H THR* 5.1 2.0 + - - -
32H LEU 3.0 25.5 + - - -
33H ASP* 4.0 18.7 + - - +
35H ASP 2.7 31.9 + - - +
36H ILE* 3.4 8.7 - - - +
37H LEU* 2.8 60.2 + - + +
138H LEU* 1.3 69.9 - - - +
140H ILE* 1.3 71.7 + - - +
141H PRO* 3.9 6.2 - - - +
364H PHE* 3.6 25.9 - - + -
365H THR 3.5 25.3 + - - +
366H GLN* 3.7 4.5 - - - +
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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