Contacts of the helix formed by residues 142 - 147 (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 VAL 142 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33L ASP 4.8 4.2 + - - +
140L ILE 5.2 0.2 - - - +
141L PRO* 1.3 72.2 - - - +
143L ALA* 1.3 65.4 + - + +
145L VAL* 3.6 8.0 - - - +
146L LYS* 3.1 30.5 + - + +
367L SER* 3.9 33.2 - - - +
369L VAL* 3.7 32.5 - - + -
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Residues in contact with ALA 143 (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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33L ASP 5.5 0.6 + - - +
34L THR* 4.5 15.9 - - + -
105L LEU* 4.2 25.3 - - + +
141L PRO* 3.1 3.9 - - + +
142L VAL* 1.3 84.3 - - + +
144L TYR* 1.3 60.3 + - - +
146L LYS* 3.9 9.6 + - - +
147L THR* 3.6 15.6 - - - +
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Residues in contact with TYR 144 (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* 4.7 9.9 - - + -
105L LEU* 3.9 19.7 - - + +
108L PHE* 3.6 28.3 - + + +
109L GLU 2.8 32.3 + - - -
110L GLU* 4.0 3.1 - - + -
112L SER 3.3 17.0 + - - -
116L MET* 4.0 25.7 + - + +
140L ILE* 4.0 15.5 - - + -
141L PRO* 2.9 23.6 + - + +
143L ALA* 1.3 74.8 - - - +
145L VAL* 1.3 66.6 + - - +
146L LYS 3.2 1.8 - - - -
147L THR* 2.8 40.0 + - + -
148L PHE* 3.2 32.5 - + - -
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Residues in contact with VAL 145 (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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140L ILE* 3.6 26.7 - - + +
141L PRO 3.0 19.3 + - - +
142L VAL* 3.3 12.1 + - - +
144L TYR* 1.3 77.3 - - - +
146L LYS* 1.3 61.2 + - + +
148L PHE* 3.0 29.2 + - - +
320L LEU* 4.2 14.8 - - + -
366L GLN* 4.3 2.5 - - - +
367L SER 4.2 10.5 - - - +
368L TRP* 3.7 19.3 - - + +
369L VAL* 4.0 5.4 - - + -
371L THR* 3.3 27.2 + - + +
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Residues in contact with LYS 146 (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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210B PRO* 3.9 25.9 - - - +
213B ARG* 5.0 5.3 - - - +
142L VAL 3.1 20.2 + - - +
143L ALA* 4.1 8.3 - - - +
144L TYR 3.2 0.6 - - - -
145L VAL* 1.3 76.3 - - + +
147L THR* 1.3 58.6 + - - +
148L PHE 3.2 7.7 + - - +
369L VAL* 3.7 33.1 + - + +
371L THR* 5.9 0.7 - - - +
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Residues in contact with THR 147 (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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110L GLU* 3.7 28.1 - - + +
111L GLY* 2.9 36.2 + - - -
143L ALA 3.6 18.4 - - - +
144L TYR* 2.8 21.9 + - + +
146L LYS* 1.3 77.4 - - + +
148L PHE* 1.3 63.4 + - - +
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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