Contacts of the helix formed by residues 311 - 321 (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 PHE 311 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269L TYR* 4.1 17.3 - - - -
295L ARG* 3.5 39.7 - - + +
298L HIS* 4.1 4.0 - - + -
302L ASP* 3.3 32.4 - - - +
310L HIS* 1.3 84.8 + - + +
312L ARG* 1.3 56.6 + - - +
314L LEU* 2.9 14.4 + - + -
315L ALA* 2.8 41.1 + - + -
326L ILE* 3.8 16.4 - - + -
327L HIS 3.6 21.5 - - - -
328L SER* 4.6 0.7 - - - -
345L PHE* 3.6 36.8 - + + -
349L LEU* 5.1 2.7 - - + -
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Residues in contact with ARG 312 (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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136L GLU* 2.7 67.2 + - - +
137L ASP* 3.9 19.5 - - - +
310L HIS* 3.0 41.0 + - + +
311L PHE* 1.3 76.9 - - - +
313L VAL* 1.3 61.4 + - + +
315L ALA* 3.5 3.3 + - - +
316L LYS* 3.1 28.8 + - - +
341L ILE* 4.2 12.3 + - - +
344L GLY 6.3 0.2 - - - -
345L PHE* 3.9 29.5 - - + +
348L LEU* 4.1 14.5 - - + +
360L ARG 4.1 6.5 + - - -
361L GLY* 3.0 42.1 + - - -
362L ILE* 4.9 2.3 - - - +
363L TYR* 4.2 1.2 - - - -
475L VAL* 5.4 0.4 - - - +
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Residues in contact with VAL 313 (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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117L PHE* 3.8 15.4 - - + -
135L LEU* 3.9 19.7 - - + +
136L GLU 3.6 24.0 - - - +
137L ASP* 3.6 23.1 - - - +
138L LEU* 4.0 12.3 - - + +
309L MET* 3.6 26.7 - - + -
310L HIS 3.1 11.0 + - - +
312L ARG* 1.3 73.9 - - - +
314L LEU* 1.3 60.1 + - - +
316L LYS* 3.3 9.3 + - - +
317L ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 314 (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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117L PHE* 4.3 12.6 - - + -
269L TYR* 2.8 27.4 + - - +
270L LEU* 4.2 24.7 - - + -
274L PHE* 4.8 0.9 - - + -
298L HIS* 4.2 25.8 - - + -
301L ILE* 4.4 23.6 - - + -
302L ASP* 4.2 11.2 - - + +
309L MET* 3.9 27.1 - - + -
310L HIS 4.2 7.2 - - - +
311L PHE* 2.9 15.9 + - + +
313L VAL* 1.3 76.9 - - - +
315L ALA* 1.3 59.6 + - - +
317L ALA* 3.5 5.6 + - - +
318L LEU* 3.2 14.9 + - - +
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Residues in contact with ALA 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L PHE* 2.8 38.3 + - + +
312L ARG* 3.7 9.9 - - - +
313L VAL 3.2 0.2 - - - -
314L LEU* 1.3 74.7 - - - +
316L LYS* 1.3 64.4 + - + +
318L LEU* 3.3 2.6 + - - +
319L ARG* 3.1 18.2 + - - +
326L ILE* 4.5 4.7 - - - -
345L PHE* 4.8 5.8 - - + -
348L LEU* 6.0 2.2 - - + -
349L LEU* 3.6 37.3 - - + +
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Residues in contact with LYS 316 (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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137L ASP* 3.0 22.0 + - - +
138L LEU* 2.6 33.4 + - + +
139L ARG* 4.6 1.2 - - - +
140L ILE* 4.1 15.5 - - + -
312L ARG 3.1 17.4 + - - +
313L VAL* 3.3 9.6 + - - +
315L ALA* 1.3 75.8 - - - +
317L ALA* 1.3 62.8 + - - +
319L ARG* 3.2 5.1 + - - +
320L LEU* 3.1 27.8 + - - +
348L LEU* 3.9 35.3 - - + +
349L LEU* 5.6 0.2 - - - -
364L PHE* 5.0 3.4 + - - +
366L GLN* 3.0 30.4 + - - +
368L TRP* 4.0 23.3 - - + -
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Residues in contact with ALA 317 (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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113L VAL* 3.7 19.3 - - + +
116L MET* 4.9 4.3 - - + -
117L PHE* 3.6 37.2 - - + -
140L ILE* 5.4 0.2 - - - +
274L PHE* 4.0 8.1 - - + -
313L VAL 3.0 10.1 + - - +
314L LEU 3.7 6.3 - - - +
316L LYS* 1.3 77.6 - - - +
318L LEU* 1.3 57.3 + - - +
320L LEU* 3.3 7.3 + - - +
321L SER* 2.9 30.6 + - - -
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Residues in contact with LEU 318 (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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269L TYR* 3.7 29.3 - - + -
277L ASN* 3.8 12.1 - - - +
293L ILE* 3.9 17.5 - - + -
314L LEU 3.2 9.1 + - - +
315L ALA 3.6 9.0 - - - +
316L LYS 3.2 0.4 - - - -
317L ALA* 1.3 73.2 - - - +
319L ARG* 1.3 62.4 + - - +
321L SER* 4.5 1.6 - - - -
322L GLY* 2.7 47.5 + - - +
323L GLY* 4.0 18.4 - - - +
326L ILE* 3.8 37.2 - - + -
349L LEU* 5.3 0.2 - - + -
374L VAL* 4.3 12.3 - - + -
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Residues in contact with ARG 319 (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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150L GLY* 3.1 23.7 - - - -
151L PRO* 3.2 6.1 - - + +
315L ALA 3.1 13.1 + - - +
316L LYS* 3.2 8.0 + - - +
318L LEU* 1.3 77.2 - - - +
320L LEU* 1.3 57.7 + - - +
348L LEU 2.8 27.4 + - - -
349L LEU* 3.3 27.3 + - + +
350L ARG 4.0 0.8 + - - -
351L ASP 2.8 32.3 + - - -
352L ASP* 4.6 1.2 - - - +
368L TRP* 3.2 39.2 - - + +
371L THR* 2.9 29.1 + - + +
372L PRO 2.9 22.1 + - - +
373L GLY* 3.6 5.3 - - - +
374L VAL* 3.9 22.9 - - + -
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Residues in contact with LEU 320 (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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113L VAL* 4.0 3.8 - - + -
116L MET* 4.5 14.1 - - + -
140L ILE* 3.6 32.3 - - + -
145L VAL* 4.2 21.5 - - + -
148L PHE* 3.5 56.7 - - + +
149L GLN 4.3 0.7 + - - -
150L GLY* 3.2 21.3 + - - -
316L LYS 3.1 12.3 + - - +
317L ALA 3.6 5.2 - - - +
319L ARG* 1.3 75.0 - - - +
321L SER* 1.3 67.1 + - - +
368L TRP* 3.9 21.3 - - + -
371L THR* 5.6 2.5 - - + +
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Residues in contact with SER 321 (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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113L VAL* 4.1 12.6 - - - +
148L PHE* 4.8 3.4 - - - -
150L GLY 4.1 2.9 + - - +
274L PHE* 4.0 13.3 + - - -
277L ASN* 3.0 22.2 + - - +
278L THR* 2.8 38.0 + - - +
281L SER* 3.1 17.4 + - - -
282L HIS* 4.8 4.3 - - - -
317L ALA 2.9 20.4 + - - -
318L LEU* 4.1 3.1 - - - -
320L LEU* 1.3 74.7 - - - +
322L GLY* 1.3 59.1 + - - +
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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