Contacts of the helix formed by residues 428 - 434 (chain A) in PDB entry 2RIO
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 LEU 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A PHE* 4.4 8.1 - - + -
311A LYS* 3.7 32.3 - - + +
312A VAL* 4.0 25.6 - - + +
315A ARG* 4.3 14.4 - - + -
418A VAL* 3.8 24.2 - - + -
422A LEU* 3.7 33.2 - - + +
425A ASP* 3.2 19.0 + - + +
427A ILE* 1.4 74.5 - - + +
429A ARG* 1.3 62.4 + - - +
430A GLU 3.2 1.3 - - - -
431A PHE* 3.2 13.2 + - + +
432A LEU* 3.2 24.6 + - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LEU 5.1 1.2 + - - -
423A SER* 2.8 31.3 + - - +
424A ASP* 4.1 10.9 - - - +
425A ASP 2.9 28.6 + - - +
426A GLN* 4.1 11.9 - - - +
428A LEU* 1.3 73.7 - - - +
430A GLU* 1.3 59.7 + - + +
432A LEU* 3.6 4.0 - - - +
433A TYR* 2.7 73.7 + - + +
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A GLN 3.9 7.7 - - - +
427A ILE* 3.3 15.7 + - - +
428A LEU 3.2 0.8 - - - -
429A ARG* 1.3 80.3 - - - +
431A PHE* 1.3 61.9 + - + +
434A SER* 2.7 43.6 + - - -
303B SER* 4.5 15.1 + - - +
396B PRO* 3.3 38.7 - - + +
397B ASP* 5.0 3.3 - - - +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 4.9 1.0 - - - +
300A TRP* 3.0 26.1 + + + -
304A LYS* 3.6 55.9 + - + +
307A GLU* 3.9 24.7 - - + -
308A PHE* 3.6 39.3 - + + -
311A LYS* 3.9 25.8 - - + -
427A ILE* 3.8 19.1 - - + -
428A LEU* 3.2 12.5 + - + +
430A GLU* 1.3 82.8 - - + +
432A LEU* 1.3 62.1 + - - +
434A SER* 4.3 2.1 + - - +
307B GLU* 4.6 4.3 - - - -
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 3.8 20.4 - - - +
300A TRP* 4.8 1.8 - - - -
308A PHE* 3.9 22.4 - - + -
415A TYR* 3.6 34.8 + - + -
418A VAL* 3.9 15.3 - - + -
419A LYS* 3.8 34.9 + - + +
422A LEU 4.8 0.7 - - - +
423A SER* 3.9 23.6 - - - -
428A LEU 3.2 16.8 + - - +
429A ARG 3.1 1.6 + - - -
431A PHE* 1.3 81.0 - - - +
433A TYR* 1.3 82.8 + - + +
434A SER 3.7 0.2 - - - -
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LYS* 6.1 5.8 - - + -
295A ARG* 3.6 32.9 + - - +
419A LYS* 4.5 17.5 + - - +
423A SER* 3.2 43.9 + - - -
429A ARG* 2.7 55.0 + - + +
430A GLU* 5.5 0.2 - - - -
432A LEU* 1.3 94.5 - - + +
434A SER* 1.3 57.4 + - - +
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 3.6 27.0 - - - +
304A LYS* 3.5 23.7 + - - -
430A GLU* 2.7 32.6 + - - -
431A PHE 4.4 0.9 + - - +
432A LEU 3.7 2.4 - - - -
433A TYR* 1.3 80.4 - - - +
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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