Contacts of the helix formed by residues 23 - 35 (chain I) 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 THR 23 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22I THR* 1.3 74.4 - - - +
24I ASP* 1.3 65.5 + - - +
26I LEU* 3.3 10.9 + - + +
27I ALA* 3.0 28.7 + - + +
84I LEU* 5.6 5.0 - - + +
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Residues in contact with ASP 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 3.2 7.6 + - - +
23I THR* 1.3 86.3 - - - +
25I GLN* 1.3 59.5 + - + +
27I ALA* 3.4 8.2 + - - +
28I ARG* 3.0 35.7 + - + +
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Residues in contact with GLN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429H GLN* 3.8 17.1 + - - +
433H GLU* 3.9 20.7 - - - +
19I PRO* 4.9 2.0 + - - +
20I PRO 3.6 6.9 + - - -
21I LEU* 3.3 23.9 - - + +
22I THR* 2.9 41.4 + - - +
24I ASP* 1.3 75.1 - - + +
26I LEU* 1.3 66.0 + - - +
28I ARG* 3.3 4.7 + - - +
29I GLN* 3.2 27.1 + - - +
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Residues in contact with LEU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I LEU* 4.1 18.6 - - + +
22I THR 2.9 13.0 + - - +
23I THR* 3.5 13.5 - - + +
25I GLN* 1.3 77.5 - - - +
27I ALA* 1.3 63.8 + - - +
29I GLN* 3.0 15.1 + - - +
30I VAL* 3.1 16.1 + - + +
84I LEU* 3.8 24.7 - - + -
87I LEU* 3.9 17.9 - - + -
101I ILE* 4.6 2.2 - - + -
115I PHE* 3.4 32.3 - - + -
117I ALA* 4.2 19.3 - - + +
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Residues in contact with ALA 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I THR* 3.0 18.3 + - + +
24I ASP* 3.4 10.1 + - - +
26I LEU* 1.3 76.0 - - - +
28I ARG* 1.3 56.7 + - - +
30I VAL* 3.2 7.6 + - - +
31I ASP* 2.9 35.2 + - - +
80I PRO* 4.9 4.1 - - + +
84I LEU* 4.2 24.7 - - + +
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Residues in contact with ARG 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432H ASN 4.2 4.8 - - - +
433H GLU* 3.1 58.5 + - + +
24I ASP* 3.0 23.5 + - + +
25I GLN* 3.5 9.0 - - - +
26I LEU 3.2 0.4 - - - -
27I ALA* 1.3 75.9 - - - +
29I GLN* 1.3 59.2 + - - +
31I ASP* 3.3 15.1 + - - +
32I TYR* 3.0 27.5 + - - +
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429H GLN* 3.9 24.4 + - - +
432H ASN* 3.0 39.4 + - - +
433H GLU* 4.3 6.8 - - - +
15I LEU* 4.0 30.2 - - + +
21I LEU* 4.5 8.1 - - + -
25I GLN 3.2 12.9 + - - +
26I LEU 3.0 9.6 + - - +
28I ARG* 1.3 76.4 - - - +
30I VAL* 1.3 62.8 + - - +
32I TYR* 3.2 11.2 + - - +
33I LEU* 3.1 20.6 + - - +
113I ILE* 5.5 4.6 - - - +
115I PHE* 3.7 28.1 - - + -
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Residues in contact with VAL 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I LEU* 3.1 14.8 + - + +
27I ALA* 3.6 8.3 - - - +
29I GLN* 1.3 72.8 - - - +
31I ASP* 1.3 66.3 + - - +
33I LEU* 3.2 13.8 + - + +
34I LEU* 3.0 25.6 + - + +
80I PRO* 3.9 20.0 - - + +
83I VAL* 3.8 34.1 - - + -
84I LEU* 4.1 21.3 - - + -
101I ILE* 4.3 22.7 - - + -
115I PHE* 4.6 4.9 - - + -
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Residues in contact with ASP 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA* 2.9 20.1 + - - +
28I ARG* 3.5 19.8 - - - +
30I VAL* 1.3 77.1 - - - +
32I TYR* 1.3 52.7 + - - +
34I LEU* 3.3 4.0 + - - +
35I ASN* 2.8 53.7 + - - +
80I PRO* 3.2 26.9 - - - +
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Residues in contact with TYR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396H ASP* 4.4 4.2 + - - -
431H ARG* 3.6 21.9 + - + -
432H ASN* 3.2 68.8 + - + +
28I ARG 3.0 8.8 + - - +
29I GLN* 3.4 11.7 - - - +
30I VAL 3.2 0.2 - - - -
31I ASP* 1.3 77.7 - - - +
33I LEU* 1.3 59.7 + - - +
35I ASN* 3.4 7.5 + - + +
36I ASN* 2.7 54.9 + - - -
38I TRP* 3.6 16.4 - + - -
113I ILE* 3.3 34.1 - - + -
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I GLN 3.1 9.8 + - - +
30I VAL* 3.2 14.8 + - + +
32I TYR* 1.3 80.0 - - - +
34I LEU* 1.3 65.1 + - + +
36I ASN* 3.3 7.3 + - - +
38I TRP* 3.1 69.4 + - + +
40I PRO* 3.9 22.4 - - + -
101I ILE* 4.2 14.1 - - + -
102I ILE 3.8 9.6 - - - +
103I GLY* 3.8 23.1 - - - +
113I ILE* 4.0 24.2 - - + -
115I PHE* 5.5 0.7 - - + -
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Residues in contact with LEU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I VAL* 3.0 22.5 + - + +
31I ASP* 3.9 3.8 - - - +
33I LEU* 1.3 75.1 - - + +
35I ASN* 1.3 62.4 + - - +
37I LYS* 2.9 26.0 + - - +
38I TRP 4.3 6.1 - - - +
40I PRO* 3.9 30.7 - - + -
77I CYS* 3.7 26.2 - - - +
78I THR* 4.1 10.1 - - - +
79I ASP 3.8 5.8 - - - -
80I PRO* 3.4 48.7 - - + -
83I VAL* 4.8 0.4 - - + -
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Residues in contact with ASN 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ASP* 2.8 41.2 + - - +
32I TYR* 3.8 8.2 - - + +
34I LEU* 1.3 75.4 - - - +
36I ASN* 1.3 64.5 + - - +
37I LYS* 3.1 12.5 + - - +
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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