Contacts of the helix formed by residues 80 - 93 (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 PRO 80 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27I ALA* 4.9 4.9 - - + +
30I VAL* 3.9 18.6 - - + +
31I ASP* 3.2 32.3 - - - +
34I LEU* 3.4 22.2 - - + -
78I THR 3.8 4.5 - - - +
79I ASP* 1.3 92.7 - - - +
81I ALA* 1.3 61.1 + - - +
83I VAL* 3.1 6.3 + - + +
84I LEU* 3.0 32.5 + - + +
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Residues in contact with ALA 81 (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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79I ASP* 3.1 22.8 + - - +
80I PRO* 1.3 79.9 - - - +
82I GLN* 1.3 57.4 + - - +
84I LEU* 3.4 10.2 + - - +
85I ASN* 2.9 39.6 + - - +
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Residues in contact with GLN 82 (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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74I MET* 3.7 15.3 - - + +
77I CYS* 3.6 22.8 - - - +
78I THR* 3.3 8.7 + - - -
79I ASP* 2.9 47.7 + - + +
81I ALA* 1.3 77.8 - - - +
83I VAL* 1.3 56.4 + - - +
85I ASN* 3.3 7.3 - - - +
86I GLU* 3.0 31.9 + - - +
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Residues in contact with VAL 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL* 3.8 28.3 - - + -
34I LEU* 4.8 1.8 - - + -
40I PRO* 3.9 29.8 - - + -
42I LEU* 4.1 20.4 - - + +
74I MET* 4.2 9.9 - - - -
77I CYS* 4.0 14.8 - - - -
79I ASP 4.3 1.3 - - - +
80I PRO* 3.5 7.2 - - + +
82I GLN* 1.3 74.1 - - - +
84I LEU* 1.3 61.5 + - - +
86I GLU* 3.1 5.4 + - - +
87I LEU* 2.9 26.3 + - - +
101I ILE* 4.3 23.3 - - + -
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Residues in contact with LEU 84 (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* 5.6 5.8 - - + +
26I LEU* 3.8 30.1 - - + -
27I ALA* 4.2 24.0 - - + +
30I VAL* 4.1 20.2 - - + -
80I PRO* 3.0 22.9 + - + +
81I ALA* 4.0 7.6 - - - +
83I VAL* 1.3 74.0 - - - +
85I ASN* 1.3 61.5 + - - +
87I LEU* 3.3 13.6 + - + +
88I GLU* 3.1 27.7 + - + +
101I ILE* 5.2 2.0 - - + -
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Residues in contact with ASN 85 (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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81I ALA* 2.9 24.3 + - - +
82I GLN* 3.3 9.6 - - - +
84I LEU* 1.3 75.1 - - - +
86I GLU* 1.3 66.9 + - + +
88I GLU* 3.2 9.4 + - - +
89I GLU* 3.0 23.7 + - - +
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Residues in contact with GLU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I LEU* 3.7 16.3 - - + +
70I TRP* 2.8 33.4 + - + +
71I LYS* 2.9 30.9 + - - +
74I MET* 3.8 21.1 - - + +
82I GLN 3.0 14.8 + - - +
83I VAL* 3.1 8.2 + - - +
85I ASN* 1.3 80.6 - - + +
87I LEU* 1.3 52.6 + - - +
89I GLU* 3.2 11.5 + - - +
90I CYS* 2.7 36.6 + - - +
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Residues in contact with LEU 87 (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* 3.9 28.5 - - + -
42I LEU* 3.6 12.9 - - + +
83I VAL 2.9 13.5 + - - +
84I LEU* 3.4 15.5 - - + +
85I ASN 3.2 0.2 - - - -
86I GLU* 1.3 76.1 - - - +
88I GLU* 1.3 64.4 + - - +
90I CYS* 3.2 1.4 + - - +
91I LYS* 2.9 47.5 + - + +
99I ILE* 3.9 28.0 - - + -
101I ILE* 4.4 10.1 - - + -
117I ALA* 4.0 26.7 - - + +
118I TYR* 4.5 2.5 - - + -
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Residues in contact with GLU 88 (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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84I LEU 3.1 17.8 + - - +
85I ASN* 3.2 10.1 + - - +
87I LEU* 1.3 82.1 - - - +
89I GLU* 1.3 57.7 - - - +
91I LYS* 2.8 39.9 + - - +
92I LYS* 2.9 29.0 + - - +
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Residues in contact with GLU 89 (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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70I TRP* 3.5 11.7 - - + -
71I LYS* 3.0 33.4 + - - -
85I ASN* 3.0 14.3 + - - +
86I GLU* 3.5 14.3 - - - +
88I GLU* 1.3 78.0 - - - +
90I CYS* 1.3 59.8 + - - +
92I LYS* 2.8 62.7 + - - +
93I GLU* 3.1 3.8 + - - +
1S MET 5.3 0.9 - - - +
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Residues in contact with CYS 90 (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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42I LEU* 4.2 7.2 - - + -
44I PHE* 4.1 18.8 - - - -
70I TRP* 3.6 43.3 - - + -
86I GLU 2.7 20.5 + - - +
87I LEU 3.7 4.3 - - - +
89I GLU* 1.3 71.4 - - - +
91I LYS* 1.3 51.9 + - - +
93I GLU* 3.2 2.8 + - - +
94I TYR* 2.7 37.4 + - - +
99I ILE* 3.7 29.8 - - + -
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Residues in contact with LYS 91 (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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87I LEU* 2.9 32.9 + - + +
88I GLU* 2.8 38.8 + - - +
90I CYS* 1.3 77.4 - - - +
92I LYS* 1.3 61.3 + - - +
94I TYR 4.4 2.0 - - - -
95I PRO* 3.1 28.8 - - - +
99I ILE* 3.7 11.9 - - + +
117I ALA 5.6 0.4 - - - +
118I TYR* 3.6 47.1 - - + -
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Residues in contact with LYS 92 (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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88I GLU 2.9 15.7 + - - +
89I GLU* 2.8 60.1 + - - +
91I LYS* 1.3 76.9 - - - +
93I GLU* 1.3 95.8 + - - +
95I PRO* 3.7 8.7 - - - +
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Residues in contact with GLU 93 (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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70I TRP* 3.5 21.6 - - + -
89I GLU* 3.1 10.8 + - - +
90I CYS 3.8 2.9 - - - +
92I LYS* 1.3 104.5 + - - +
94I TYR* 1.3 84.1 + - + +
95I PRO* 3.5 6.7 - - - +
96I ASN* 5.1 0.3 - - - +
3S VAL* 4.3 16.8 + - - +
5S PRO* 6.0 1.4 - - - +
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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