Contacts of the helix formed by residues 68 - 76 (chain F) in PDB entry 2RHB
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 GLU 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66F VAL 3.5 1.6 + - - -
67F PRO* 1.3 73.0 - - - +
69F ILE* 1.3 67.4 + - - +
70F LYS* 3.2 16.7 + - + -
71F ILE* 3.1 37.5 + - + +
72F LEU 3.6 3.3 + - - -
159F GLN* 3.5 19.9 + - - +
160F ALA* 4.8 1.6 - - - +
161F SER* 4.4 14.6 - - - +
166F THR* 3.2 41.7 + - + +
197F SER* 2.7 33.4 + - - -
272F ASP* 4.6 7.5 - - - +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F PRO 3.5 1.5 + - - +
68F GLU* 1.3 72.2 - - - +
70F LYS* 1.3 57.2 + - - +
72F LEU* 3.1 11.0 + - + +
73F ASN* 2.8 53.3 + - - +
85F ILE* 4.0 15.7 - - + -
86F TRP 3.7 10.1 - - - +
87F ASP* 3.4 52.3 - - + +
88F TYR 4.9 0.7 - - - +
94F ALA* 3.9 22.9 - - + +
95F HIS* 6.2 0.4 - - - +
272F ASP* 5.0 12.1 + - + +
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Residues in contact with LYS 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLU* 3.5 17.8 + - + -
69F ILE* 1.3 78.8 - - - +
71F ILE* 1.3 71.4 - - + +
73F ASN* 3.4 9.2 + - - +
74F ASN* 3.0 36.5 + - - +
195F THR* 3.4 26.0 - - - +
197F SER* 2.7 35.7 + - - +
272F ASP* 3.9 26.1 + - - +
273F SER* 4.0 35.8 + - - +
274F THR* 4.2 12.3 - - - +
323F ASP* 4.4 7.2 - - - +
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Residues in contact with ILE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F PRO* 5.0 1.6 - - + -
68F GLU* 3.1 38.3 + - + +
70F LYS* 1.3 85.6 - - + +
72F LEU* 1.3 60.7 + - - +
74F ASN* 3.0 8.7 + - - +
75F LEU* 2.8 46.2 + - + +
157F PRO* 4.4 23.8 - - + -
159F GLN 5.6 0.7 - - - +
178F TYR* 3.8 26.0 - - + +
194F PHE* 5.3 0.4 - - + -
323F ASP* 4.3 24.2 - - + +
324F TYR* 4.2 16.2 - - + -
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F PRO* 3.8 37.2 - - + +
68F GLU 3.6 2.2 + - - +
69F ILE* 3.1 15.4 + - + +
71F ILE* 1.3 75.4 - - - +
73F ASN* 1.3 64.6 + - - +
75F LEU* 4.5 6.5 - - + -
76F GLY 3.1 4.3 + - - -
77F VAL* 3.0 48.5 + - + +
85F ILE* 3.9 29.8 - - + -
95F HIS* 4.7 10.3 - - - +
122F LEU* 3.6 39.5 - - + -
141F VAL* 5.6 0.4 - - + -
178F TYR* 5.3 3.1 - - + -
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Residues in contact with ASN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASP* 5.1 16.6 + - + +
38D ILE* 5.9 2.8 - - - +
69F ILE* 2.8 44.9 + - - +
70F LYS* 3.6 6.4 - - - +
72F LEU* 1.3 75.2 - - - +
74F ASN* 1.3 64.9 + - - +
76F GLY* 3.2 14.3 + - - -
77F VAL 5.0 5.7 - - - +
94F ALA* 5.4 2.8 - - - +
95F HIS* 5.3 7.1 + - - -
271F MET* 4.7 16.4 - - - +
272F ASP 4.2 14.5 + - - -
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Residues in contact with ASN 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LYS 3.0 25.8 + - - +
71F ILE 3.0 3.1 + - - +
73F ASN* 1.3 77.1 - - - +
75F LEU* 1.3 64.5 + - - +
76F GLY* 3.5 0.7 + - - -
180F LYS* 5.2 1.2 + - - -
274F THR* 2.9 29.7 + - - -
323F ASP* 2.7 34.4 + - - +
324F TYR* 3.7 17.2 - - + +
325F ALA* 3.6 17.6 - - + +
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ILE* 2.8 22.9 + - + +
72F LEU* 3.7 8.5 - - + +
74F ASN* 1.3 76.3 - - - +
76F GLY* 1.3 59.5 + - - +
77F VAL* 4.1 9.2 - - + -
120F THR* 5.0 0.7 + - - +
141F VAL* 3.9 22.1 - - + +
178F TYR* 3.5 39.3 - - + -
180F LYS* 2.8 36.9 + - + +
189F LEU* 4.4 16.2 - - + -
324F TYR* 3.3 44.0 - - + +
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Residues in contact with GLY 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F LEU 3.1 3.2 + - - -
73F ASN* 3.2 14.4 + - - -
74F ASN 4.5 0.4 - - - -
75F LEU* 1.3 79.0 - - - +
77F VAL* 1.3 66.1 + - - +
78F ASP* 2.9 23.1 + - - +
120F THR* 3.5 11.1 + - - -
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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