Contacts of the helix formed by residues 71 - 80 (chain F) in PDB entry 1I94
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 ARG 71 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F TYR* 4.1 32.1 - - + +
67F MET* 5.7 2.2 - - + -
68F PRO* 2.8 16.2 + - + +
69F GLU 2.6 6.5 + - - -
70F ASP* 1.3 74.2 - - - +
72F VAL* 1.3 53.4 + - - +
73F ASN 3.2 2.5 - - - -
74F ASP* 2.5 45.3 + - + +
75F LEU* 3.4 3.3 + - - -
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Residues in contact with VAL 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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720A A 3.9 24.7 - - - +
67F MET* 5.4 9.7 - - + +
68F PRO 4.3 1.0 + - - -
69F GLU* 3.0 17.6 + - - +
71F ARG* 1.3 74.6 - - - +
73F ASN* 1.3 58.9 + - - +
74F ASP 2.8 7.3 + - - -
75F LEU* 3.1 16.0 + - - +
76F ALA* 3.2 13.9 + - - +
90F VAL* 5.6 9.9 - - + -
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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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653A G 5.0 20.9 + - - +
654A G 5.8 4.6 - - - +
720A A 4.9 22.1 + - + +
69F GLU 4.7 0.6 + - - -
70F ASP 5.5 0.2 - - - -
71F ARG 2.9 3.0 + - - -
72F VAL* 1.3 75.5 - - - +
74F ASP* 1.3 56.1 + - - +
76F ALA* 4.2 11.8 - - - +
77F ARG* 4.1 12.0 + - - +
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Residues in contact with ASP 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 ASP 5.4 1.1 - - - +
71F ARG* 2.5 28.2 + - + +
73F ASN* 1.3 72.1 - - - +
75F LEU* 1.3 59.5 + - - +
76F ALA 3.2 0.7 - - - -
77F ARG* 2.8 27.9 + - - +
78F GLU* 3.0 7.7 + - - +
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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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29F ALA* 6.0 3.8 - - + +
30F LEU* 5.6 9.6 - - - +
33F TYR* 5.3 11.2 - - + -
71F ARG* 3.4 4.9 + - + +
72F VAL* 3.1 10.2 + - - +
74F ASP* 1.3 72.4 - - - +
76F ALA* 1.3 53.8 + - - +
77F ARG 2.7 9.2 + - - -
78F GLU* 2.7 9.5 + - - +
79F LEU* 2.7 37.4 + - + +
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Residues in contact with ALA 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 VAL 3.2 14.0 + - - +
73F ASN* 4.2 11.9 - - - +
75F LEU* 1.3 79.5 - - - +
77F ARG* 1.3 58.4 + - - +
79F LEU* 4.0 7.7 - - - +
80F ARG* 3.5 21.5 + - - +
88F VAL* 4.5 13.5 - - + +
90F VAL* 5.3 13.5 - - + +
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Residues in contact with ARG 77 (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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73F ASN 4.1 8.9 + - - +
74F ASP* 2.8 19.6 + - - +
75F LEU 2.7 1.0 + - - -
76F ALA* 1.3 77.1 - - - +
78F GLU* 1.3 57.3 + - - +
79F LEU 3.1 1.3 - - - -
80F ARG* 2.9 22.4 + - - +
81F ILE* 3.2 11.3 + - - +
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Residues in contact with GLU 78 (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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29F ALA* 5.4 13.3 - - + +
74F ASP 3.0 6.4 + - - +
75F LEU* 2.7 14.5 + - - +
77F ARG* 1.3 72.8 - - - +
79F LEU* 1.3 62.8 + - - +
80F ARG 3.2 0.2 - - - -
81F ILE* 3.6 18.1 + - - +
82F ARG* 4.5 3.6 + - - +
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Residues in contact with LEU 79 (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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26F ILE* 6.4 3.6 - - + +
29F ALA* 6.0 4.7 - - + +
75F LEU* 2.7 21.3 + - + +
76F ALA* 4.2 7.4 - - - +
78F GLU* 1.3 74.5 - - - +
80F ARG* 1.3 56.5 + - - +
81F ILE 3.2 4.4 + - - -
82F ARG* 3.7 6.6 + - - +
85F VAL* 3.4 23.5 - - + +
88F VAL* 4.7 12.8 - - + -
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Residues in contact with ARG 80 (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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655A U 5.7 9.6 - - - +
76F ALA 3.5 17.2 + - - +
77F ARG* 2.9 9.4 + - - +
79F LEU* 1.3 77.5 - - - +
81F ILE* 1.3 58.3 + - - +
82F ARG 3.3 6.1 - - - +
85F VAL* 4.8 8.5 - - - +
87F ARG* 6.5 0.2 - - - -
88F VAL* 5.0 10.8 - - + +
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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