Contacts of the helix formed by residues 67 - 71 (chain B) in PDB entry 1FBA
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B THR 3.8 5.8 - - - +
66B ASP* 1.3 88.6 - - - +
68B LYS* 1.3 60.2 + - - -
69B LEU* 2.9 7.3 + - + -
70B ALA* 3.0 22.1 + - - +
71B GLU* 4.3 1.2 + - - +
100B LYS* 4.5 30.7 - - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASP* 2.8 31.5 + - - +
67B PRO* 1.3 76.5 - - - +
69B LEU* 1.3 62.9 + - - +
71B GLU* 3.0 49.3 + - - +
72B ASN* 4.3 3.0 + - - +
328B LEU* 4.3 25.7 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 5.2 6.1 - - + -
62B LEU 4.2 11.0 - - - +
65B THR* 4.0 19.5 - - + +
66B ASP 2.9 15.1 + - - +
67B PRO* 2.9 1.1 - - + -
68B LYS* 1.3 78.5 - - - +
70B ALA* 1.3 56.2 - - - +
71B GLU 3.0 0.2 - - - -
72B ASN* 3.0 8.2 + - - +
73B ILE* 2.9 55.8 + - + +
76B VAL* 6.3 0.4 - - + -
97B LEU* 6.3 1.3 - - + -
100B LYS* 6.3 2.9 - - + +
102B ILE* 4.6 15.9 - - + -
327B LEU* 4.1 23.1 - - + +
328B LEU* 3.8 18.1 - - + +
331B ALA* 3.9 18.2 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.4 22.0 + - - -
67B PRO* 3.0 15.1 + - - +
69B LEU* 1.3 74.6 - - - +
71B GLU* 1.3 63.2 + - - +
72B ASN 3.2 0.2 - - - -
73B ILE 3.6 16.4 - - - +
100B LYS* 3.2 29.2 - - + +
101B GLY 5.2 2.0 - - - +
102B ILE* 4.2 15.1 - - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO 5.1 0.7 - - - +
26B GLY 3.4 5.0 - - - +
27B LYS* 3.3 22.0 - - - +
67B PRO 4.3 0.9 + - - +
68B LYS* 3.0 41.4 + - - +
69B LEU 3.0 0.8 - - - -
70B ALA* 1.3 80.3 - - - +
72B ASN* 1.3 70.7 + - - +
332B LYS* 5.6 3.6 - - - +
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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