Contacts of the strand formed by residues 73 - 78 (chain C) 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 ILE 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LYS* 4.6 0.7 - - - -
28C GLY 3.4 3.4 - - - +
30C LEU* 4.0 11.9 - - + +
69C LEU* 3.0 41.2 + - + +
70C ALA* 3.5 21.8 - - - +
72C ASN* 1.3 87.1 - - - +
74C SER* 1.3 59.1 + - - +
75C GLY 3.5 22.4 - - - +
76C VAL* 4.0 17.5 - - + -
101C GLY 5.6 0.2 - - - +
102C ILE* 3.9 16.2 - - + +
299C PHE* 3.9 22.2 - - + -
305C LEU* 4.1 13.7 - - + -
327C LEU* 5.8 1.1 - - + -
331C ALA* 3.9 16.2 - - + -
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS 3.8 7.6 - - - -
22C ILE* 2.6 47.6 + - - +
27C LYS* 3.9 20.3 - - - +
28C GLY 2.9 18.6 + - - -
72C ASN 3.9 1.6 - - - -
73C ILE* 1.3 74.1 - - - +
75C GLY* 1.3 58.7 + - - +
101C GLY 4.4 2.3 - - - +
102C ILE* 3.8 3.7 - - - -
103C ILE* 3.0 32.6 + - - +
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 5.7 1.1 - - - -
29C ILE* 3.3 12.0 - - - -
30C LEU 2.9 24.3 + - - -
73C ILE* 3.4 6.7 - - - +
74C SER* 1.3 86.9 + - - +
76C VAL* 1.3 64.5 + - - -
102C ILE* 3.6 4.0 - - - +
103C ILE* 3.1 14.8 - - - -
144C PHE* 4.3 10.8 - - - -
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.1 28.7 - - + +
32C ALA* 4.2 6.3 - - + -
63C PHE* 3.8 25.6 - - + -
69C LEU* 6.0 1.1 - - + -
73C ILE* 4.0 7.4 - - + -
75C GLY* 1.3 78.4 - - - +
77C ILE* 1.3 69.2 + - - +
78C LEU* 3.7 17.9 + - + +
97C LEU* 4.3 17.7 - - + -
102C ILE* 3.7 19.1 - - + -
103C ILE 3.1 7.4 + - - +
104C LEU* 3.9 2.8 - - + -
105C GLY 3.0 23.3 + - - +
144C PHE* 4.2 1.7 - - - -
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.7 10.8 - - + -
30C LEU 2.8 9.9 + - - -
31C ALA* 4.1 17.5 - - + -
32C ALA* 2.9 33.8 + - - +
33C ASP* 3.5 25.1 - - + +
76C VAL* 1.3 72.7 - - - +
78C LEU* 1.3 66.8 + - - +
105C GLY 3.6 6.7 - - - +
107C LYS 4.1 6.1 - - - +
144C PHE* 3.5 26.5 - - + -
146C LYS* 4.0 32.8 - - + -
185C ILE* 4.7 5.6 - - + -
229C LYS* 4.2 5.6 - - + +
300C SER* 3.8 22.0 - - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA 4.4 2.5 - - - +
33C ASP* 3.7 8.0 - - - +
63C PHE* 3.6 34.5 - - + -
76C VAL* 3.8 17.7 - - + +
77C ILE* 1.3 73.3 - - - +
79C PHE* 1.3 68.2 + - - +
82C THR* 4.2 9.4 - - + +
83C LEU* 3.9 39.5 - - + +
93C PHE* 6.1 1.3 - - + -
94C ALA* 5.6 3.6 - - - +
97C LEU* 4.5 4.7 - - + -
104C LEU* 4.4 20.2 - - + -
105C GLY 2.8 18.7 + - - +
106C ILE* 3.4 9.4 - - + +
107C LYS 3.2 25.1 + - - -
142C CYS* 5.5 0.4 - - - -
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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