Contacts of the helix formed by residues 93 - 99 (chain D) 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 PHE 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D ARG* 3.5 26.9 - - + -
59D ARG* 4.0 10.5 - - + -
60D GLN* 3.8 23.3 - - + -
63D PHE* 3.8 23.3 - + + -
78D LEU* 6.3 2.2 - - + -
82D THR* 3.8 21.3 - - + +
83D LEU* 6.1 0.2 - - - -
85D GLN* 3.0 54.1 + - + +
86D LYS 3.9 9.4 - - - -
87D ALA* 3.7 25.1 - - + -
91D THR 3.4 2.0 + - - -
92D PRO* 1.3 70.3 - - - +
94D ALA* 1.3 60.8 + - - +
96D ILE* 3.2 15.3 + - + +
97D LEU* 3.0 31.1 + - + +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LEU* 5.7 2.0 - - - +
83D LEU* 4.2 25.7 + - + +
85D GLN 4.8 0.2 + - - -
92D PRO* 3.1 7.2 - - + +
93D PHE* 1.3 77.4 - - - +
95D GLU* 1.3 58.0 + - - +
97D LEU* 3.6 2.6 + - - -
98D LYS* 3.0 38.8 + - + +
104D LEU* 3.7 25.4 - - + +
140D ASP 4.7 7.6 - - - +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D THR* 3.9 15.5 - - + +
92D PRO* 3.0 34.8 + - + +
94D ALA* 1.3 79.0 - - - +
96D ILE* 1.3 59.2 + - - +
98D LYS* 4.2 3.9 - - - +
99D LYS* 3.0 33.1 + - + +
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D PHE* 3.4 32.8 - - + +
64D SER* 4.7 6.5 - - - -
87D ALA* 3.6 31.2 - - + -
89D ASP* 5.9 0.4 - - - +
91D THR* 3.5 24.5 - - + +
92D PRO 3.1 10.8 + - - +
93D PHE* 3.2 18.6 + - + +
95D GLU* 1.3 78.6 - - - +
97D LEU* 1.3 61.3 + - - +
99D LYS* 3.6 5.5 + - - +
100D LYS* 3.5 33.1 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D PHE* 3.6 63.0 - - + +
69D LEU* 6.3 1.3 - - + -
76D VAL* 4.5 11.4 - - + -
78D LEU* 4.4 11.7 - - + -
93D PHE 3.0 21.9 + - - +
94D ALA 4.1 0.4 - - - +
96D ILE* 1.3 75.4 - - - +
98D LYS* 1.3 64.1 + - - +
100D LYS* 3.3 12.0 + - + +
101D GLY 3.5 0.2 + - - -
102D ILE* 3.1 45.5 + - + +
104D LEU* 3.7 29.4 - - + -
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA* 3.0 25.4 + - + +
95D GLU* 4.2 4.3 - - - +
96D ILE 3.4 0.2 - - - -
97D LEU* 1.3 74.3 - - - +
99D LYS* 1.3 66.5 + - - +
101D GLY* 3.0 15.4 + - - -
102D ILE 3.9 12.1 - - - +
103D ILE* 5.7 1.3 - - - +
104D LEU* 4.0 19.5 - - + +
141D GLY* 3.5 36.8 + - - +
143D ASP* 4.7 10.7 + - - -
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Residues in contact with LYS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLU* 3.0 20.1 + - + +
96D ILE* 3.8 7.2 - - - +
97D LEU 3.3 0.2 - - - -
98D LYS* 1.3 77.0 - - - +
100D LYS* 1.3 62.0 + - + +
101D GLY 3.5 0.9 + - - -
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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