Contacts of the helix formed by residues 86 - 93 (chain D) in PDB entry 1FS1
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 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D HIS* 6.4 0.2 - - - +
65D HIS* 5.6 1.6 - - - +
84D ASP 3.4 9.2 - - - +
85D ILE* 1.3 90.1 - - + +
87D VAL* 1.3 66.9 + - - +
88D TRP* 4.4 5.8 - - + +
89D ASP* 3.1 30.5 + - + +
90D GLN* 2.9 18.2 + - - +
118D VAL* 4.8 4.3 - - + -
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Residues in contact with VAL 87 (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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85D ILE 3.4 1.4 + - - +
86D PRO* 1.3 71.5 - - - +
88D TRP* 1.3 64.2 + - - +
90D GLN* 3.1 20.5 + - + +
91D GLU* 3.0 28.0 + - + +
94D LYS* 6.0 1.1 - - - +
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Residues in contact with TRP 88 (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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3B SER 5.9 0.2 + - - -
5B LYS* 3.5 19.9 - - - +
15B GLU* 3.4 25.2 + - - -
60D GLN* 4.1 10.1 - - + -
61D TRP* 4.0 10.1 - + - -
64D HIS* 3.2 70.8 + + + +
86D PRO* 3.2 4.8 - - + +
87D VAL* 1.3 79.0 - - - +
89D ASP* 1.3 75.2 + - - +
91D GLU* 3.1 26.9 - - + +
92D PHE* 2.8 57.8 + + + +
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Residues in contact with ASP 89 (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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61D TRP* 2.9 14.6 + - - -
64D HIS* 5.3 0.5 + - - -
65D HIS* 2.6 42.1 + - - -
85D ILE* 3.8 3.1 - - + -
86D PRO* 3.1 34.0 + - - +
88D TRP* 1.3 82.9 - - - +
90D GLN* 1.3 67.2 + - - +
92D PHE* 4.1 2.7 - - - -
93D LEU* 2.8 32.4 + - + +
118D VAL* 3.7 25.5 - - + +
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Residues in contact with GLN 90 (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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85D ILE* 2.8 41.7 + - + +
86D PRO 2.9 15.3 + - - +
87D VAL* 3.1 20.9 + - + +
89D ASP* 1.3 77.7 - - - +
91D GLU* 1.3 61.2 + - - +
93D LEU* 3.3 5.9 + - - +
94D LYS* 2.9 41.2 + - - +
122D THR* 5.8 0.9 - - - -
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Residues in contact with GLU 91 (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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5B LYS* 5.2 8.9 + - - +
43B ASP* 5.7 1.0 - - - +
87D VAL* 3.0 17.5 + - + +
88D TRP* 3.1 43.2 - - + +
90D GLN* 1.3 75.2 - - - +
92D PHE* 1.3 67.3 + - - +
94D LYS* 3.0 35.3 + - + +
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Residues in contact with PHE 92 (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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5B LYS* 6.0 0.9 - - - -
15B GLU* 5.9 0.2 - - - -
57D LYS* 3.2 45.0 + - + -
60D GLN* 3.4 31.0 - - + -
61D TRP* 3.7 31.9 - + + -
88D TRP* 2.8 44.7 + + + +
89D ASP* 3.5 3.6 - - - +
91D GLU* 1.3 80.4 - - - +
93D LEU* 1.3 80.8 + - + +
94D LYS 3.3 3.3 + - - -
95D VAL* 3.5 16.8 - - - +
103D LEU* 4.4 11.7 - - + -
115D LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 93 (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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85D ILE* 5.3 0.4 - - + -
89D ASP* 2.8 25.7 + - + +
90D GLN* 3.3 6.0 + - - +
91D GLU 3.2 0.4 - - - -
92D PHE* 1.3 97.4 - - + +
94D LYS* 1.3 59.7 + - - +
95D VAL* 2.8 20.0 + - + +
100D LEU* 4.4 9.0 - - + +
103D LEU* 3.9 20.0 - - + -
118D VAL* 3.7 36.1 - - + +
119D THR* 3.9 14.6 - - + -
122D THR* 3.4 40.8 - - + +
126D MET* 6.1 0.2 - - - +
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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