Contacts of the helix formed by residues 88 - 92 (chain N) in PDB entry 3FKS
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 GLY 88 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87N VAL* 1.3 77.6 - - - +
89N ARG* 1.3 60.7 + - - -
90N GLU 3.3 2.2 - - - -
91N THR* 2.9 19.6 + - - -
92N LEU 4.5 0.3 + - - -
239N ILE* 5.4 0.2 - - - +
242N TYR* 4.0 26.8 - - - +
243N PHE* 2.9 25.2 - - - -
247N GLU* 5.0 1.6 - - - -
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Residues in contact with ARG 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP 4.7 5.1 + - - -
119B GLY* 2.9 31.3 + - - -
120B LYS* 3.5 23.0 - - - +
121B GLY* 4.9 8.3 - - - +
88N GLY* 1.3 70.3 - - - -
90N GLU* 1.3 61.3 + - + +
91N THR 3.0 7.2 + - - -
92N LEU* 3.2 35.5 + - + +
181N PHE* 3.6 26.2 - - - -
212N GLU* 3.4 22.6 + - - -
243N PHE* 4.2 4.0 - - + -
247N GLU* 3.5 31.7 + - - +
249N GLN* 4.0 5.9 - - - +
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Residues in contact with GLU 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLY* 5.8 0.3 - - - -
122B PRO* 4.5 19.0 - - + +
87N VAL 5.3 0.4 - - - +
88N GLY* 3.3 1.4 - - - -
89N ARG* 1.3 78.0 - - + +
91N THR* 1.3 58.7 + - - +
92N LEU 3.5 2.2 - - - +
94N ARG* 3.9 9.7 + - - +
109N ILE* 3.0 28.7 - - + +
110N LYS* 3.3 39.9 + - - +
111N SER* 4.0 15.5 - - - +
112N LYS 5.3 1.1 - - - +
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Residues in contact with THR 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N PRO* 3.3 48.7 - - + +
87N VAL* 4.3 4.9 - - - +
88N GLY 2.9 17.8 + - - -
90N GLU* 1.3 82.1 - - - +
92N LEU* 1.3 65.9 + - - +
93N GLY 3.2 0.2 + - - -
94N ARG* 3.1 28.5 + - - +
96N ILE* 5.1 12.4 - - + +
109N ILE* 4.5 5.2 - - + -
111N SER* 5.1 0.9 - - - +
216N ALA* 4.0 12.6 - - - +
239N ILE* 4.2 16.7 - - + +
243N PHE* 4.6 1.2 - - - -
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Residues in contact with LEU 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N ARG* 3.2 38.2 + - + +
90N GLU 4.6 1.4 - - - +
91N THR* 1.3 78.8 + - - +
93N GLY* 1.3 60.5 + - - +
94N ARG* 4.0 4.7 - - - +
181N PHE* 3.3 55.9 - - + -
182N SER 4.5 1.6 - - - +
183N VAL* 6.3 0.2 - - + -
212N GLU* 5.5 2.9 - - + +
213N SER* 4.0 17.1 + - - +
214N LYS 3.7 2.0 - - - +
215N VAL* 3.6 28.9 - - - +
216N ALA* 4.1 7.0 - - + +
243N PHE* 4.6 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