Contacts of the helix formed by residues 109 - 112 (chain F) in PDB entry 1I43
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 109 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F THR 4.6 6.3 - - - -
85F SER 3.0 24.6 + - - -
87F TYR* 3.9 9.4 - - - -
108F TYR* 1.3 73.5 - - - +
110F ARG* 1.3 60.3 + - - +
111F TYR 3.0 0.2 - - - -
112F GLY* 3.0 26.4 + - - +
113F ASN* 5.2 1.7 - - - +
294F ALA* 4.8 6.1 - - - +
270H LEU* 4.0 11.9 - - - -
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F TYR* 3.1 23.5 + - + -
109F GLY* 1.3 75.0 - - - +
111F TYR* 1.3 90.3 + - + +
112F GLY 3.5 0.4 - - - -
288F HIS* 4.9 6.4 + - - +
289F HIS* 3.0 41.4 + - - +
292F GLY* 3.7 25.1 - - - -
294F ALA* 4.5 15.0 - - + +
137H SER* 3.9 10.5 - - - +
139H MET* 3.3 26.0 - - - +
163H TYR* 3.2 25.5 + - - -
165H LYS* 4.3 4.4 - - - +
270H LEU* 3.6 20.3 - - + +
500H PLP 2.8 30.2 + - - -
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Residues in contact with TYR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PHE* 3.5 24.4 - - - +
107F GLU* 3.9 11.0 - - + -
108F TYR* 2.9 34.5 + + + +
110F ARG* 1.3 108.7 + - + +
112F GLY* 1.3 55.1 + - - +
285F ARG* 5.4 4.5 + - - -
289F HIS* 3.6 55.1 + + + +
165H LYS* 3.2 31.2 + - - +
607H PMC 2.8 30.8 + - - +
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Residues in contact with GLY 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F TYR* 3.2 11.6 + - - -
106F PHE* 3.8 16.4 - - - -
108F TYR 3.6 0.8 + - - -
109F GLY* 3.0 21.7 + - - +
110F ARG 3.5 1.0 - - - -
111F TYR* 1.3 81.6 - - - +
113F ASN* 1.3 65.1 + - - +
116F THR* 5.2 3.6 - - - -
117F VAL* 5.8 1.6 - - - -
285F ARG* 6.3 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