Contacts of the helix formed by residues 108 - 111 (chain B) in PDB entry 3I58
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 LEU 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 11.2 - - + -
111A VAL* 3.8 17.0 - - + +
20B MET* 3.7 33.7 - - + -
23B ARG* 4.4 7.6 - - - +
99B MET* 4.0 26.2 - - + +
104B GLY 3.5 16.8 - - - +
105B ARG* 3.5 9.4 - - - +
106B GLY 3.2 1.0 - - - -
107B ASP* 1.3 75.7 - - - +
109B GLY* 1.3 61.0 + - - +
110B PHE 3.0 2.0 + - - -
111B VAL* 3.1 27.4 + - - +
127B ARG* 3.5 27.5 - - - +
128B TYR* 4.1 9.2 - - - +
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG 4.0 0.6 + - - -
106B GLY 2.8 17.4 + - - -
108B LEU* 1.3 77.4 - - - +
110B PHE* 1.3 64.7 + - - +
111B VAL* 3.1 0.4 - - - -
112B GLU* 3.0 13.7 + - - +
123B ALA* 3.6 19.3 - - - +
124B TYR* 4.9 9.9 - - - -
127B ARG* 4.0 19.6 - - - +
128B TYR* 4.9 3.1 - - - -
292B THR* 4.7 4.3 - - - -
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 5.7 0.2 - - - -
16A LEU* 4.2 13.0 - - + -
17A ALA* 3.8 42.6 - - + -
20A MET* 3.4 20.8 - - + +
106B GLY 4.3 0.2 + - - -
107B ASP* 2.8 31.8 + - + +
109B GLY* 1.3 72.8 - - - +
111B VAL* 1.3 56.9 + - - +
112B GLU 2.8 6.3 - - - -
113B LEU* 2.8 43.2 + - + +
285B GLY 4.6 0.2 - - - -
288B LEU* 3.9 11.7 - - + -
289B ARG* 3.5 52.0 - - + -
292B THR* 3.5 30.4 + - + -
293B TYR* 5.2 0.4 - + - -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 5.9 4.5 - - + -
20A MET* 3.7 27.6 - - + +
99A MET* 5.0 4.0 - - - +
108A LEU* 4.3 22.0 - - + +
111A VAL* 3.3 33.7 - - + -
127A ARG* 3.6 28.5 + - - +
16B LEU* 5.7 3.6 - - + -
20B MET* 6.3 0.2 - - - -
108B LEU* 3.1 15.2 + - - +
110B PHE* 1.3 76.5 - - + +
112B GLU* 1.3 72.5 + - + +
113B LEU 3.4 0.4 - - - -
114B ALA 5.3 0.2 + - - -
127B ARG* 4.1 14.1 - - - +
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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