Contacts of the helix formed by residues 105 - 111 (chain H) in PDB entry 1SMK
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 GLN 105 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E ASP 5.6 0.6 + - - -
233E LYS* 4.9 7.3 - - - +
234E PRO* 3.6 43.0 - - + +
235E PRO* 4.0 2.9 - - - +
76H TYR* 4.4 0.8 - - - -
99H GLY 4.3 0.2 - - - +
100H PHE* 3.4 25.8 - - + +
101H LEU* 3.0 43.8 + - - +
102H GLY 3.2 3.7 + - - +
103H GLN 2.9 0.8 - - - -
104H GLN* 1.3 104.9 - - + +
106H LEU* 1.3 63.5 + - - +
107H GLU 3.5 2.0 - - - -
108H ALA* 3.7 9.3 + - - +
109H ALA* 3.4 15.9 + - - +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LEU* 4.4 3.4 - - + -
76H TYR* 3.8 40.4 - - + -
102H GLY 3.9 1.4 + - - -
103H GLN* 3.3 37.8 + - - +
105H GLN* 1.3 76.0 - - - +
107H GLU* 1.3 68.4 + - - +
109H ALA* 3.4 1.8 + - + +
110H LEU* 3.0 49.1 + - + +
143H THR 4.2 8.1 - - - +
144H LEU* 4.1 12.3 - - + +
146H GLU 4.1 17.5 - - - +
147H GLY* 4.4 5.2 - - - -
151H CYS* 5.9 0.2 - - - -
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLN 5.2 0.2 + - - -
105H GLN 3.5 0.2 - - - -
106H LEU* 1.3 79.7 - - - +
108H ALA* 1.3 55.7 + - - +
111H THR* 2.5 47.9 + - - +
150H LYS* 3.4 31.6 + - - +
151H CYS* 3.3 30.7 - - + -
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E PRO* 4.7 13.0 - - + -
235E PRO 5.2 2.0 - - - +
74H HIS* 3.9 11.3 + - - -
100H PHE* 3.5 27.2 - - + -
105H GLN* 3.7 11.6 - - - +
106H LEU 3.2 0.2 - - - -
107H GLU* 1.3 81.0 - - - +
109H ALA* 1.3 63.5 + - - +
111H THR* 3.7 11.8 + - - +
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Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ALA* 4.2 2.6 - - + +
50H LEU* 5.2 2.7 - - + -
74H HIS* 2.8 35.0 + - + +
76H TYR* 4.1 19.3 - - + -
100H PHE* 3.4 32.4 - - + -
105H GLN 3.4 7.9 + - - +
106H LEU 3.4 4.6 + - - +
107H GLU 3.3 0.6 - - - -
108H ALA* 1.3 79.2 - - - +
110H LEU* 1.3 65.1 + - + +
113H MET* 3.3 10.0 - - - +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ALA* 4.8 2.7 - - + -
50H LEU* 4.0 27.6 - - + -
106H LEU* 3.0 44.5 + - + +
109H ALA* 1.3 77.4 - - - +
111H THR* 1.3 65.5 + - - +
112H GLY 3.3 0.7 + - - -
113H MET* 3.1 21.0 + - - +
116H ILE* 3.6 31.4 - - + -
144H LEU 4.4 1.3 - - - +
147H GLY 3.2 31.6 - - - +
148H ILE* 3.7 7.4 - - + +
151H CYS* 3.8 14.6 - - + -
152H CYS* 3.4 11.1 - - - -
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Residues in contact with THR 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H HIS* 4.7 1.4 - - - -
107H GLU* 2.5 45.9 + - - +
108H ALA* 4.0 10.0 - - - +
109H ALA 3.5 1.7 - - - +
110H LEU* 1.3 71.4 - - - +
112H GLY* 1.3 66.0 + - - +
113H MET* 3.2 16.3 + - - +
151H CYS* 3.3 13.8 - - - +
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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