Contacts of the helix formed by residues 102 - 111 (chain A) 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 GLY 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TYR* 3.2 21.9 - - - -
77A ASP 3.1 14.2 + - - -
78A VAL* 4.1 11.6 - - - +
101A LEU* 1.3 75.2 - - - +
103A GLN* 1.3 65.1 + - - -
104A GLN* 3.0 14.6 - - - -
105A GLN 2.9 13.0 + - - -
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 3.4 11.3 + - - +
78A VAL* 5.3 1.6 - - - +
102A GLY* 1.3 72.0 - - - -
104A GLN* 1.3 62.8 + - - +
105A GLN 2.9 6.1 + - - -
106A LEU* 3.1 35.1 + - - +
107A GLU* 4.5 1.7 + - - +
143A THR* 4.4 17.4 + - - -
147A GLY* 6.0 1.4 - - - -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU 4.1 2.7 - - - +
102A GLY* 3.0 11.0 - - - -
103A GLN* 1.3 91.2 + - - +
105A GLN* 1.3 71.9 + - + +
107A GLU* 5.2 3.8 + - - +
108A ALA* 5.5 0.5 + - - +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 4.5 2.0 - - - -
99A GLY 4.3 4.2 - - - +
100A PHE* 3.7 18.0 - - + +
101A LEU* 2.7 52.6 + - - +
102A GLY 2.9 4.3 + - - +
104A GLN* 1.3 90.8 - - + +
106A LEU* 1.3 66.0 + - - +
107A GLU 3.2 2.9 - - - -
108A ALA* 3.0 12.9 + - + +
109A ALA* 2.9 21.3 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.1 8.7 - - + -
76A TYR* 3.6 44.4 - - + +
102A GLY 3.5 3.8 + - - -
103A GLN* 3.1 35.1 + - - +
105A GLN* 1.3 76.9 - - - +
107A GLU* 1.3 63.3 + - - +
109A ALA* 3.1 2.3 + - + +
110A LEU* 2.9 55.1 + - + +
143A THR* 4.4 3.6 - - - +
144A LEU* 4.0 30.3 - - + +
147A GLY* 4.3 10.8 - - - -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLN 4.5 2.0 + - - +
104A GLN 5.5 3.8 - - - +
105A GLN* 3.2 1.0 - - - +
106A LEU* 1.3 77.6 - - - +
108A ALA* 1.3 56.0 + - - +
110A LEU* 4.1 0.3 - - - +
111A THR* 2.7 44.7 + - - +
150A LYS* 2.8 39.5 + - - +
151A CYS* 3.6 23.5 - - - -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 3.9 9.0 + - - -
98A ARG* 5.3 4.4 + - - +
100A PHE* 3.6 23.9 - - + -
104A GLN 5.5 0.6 + - - +
105A GLN* 3.0 15.4 + - + +
107A GLU* 1.3 80.1 - - - +
109A ALA* 1.3 63.6 + - - +
111A THR* 4.1 10.5 + - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.1 2.6 - - + +
50A LEU* 5.2 2.5 - - + -
74A HIS* 2.8 28.9 + - + +
76A TYR* 4.0 19.3 - - + -
100A PHE* 3.4 38.7 - - + -
105A GLN 2.9 7.6 + - - +
106A LEU* 3.1 10.3 + - + +
108A ALA* 1.3 78.3 - - - +
110A LEU* 1.3 60.2 + - + +
113A MET* 3.4 8.7 - - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.6 1.8 - - + -
50A LEU* 3.9 30.1 - - + -
106A LEU* 2.9 40.8 + - + +
109A ALA* 1.3 77.0 - - - +
111A THR* 1.3 65.5 + - - +
112A GLY 3.2 0.5 + - - -
113A MET* 3.0 23.1 + - - +
116A ILE* 3.9 23.8 - - + -
144A LEU 4.4 0.7 - - - +
147A GLY* 3.3 36.1 - - - +
148A ILE* 3.5 13.2 - - + +
151A CYS* 3.7 13.9 - - + -
152A CYS* 3.6 11.6 - - - +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 4.7 2.4 - - - -
107A GLU* 2.7 35.3 + - - +
108A ALA* 4.4 10.8 - - - +
109A ALA 3.7 0.6 - - - -
110A LEU* 1.3 72.7 - - - +
112A GLY* 1.3 63.7 + - - +
113A MET* 3.5 10.7 + - - +
151A CYS* 3.9 21.8 - - - +
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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