Contacts of the helix formed by residues 102 - 108 (chain D) in PDB entry 1SA0
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 ASN 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D GLY* 4.1 9.2 - - - +
101D ASN* 1.3 80.0 - - - +
103D TRP* 1.3 63.8 + - - +
104D ALA* 3.8 5.3 - - - +
105D LYS* 2.8 41.6 + - + +
106D GLY 3.8 2.3 + - - -
144D GLY* 4.0 6.8 - - - +
182D VAL* 5.6 0.4 - - + -
186D ASN* 3.7 4.9 - - - -
407D TRP* 3.4 27.1 + - + +
408D TYR* 3.2 34.2 - - + -
411D GLU* 4.6 2.1 - - - +
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Residues in contact with TRP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN* 1.3 67.6 - - - +
104D ALA* 1.3 83.0 + - - +
106D GLY* 2.7 17.0 + - - -
107D HIS* 3.1 41.7 + + + -
108D TYR* 3.6 25.1 - + - -
144D GLY* 4.3 8.7 - - - -
147D SER* 3.1 40.9 + - - -
148D GLY* 3.6 4.4 - - - -
151D THR* 3.6 4.0 + - - -
186D ASN* 2.8 27.0 + - - +
189D LEU* 3.7 50.9 - - + +
190D SER* 3.4 11.7 + - - +
193D GLN* 3.4 24.5 - - - -
408D TYR* 3.7 8.1 - - + -
413D MET* 4.1 3.6 - - - -
417D GLU* 4.0 6.3 - - - -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASN* 3.8 7.0 - - - +
103D TRP* 1.3 90.6 - - - +
105D LYS* 1.3 65.4 + - - +
107D HIS 3.0 0.9 + - - -
108D TYR* 2.9 33.8 + - + +
109D THR* 4.6 1.6 - - - -
408D TYR* 3.8 24.1 - - + -
411D GLU* 3.9 19.3 - - + -
413D MET* 3.9 15.9 - - + -
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLY* 5.3 8.7 - - - -
99D ALA 4.5 3.1 - - - +
100D GLY* 4.0 24.7 - - - +
102D ASN* 2.8 30.0 + - + +
104D ALA* 1.3 72.5 - - - +
106D GLY* 1.3 51.8 + - - +
109D THR* 3.5 9.9 + - - -
110D GLU* 2.9 46.5 + - + -
111D GLY 2.7 28.6 + - - -
411D GLU* 3.2 29.4 - - + +
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Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 5.2 5.2 - - - -
102D ASN 3.8 2.4 + - - -
103D TRP 2.7 14.4 + - - -
105D LYS* 1.3 75.4 - - - +
107D HIS* 1.3 55.1 + - - -
108D TYR 3.5 0.4 - - - -
110D GLU 4.9 0.2 - - - -
111D GLY* 3.1 20.7 - - - -
144D GLY 4.1 10.5 + - - -
145D THR* 5.4 1.8 - - - -
148D GLY 3.4 6.7 - - - -
149D MET* 3.0 30.2 - - - -
152D LEU* 4.1 1.9 - - - +
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Residues in contact with HIS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TRP* 3.1 43.0 + + + +
104D ALA 3.0 2.4 + - - +
106D GLY* 1.3 75.8 - - - +
108D TYR* 1.3 83.3 + + - +
148D GLY 2.9 23.9 + - - +
151D THR* 3.7 6.5 + - - -
152D LEU* 3.1 55.5 + - + +
155D SER* 4.8 4.4 - - - -
193D GLN* 3.2 26.4 + - - -
126E LYS 5.9 0.8 + - - -
130E ALA* 5.3 1.3 - - + +
134E ARG* 5.2 0.7 + - - -
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Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TRP* 3.6 22.0 - + - -
104D ALA* 2.9 20.8 + - + +
106D GLY 3.5 1.8 - - - -
107D HIS* 1.3 102.1 - + + +
109D THR* 1.3 66.1 + - + +
112D ALA* 2.9 32.3 + - - +
411D GLU 5.0 8.5 - - - +
412D GLY 6.0 0.4 - - - -
413D MET* 3.6 25.1 - - + -
417D GLU* 2.6 30.0 + - - -
129E HIS* 3.9 9.5 + + - -
130E ALA* 3.5 42.6 - - + -
133E VAL* 4.9 10.5 - - + +
134E ARG* 3.3 19.6 + - + +
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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