Contacts of the helix formed by residues 134 - 142 (chain N) in PDB entry 3SDI
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 ILE 134 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362 GLY* 4.9 0.2 - - - -
2N SER* 5.6 0.4 - - - -
126N ILE* 4.0 15.0 - - + -
131N SER* 3.0 24.8 + - - +
133N PHE* 1.3 85.3 - - + +
135N TYR* 1.3 60.2 + - - +
136N GLY 3.3 2.2 - - - -
137N TYR* 3.8 11.2 - - + -
138N CYS* 2.8 51.5 + - - +
158N SER* 3.3 36.8 - - - +
159N LEU* 4.7 8.3 - - + -
161N GLN* 3.8 12.1 - - + -
162N ALA* 3.6 27.8 - - + +
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Residues in contact with TYR 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332 PHE* 4.2 11.2 - + + -
1652 TRP* 3.3 64.9 + + + +
24M LEU* 3.7 25.3 - - + +
26M ARG* 3.7 31.4 + - + -
124N TYR* 5.0 0.2 + - - -
126N ILE* 3.7 32.1 + - + -
131N SER* 3.2 39.1 + - - -
132N THR* 3.6 19.4 + - + +
133N PHE 3.6 1.6 - - - -
134N ILE* 1.3 76.1 - - - +
136N GLY* 1.3 56.8 + - - +
138N CYS* 4.1 0.7 - - - +
139N ASP* 3.0 25.8 + - - +
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Residues in contact with GLY 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332 PHE 3.0 19.5 + - - -
1342 ILE* 4.9 0.2 - - - -
1372 TYR* 4.2 9.9 - - - -
1612 GLN* 3.0 29.4 + - - -
1652 TRP* 3.8 2.0 - - - +
135N TYR* 1.3 75.3 - - - +
137N TYR* 1.3 65.0 + - - +
140N LYS* 3.2 28.8 + - - +
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Residues in contact with TYR 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332 PHE 4.6 0.4 + - - -
1362 GLY* 4.4 4.0 - - - -
1372 TYR* 3.9 31.6 - + - +
1402 LYS* 3.6 39.5 - - + -
1412 ASN* 5.2 1.6 - - - -
134N ILE* 3.3 17.4 + - + +
136N GLY* 1.3 75.2 - - - +
138N CYS* 1.3 64.2 + - - +
140N LYS 3.2 1.2 + - - -
141N ASN* 3.2 58.4 + - + +
154N PHE* 4.6 5.6 - + - -
157N HIS* 3.2 31.0 + - + +
158N SER* 3.6 40.8 - - - -
161N GLN* 5.0 3.4 - - + -
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Residues in contact with CYS 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N MET* 4.0 14.8 - - - -
124N TYR* 3.6 22.7 - - + +
126N ILE* 4.1 9.4 - - + -
134N ILE* 2.8 41.0 + - - +
135N TYR 4.1 2.0 - - - +
137N TYR* 1.3 69.0 - - - +
139N ASP* 1.3 66.4 + - - +
140N LYS 3.0 2.6 + - - -
142N PHE* 3.1 28.9 + - - +
154N PHE* 4.0 8.3 - - + -
158N SER* 3.3 27.6 - - - -
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Residues in contact with ASP 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1612 GLN* 3.2 24.1 - - - +
1642 LYS* 2.8 33.1 + - - -
1652 TRP* 3.7 22.8 - - + -
124N TYR* 3.5 10.3 + - - -
135N TYR 3.0 20.0 + - - +
138N CYS* 1.3 76.7 - - - +
140N LYS* 1.3 61.0 + - - +
142N PHE* 4.5 7.8 + - - +
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Residues in contact with LYS 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372 TYR* 3.7 37.7 - - + -
1572 HIS* 4.0 19.6 + - - +
1602 SER* 4.7 4.9 + - - -
1612 GLN* 4.1 23.4 + - + +
1872 LEU* 2.9 45.7 + - - +
136N GLY 3.2 18.5 + - - +
137N TYR 3.7 0.7 - - - +
138N CYS 3.0 1.0 - - - -
139N ASP* 1.3 81.2 - - - +
141N ASN* 1.3 72.7 + - - +
142N PHE 3.7 1.3 - - - +
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Residues in contact with ASN 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372 TYR* 5.1 4.0 - - - -
137N TYR* 3.2 46.2 + - + +
140N LYS* 1.3 88.7 - - - +
142N PHE* 1.3 62.1 - - - +
143N ARG* 3.5 21.7 + - - -
146N MET* 4.6 2.3 - - - +
154N PHE* 4.1 21.4 - - + -
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Residues in contact with PHE 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N VAL* 3.7 31.0 - - + -
7N THR* 4.0 10.5 - - - -
123N PRO* 3.7 29.4 - - + -
124N TYR* 3.7 36.1 - + + -
138N CYS 3.1 18.2 + - - +
139N ASP 4.5 6.0 + - - +
140N LYS 3.7 2.0 - - - +
141N ASN* 1.3 76.7 - - - +
143N ARG* 1.3 81.9 + - - +
144N GLU* 3.9 24.7 - - + -
146N MET* 4.7 4.5 - - - -
154N PHE* 3.8 17.0 - + + -
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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