Contacts of the helix formed by residues 140 - 147 (chain B) in PDB entry 3S9L
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 PHE 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.0 17.5 - - + -
138B THR* 3.1 37.9 - - - -
139B ASP* 1.3 73.2 + - - +
141B THR* 1.3 64.6 + - - +
142B SER 3.2 2.2 - - - -
143B THR* 3.2 7.1 + - - -
144B ILE* 2.9 33.6 + - + +
424B ALA* 4.9 5.8 - - + +
425B LEU* 3.9 17.0 - - + -
428B LYS* 3.7 27.8 - - + -
432B MET* 4.8 2.0 - - + -
584B ASN* 3.2 12.1 - - - +
587B ALA* 3.7 23.1 - - + -
588B ARG* 4.0 18.4 - - + -
591B ALA* 3.5 32.1 - - + -
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Residues in contact with THR 141 (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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139B ASP* 3.1 14.6 - - - +
140B PHE* 1.3 79.0 - - - +
142B SER* 1.3 66.9 + - - +
144B ILE* 3.5 9.2 + - - +
145B LYS* 3.3 14.9 + - - +
573B TYR* 2.5 43.2 + - - +
577B ILE* 3.9 11.5 - - - +
583B LEU* 4.4 2.7 - - - +
584B ASN* 3.4 33.7 - - + +
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Residues in contact with SER 142 (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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139B ASP* 2.7 40.0 + - - +
141B THR* 1.3 73.8 - - - +
143B THR* 1.3 58.6 + - - +
144B ILE 3.1 0.4 - - - -
145B LYS* 3.0 9.4 + - - +
146B LEU* 2.7 35.1 + - - +
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Residues in contact with THR 143 (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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139B ASP 3.1 17.4 + - - -
140B PHE* 3.2 10.0 + - - -
142B SER* 1.3 80.7 + - - +
144B ILE* 1.3 60.0 + - - +
146B LEU* 3.6 12.6 + - + +
147B LEU* 3.1 26.8 + - + +
168B TYR* 5.8 3.4 - - - +
424B ALA* 4.1 27.8 - - + +
427B LEU* 4.7 16.8 - - + -
428B LYS* 6.1 2.1 - - + +
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Residues in contact with ILE 144 (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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140B PHE* 2.9 22.2 + - + +
141B THR* 3.8 5.2 - - - +
142B SER 3.1 0.2 - - - -
143B THR* 1.3 75.6 - - - +
145B LYS* 1.3 61.9 + - - +
147B LEU* 3.5 5.2 + - - +
148B ASN* 2.8 37.2 + - - +
416B ALA* 4.3 17.5 - - + +
420B GLY 4.5 8.7 - - - +
421B VAL* 4.6 18.6 - - + +
424B ALA* 3.7 22.0 - - + -
488B VAL* 6.5 0.2 - - + -
573B TYR* 4.2 15.6 - - + -
576B LEU* 4.4 6.3 - - + -
583B LEU* 3.9 26.0 - - + -
587B ALA* 5.0 9.4 - - + -
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Residues in contact with LYS 145 (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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141B THR 3.3 11.2 + - - +
142B SER* 3.0 13.6 + - - +
144B ILE* 1.3 77.6 - - - +
146B LEU* 1.3 65.0 + - - +
147B LEU 3.1 0.4 - - - -
148B ASN* 3.0 21.6 + - - +
149B GLU* 3.8 5.0 + - - +
573B TYR* 4.0 29.4 - - + +
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Residues in contact with LEU 146 (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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142B SER 2.7 16.3 + - - +
143B THR* 3.8 13.0 - - + +
144B ILE 3.4 0.2 - - - -
145B LYS* 1.3 78.0 - - - +
147B LEU* 1.3 62.1 + - + +
148B ASN 3.4 0.5 + - - -
149B GLU* 3.4 34.4 - - - +
152B TYR* 3.6 19.3 - - + +
168B TYR* 4.0 37.5 - - + +
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Residues in contact with LEU 147 (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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143B THR* 3.1 19.7 + - + +
144B ILE* 3.8 7.9 - - - +
145B LYS 3.1 1.0 - - - -
146B LEU* 1.3 81.2 - - + +
148B ASN* 1.3 62.8 - - - +
149B GLU 3.4 1.6 - - - -
152B TYR* 3.4 27.3 - - + +
155B ARG* 4.0 14.6 + - - +
165B LEU* 3.7 30.7 - - + -
168B TYR* 4.2 17.3 - - + -
420B GLY* 3.3 31.4 - - - +
423B THR* 4.0 12.1 - - + -
424B ALA* 3.9 17.7 - - + +
427B LEU* 4.8 7.2 - - + -
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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