Contacts of the helix formed by residues 138 - 146 (chain B) in PDB entry 1DY7
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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A MET* 4.3 8.3 - - - -
292A GLN 3.7 7.4 - - - -
293A GLU* 3.5 18.2 + - - -
294A TYR 5.5 0.4 - - - -
136B GLU* 4.1 2.0 - - - +
137B PHE* 1.3 75.7 - - - +
139B MET* 1.3 61.4 + - - -
140B LYS 3.3 2.9 - - - -
141B GLU* 3.1 8.9 + - - +
142B MET* 2.9 30.4 + - - +
281B ILE* 3.8 8.5 - - - -
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Residues in contact with MET 139 (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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290A ASP 5.6 1.6 - - - +
291A GLU 3.2 22.9 - - - +
292A GLN* 3.0 49.0 + - + +
293A GLU* 3.3 0.8 + - - -
138B GLY* 1.3 71.4 - - - -
140B LYS* 1.3 58.3 + - - +
142B MET* 4.5 0.9 - - - -
143B ARG* 2.8 48.5 + - - +
278B PRO* 3.5 51.8 - - - +
279B LYS 4.2 2.7 - - - +
281B ILE* 3.4 13.9 - - + +
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Residues in contact with LYS 140 (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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293A GLU* 2.9 21.2 + - - +
139B MET* 1.3 76.4 - - - +
141B GLU* 1.3 73.7 + - + +
143B ARG* 3.4 6.1 + - - +
144B GLU* 3.0 60.5 + - + +
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Residues in contact with GLU 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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293A GLU* 5.3 3.5 - - - +
135B PRO* 5.4 1.8 - - - +
136B GLU* 2.7 28.5 - - - +
137B PHE* 2.9 39.6 - - + -
138B GLY 3.1 10.8 + - - +
140B LYS* 1.3 91.2 + - + +
142B MET* 1.3 67.1 + - - +
144B GLU* 3.3 13.9 + - - +
145B SER* 3.2 21.5 + - - -
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Residues in contact with MET 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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137B PHE* 3.7 13.5 - - + +
138B GLY 2.9 15.5 + - - +
139B MET 3.8 3.4 - - - +
141B GLU* 1.3 77.3 - - - +
143B ARG* 1.3 61.6 + - - +
145B SER* 2.7 23.9 + - - -
146B TRP* 3.0 11.1 + - - +
236B ILE* 3.5 5.3 - - + +
237B LYS 3.5 17.3 - - - +
238B ILE* 3.5 17.7 - - - +
267B GLN* 3.4 29.2 - - - +
269B VAL* 3.9 29.6 - - + -
278B PRO* 4.1 18.2 - - + -
281B ILE* 3.8 28.9 - - + -
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Residues in contact with ARG 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 MET* 2.8 38.2 + - - +
140B LYS* 3.9 5.2 - - - +
142B MET* 1.3 74.8 - - - +
144B GLU* 1.3 62.8 + - - +
146B TRP* 3.2 49.0 + - + +
277B GLU* 3.3 28.7 + - - +
278B PRO* 3.8 19.2 + - + +
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Residues in contact with GLU 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 LYS* 3.0 55.8 + - + +
141B GLU* 3.6 13.2 - - - +
142B MET 3.2 0.4 - - - -
143B ARG* 1.3 77.2 - - + +
145B SER* 1.3 59.8 - - - +
146B TRP 3.6 2.4 + - - +
147B LYS* 4.6 5.9 - - - +
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Residues in contact with SER 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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137B PHE* 4.8 2.0 - - - -
141B GLU 3.2 9.6 + - - -
142B MET 2.7 16.0 + - - -
144B GLU* 1.3 77.0 - - - +
146B TRP* 1.3 56.5 + - - +
147B LYS* 2.7 36.1 + - - +
235B GLU* 3.7 5.5 - - - +
236B ILE* 3.4 4.4 - - - +
237B LYS* 2.9 45.3 + - - -
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Residues in contact with TRP 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 MET 3.0 14.3 + - - +
143B ARG* 3.2 53.5 + - + +
144B GLU 4.6 1.9 - - - +
145B SER* 1.3 75.1 - - - +
147B LYS* 1.3 69.5 + - - +
148B VAL* 3.6 22.6 - - + +
235B GLU 3.4 13.5 - - - -
236B ILE* 3.7 12.6 - - + -
275B THR* 2.8 30.7 + - + -
276B LEU* 4.1 11.9 - - + -
277B GLU* 3.5 39.7 - - + +
278B PRO* 4.2 7.9 - - + -
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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