Contacts of the helix formed by residues 282 - 289 (chain B) in PDB entry 1ES7
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 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASN* 3.2 21.7 + - - -
62A ILE* 3.9 8.2 - - - +
280B TYR 3.3 1.0 + - - -
281B GLU* 1.3 73.9 - - - +
283B SER* 1.3 63.1 + - - +
284B ASP* 3.3 14.0 + - - -
285B PHE* 3.2 21.2 + - - +
286B GLN* 3.3 20.5 + - - +
603C TYR* 6.0 1.8 - - - -
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B HIS* 3.2 37.9 + - - -
278B MET* 3.7 15.9 - - - -
279B LYS 3.5 11.9 + - - -
280B TYR* 2.7 26.0 + - - -
281B GLU 3.2 1.6 + - - -
282B GLY* 1.3 75.7 - - - +
284B ASP* 1.3 63.3 + - - +
287B CYS* 2.8 35.0 + - - +
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Residues in contact with ASP 284 (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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280B TYR 5.9 0.4 - - - -
282B GLY* 3.7 12.2 + - - -
283B SER* 1.3 77.6 + - - +
285B PHE* 1.3 77.4 + - - -
287B CYS* 4.7 3.1 - - - +
288B LYS* 3.2 32.5 + - + +
531C TRP* 4.1 19.2 - - + -
591C TYR* 5.4 3.8 - - + -
601C LYS* 4.1 8.8 - - - +
603C TYR* 3.1 33.4 + - - -
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Residues in contact with PHE 285 (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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59A ASN* 4.1 10.5 - - - -
62A ILE* 3.8 16.8 - - + -
63A VAL* 4.1 18.8 - - + -
66A LEU* 3.6 18.6 - - + +
282B GLY* 3.2 16.1 + - - +
283B SER 3.1 0.8 - - - -
284B ASP* 1.3 90.3 + - - +
286B GLN* 1.3 58.0 + - - +
288B LYS* 3.8 1.9 - - - +
289B ASP 3.0 22.2 + - - -
523C PHE* 6.0 0.9 - + - -
528C TRP* 3.8 32.2 - + - -
531C TRP* 4.1 20.9 - + - -
532C ILE* 4.8 0.9 - - + -
589C MET* 3.8 14.8 - - + -
603C TYR* 3.6 33.9 - + - -
606C MET* 3.7 24.7 - - + -
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Residues in contact with GLN 286 (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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49A PHE* 3.4 35.2 - - + -
50A PRO* 3.1 13.2 - - + +
51A LEU* 2.7 43.0 + - - +
62A ILE* 3.2 39.7 - - + +
65A THR* 6.0 0.2 - - - +
66A LEU* 4.8 0.2 - - - -
278B MET* 3.7 34.6 - - + +
279B LYS 5.4 0.4 + - - -
281B GLU 5.4 1.6 + - - -
282B GLY 3.4 13.6 + - - +
283B SER 3.2 1.4 + - - -
285B PHE* 1.3 75.1 - - - +
287B CYS* 1.3 63.5 + - - +
288B LYS 3.5 0.2 + - - -
289B ASP 3.6 2.9 + - - -
299B ILE* 3.6 10.6 - - - +
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Residues in contact with CYS 287 (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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258B HIS* 4.3 13.0 - - - -
278B MET* 3.5 13.5 - - - -
283B SER 2.8 25.4 + - - +
284B ASP* 4.7 3.1 - - - +
286B GLN* 1.3 72.5 - - - +
288B LYS* 1.3 63.8 + - + +
299B ILE* 3.9 17.2 - - - +
300B GLU* 5.7 0.3 - - - -
301B CYS* 2.0 54.4 + - + +
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Residues in contact with LYS 288 (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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284B ASP* 3.2 23.7 + - + +
285B PHE 3.8 2.9 - - - +
286B GLN 3.2 0.2 - - - -
287B CYS* 1.3 79.3 - - + +
289B ASP* 1.3 77.7 + - - +
290B SER 5.3 0.2 - - - -
291B PRO* 5.6 0.9 - - - +
528C TRP* 4.6 2.2 - - + +
530C ASP* 4.4 8.8 + - - +
531C TRP* 3.7 60.0 - - + +
592C LEU 5.7 1.9 + - - -
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Residues in contact with ASP 289 (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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49A PHE* 3.8 9.5 - - - -
66A LEU* 3.3 11.3 - - - +
285B PHE 3.0 14.3 + - - -
286B GLN 3.6 4.4 + - - +
287B CYS 3.4 0.8 - - - -
288B LYS* 1.3 85.1 - - - +
290B SER* 1.3 81.2 + - - +
291B PRO* 4.1 1.9 - - - +
293B ALA* 5.4 0.2 - - - +
297B ARG* 2.6 58.8 + - - +
299B ILE* 4.1 19.3 + - + +
528C TRP* 2.9 21.5 + - - -
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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