Contacts of the helix formed by residues 256 - 262 (chain D) in PDB entry 6IWQ
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 GLU 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D GLU* 5.7 3.7 - - - +
255D LYS* 1.3 95.2 + - - +
257D LYS* 1.3 65.1 + - - +
258D LEU 3.1 1.7 - - - +
259D ASP* 3.1 25.3 + - - +
260D GLU* 2.9 27.4 + - - +
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Residues in contact with LYS 257 (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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220D TRP* 3.4 50.3 - - + +
252D GLU 4.5 0.7 - - - +
253D HIS* 3.6 29.6 - - + +
255D LYS 2.6 12.9 + - - +
256D GLU* 1.3 73.9 - - - +
258D LEU* 1.3 55.6 + - - +
260D GLU* 3.4 5.0 + - - +
261D TYR* 2.9 28.1 + - + +
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Residues in contact with LEU 258 (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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215D PHE* 3.9 28.0 - - + -
220D TRP* 3.9 9.4 - - + -
223D LEU* 4.4 6.5 - - + -
224D MET* 3.0 37.2 - - + -
244D LEU* 4.7 5.2 - - + -
253D HIS 3.8 3.8 + - - +
254D LEU* 3.5 35.7 - - + +
256D GLU 3.1 0.8 - - - +
257D LYS* 1.3 80.9 - - - +
259D ASP* 1.3 55.4 + - - +
261D TYR* 3.7 0.2 - - - +
262D ILE* 2.5 61.6 + - + +
271D VAL* 4.8 7.0 - - + -
273D ARG* 4.0 9.6 - - - +
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Residues in contact with ASP 259 (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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256D GLU* 3.1 32.3 + - - +
258D LEU* 1.3 79.5 - - - +
260D GLU* 1.3 64.4 + - + +
262D ILE* 3.5 11.3 + - - +
263D LYS* 3.5 16.5 + - - +
271D VAL* 4.1 17.6 - - - +
273D ARG* 3.5 17.2 + - - -
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Residues in contact with GLU 260 (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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256D GLU 2.9 16.4 + - - +
257D LYS* 3.8 5.2 - - - +
259D ASP* 1.3 78.0 - - + +
261D TYR* 1.3 59.1 + - - +
263D LYS* 2.9 44.0 - - - +
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Residues in contact with TYR 261 (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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185D LEU* 3.6 11.2 - - + +
220D TRP* 3.0 47.1 - + + -
224D MET* 3.9 13.0 - - + -
228D HIS* 2.7 29.3 + - - -
257D LYS* 2.9 10.7 + - + +
258D LEU 3.7 2.2 - - - +
260D GLU* 1.3 71.0 - - - +
262D ILE* 1.3 72.4 + - + +
263D LYS 2.9 10.7 + - - -
264D LEU* 3.1 26.1 + - + +
265D TRP* 3.6 24.2 - + - -
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Residues in contact with ILE 262 (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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224D MET* 3.9 7.4 - - + -
244D LEU* 4.7 3.6 - - + -
258D LEU* 2.5 56.3 + - + +
259D ASP* 3.8 9.0 - - - +
260D GLU 3.3 0.6 - - - -
261D TYR* 1.3 87.3 - - + +
263D LYS* 1.3 56.3 + - - +
264D LEU 2.3 22.6 - - - +
265D TRP* 3.9 11.5 - - + +
266D ASN 4.6 0.7 + - - -
267D GLY 4.6 3.5 + - - -
269D VAL* 3.1 49.1 - - + +
270D LYS* 4.5 2.5 - - - +
271D VAL* 4.7 10.5 - - + -
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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