Contacts of the helix formed by residues 253 - 260 (chain D) in PDB entry 6BCH
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 ASN 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D VAL* 3.8 1.6 - - + +
252D THR* 1.3 77.1 - - - +
254D LEU* 1.3 64.2 + - - +
255D ASN* 2.8 29.9 + - - +
256D ASP* 2.8 42.3 + - + +
257D ILE* 3.1 23.2 + - - +
6E A 3.8 25.8 + - - -
7E A 3.3 17.9 + - - +
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Residues in contact with LEU 254 (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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205D SER* 4.1 17.7 - - - +
252D THR 3.2 5.3 + - - -
253D ASN* 1.3 71.4 - - - +
255D ASN* 1.3 59.8 + - + +
257D ILE* 3.3 7.0 + - + +
258D LYS* 2.9 24.5 + - + +
285D VAL* 4.3 18.4 - - + +
288D ILE* 3.9 32.1 - - + +
289D ASP* 4.7 17.5 - - + +
293D HIS* 6.0 0.4 - - + -
5E T 5.5 8.7 - - - +
6E A 2.9 29.3 + - - +
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Residues in contact with ASN 255 (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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253D ASN* 2.8 24.3 + - - +
254D LEU* 1.3 77.4 - - + +
256D ASP* 1.3 64.7 + - - +
258D LYS* 3.6 14.4 - - + -
259D GLU* 3.0 30.3 + - + +
260D LYS* 4.8 0.5 - - - +
6E A 4.5 2.9 + - - -
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Residues in contact with ASP 256 (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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227D ASN* 5.1 1.4 - - - +
228D CYS* 3.9 30.6 - - + +
229D GLY 5.2 0.7 + - - -
251D VAL* 4.1 7.7 - - + +
253D ASN* 2.8 42.2 + - + +
255D ASN* 1.3 80.0 - - - +
257D ILE* 1.3 61.7 + - - +
260D LYS* 2.8 45.5 + - - +
261D ILE* 3.1 6.3 + - - +
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Residues in contact with ILE 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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205D SER* 3.2 43.7 - - - +
207D PHE* 5.1 0.7 - - + -
251D VAL* 3.9 24.7 - - + +
252D THR 4.1 4.0 - - - +
253D ASN 3.1 20.2 + - - +
254D LEU* 3.3 6.5 - - - +
255D ASN 3.3 0.2 - - - -
256D ASP* 1.3 79.3 - - - +
258D LYS* 1.3 60.0 + - - +
261D ILE* 4.0 7.6 - - + -
262D ILE* 3.1 33.0 + - + +
281D TRP* 3.7 32.1 - - + -
285D VAL* 3.9 28.3 - - + -
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Residues in contact with LYS 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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254D LEU* 2.9 19.5 + - + +
255D ASN* 3.6 13.0 - - + -
256D ASP 3.3 0.2 - - - -
257D ILE* 1.3 80.0 - - + +
259D GLU* 1.3 58.8 + - + +
262D ILE* 4.4 9.3 - - - +
263D PRO* 3.5 18.2 - - - +
285D VAL* 5.3 5.8 - - + -
289D ASP* 5.0 12.3 - - - +
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Residues in contact with GLU 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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255D ASN* 3.0 22.5 + - + +
258D LYS* 1.3 77.6 - - + +
260D LYS* 1.3 77.7 + - + +
263D PRO* 4.0 13.0 - - - +
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Residues in contact with LYS 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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226D LEU* 4.1 9.6 - - - +
227D ASN* 3.1 43.5 - - - +
228D CYS* 4.4 6.3 - - - -
255D ASN 4.8 0.4 - - - +
256D ASP* 2.8 31.9 + - + +
258D LYS 3.6 1.0 - - - -
259D GLU* 1.3 95.4 - - + +
261D ILE* 1.3 65.6 + - + +
262D ILE 3.6 0.7 - - - -
263D PRO* 3.5 4.6 - - - +
264D PHE* 3.3 22.9 + - - +
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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