Contacts of the helix formed by residues 260 - 268 (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 LYS 260 (chain D).
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Specific contacts
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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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Residues in contact with ILE 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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187D PHE* 4.6 0.4 - - + -
207D PHE* 4.1 28.7 - - + -
226D LEU* 4.2 24.5 - - + -
228D CYS* 3.9 20.4 - - - -
251D VAL* 4.2 15.9 - - + -
256D ASP 3.1 11.2 + - - +
257D ILE* 3.8 15.0 - - + +
260D LYS* 1.3 73.2 - - - +
262D ILE* 1.3 61.8 + - - +
264D PHE* 3.2 6.7 + - - +
265D PHE* 2.9 50.3 + - + -
278D TYR* 5.2 0.2 - - + -
281D TRP* 4.5 17.3 - - + -
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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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257D ILE* 3.1 19.0 + - + +
258D LYS* 4.4 6.3 - - - +
261D ILE* 1.3 76.0 - - - +
263D PRO* 1.3 74.4 - - + +
266D ASN* 2.9 39.9 + - - +
278D TYR* 3.1 18.5 + - - +
281D TRP* 4.2 14.4 - - + -
282D CYS* 3.8 30.5 - - + +
285D VAL* 4.2 24.2 - - + -
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Residues in contact with PRO 263 (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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258D LYS 3.5 19.3 - - - +
259D GLU* 4.0 13.5 - - - +
260D LYS 3.5 14.4 - - - +
262D ILE* 1.3 95.7 - - + +
264D PHE* 1.3 60.2 + - - +
266D ASN* 3.2 9.8 + - + +
267D LYS* 3.0 30.8 + - + +
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Residues in contact with PHE 264 (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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174D SER* 3.8 11.9 - - - -
177D VAL* 3.5 41.1 - - + -
178D ALA 4.8 0.7 - - - -
225D TYR* 3.6 24.5 - + - -
226D LEU* 4.1 17.3 - - + -
260D LYS 3.3 13.6 + - - +
261D ILE* 3.2 10.7 + - - +
262D ILE 3.2 0.4 - - - -
263D PRO* 1.3 80.1 - - - +
265D PHE* 1.3 77.2 + + - +
267D LYS* 3.2 2.3 + - - -
268D ASN* 2.6 71.1 + - + +
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Residues in contact with PHE 265 (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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177D VAL* 4.5 2.7 - - + -
178D ALA* 4.6 2.5 - - - -
181D THR* 3.1 44.6 - - + -
187D PHE* 4.0 9.9 - + - -
207D PHE* 3.8 22.4 - + - -
226D LEU* 5.4 3.1 - - + -
261D ILE* 2.9 49.0 + - + -
262D ILE 3.8 0.4 - - - -
264D PHE* 1.3 99.0 - + - +
266D ASN* 1.3 62.0 + - - +
268D ASN 3.2 27.4 - - - +
269D HIS* 3.7 8.3 + - - -
270D ILE* 3.7 18.6 + - + -
278D TYR* 3.3 29.7 - + + +
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Residues in contact with ASN 266 (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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262D ILE* 2.9 36.5 + - - +
263D PRO* 3.4 8.9 - - + +
264D PHE 3.1 0.2 - - - -
265D PHE* 1.3 81.2 - - - +
267D LYS* 1.3 75.9 + - - +
269D HIS* 3.1 22.3 + - - -
278D TYR* 3.5 17.7 + - - -
279D ARG* 4.4 13.3 + - - +
282D CYS* 5.0 0.3 - - - -
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Residues in contact with LYS 267 (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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175D ASN* 5.3 1.0 - - - +
263D PRO* 3.0 18.1 + - + +
264D PHE* 3.8 2.2 - - - +
266D ASN* 1.3 98.5 + - - +
268D ASN* 1.3 68.1 + - - +
269D HIS* 3.3 16.8 + - - -
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Residues in contact with ASN 268 (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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174D SER* 2.7 33.5 + - - +
175D ASN* 3.6 14.1 - - - +
178D ALA* 3.9 18.7 - - + +
264D PHE* 2.6 61.4 + - + +
265D PHE* 3.2 25.8 - - - +
267D LYS* 1.3 80.5 - - - +
269D HIS* 1.3 64.3 + - - +
270D ILE 3.5 0.9 + - - -
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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