Contacts of the helix formed by residues 267 - 277 (chain A) in PDB entry 3BMW
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 ASP 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A LYS* 5.2 3.6 - - - -
259A TRP* 3.2 24.4 + - - -
261A LEU* 3.9 22.2 - - + +
265A GLU* 4.2 11.0 + - - +
266A ILE* 1.3 79.3 - - - +
268A VAL* 1.3 59.3 + - - +
269A ASN* 2.9 28.4 + - - +
270A ASN* 3.0 30.3 + - + +
271A THR* 3.5 7.6 + - - -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ILE* 4.3 11.6 - - + +
267A ASP* 1.3 72.9 + - - +
269A ASN* 1.3 70.9 + - - +
271A THR* 3.4 11.3 + - - -
272A TYR* 3.1 27.4 + - - +
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.5 43.6 + - + +
259A TRP* 3.6 21.2 - - + -
267A ASP* 2.9 18.4 + - - +
268A VAL* 1.3 84.3 - - - +
270A ASN* 1.3 59.1 + - - +
272A TYR* 3.8 9.2 - - - +
273A PHE* 3.0 29.6 + - - +
621A PRO* 6.1 1.0 - - - +
635A TYR* 5.4 1.6 + - - -
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A TRP* 3.5 51.7 + - + +
261A LEU* 3.5 20.5 - - - +
267A ASP* 3.0 20.0 + - + +
269A ASN* 1.3 76.4 - - - +
271A THR* 1.3 68.3 + - - +
273A PHE* 3.4 1.2 + - - +
274A ALA* 3.1 19.2 + - - +
281A LEU* 3.5 19.3 - - - +
282A LEU 5.3 2.6 + - - -
285A ARG* 4.9 1.6 + - - -
315A TYR* 2.7 28.0 + - - -
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASP 3.5 7.4 + - - -
268A VAL* 3.4 12.2 + - - -
270A ASN* 1.3 82.1 + - - +
272A TYR* 1.3 64.3 + - - +
274A ALA* 3.3 4.2 + - - +
275A ASN* 3.1 29.5 + - - +
285A ARG* 4.1 18.2 + - - -
314A ASP* 3.5 38.5 + - + +
315A TYR* 4.1 8.0 - - + -
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 6.1 0.4 - - - -
237A PHE* 3.6 47.1 - + + -
268A VAL 3.1 17.1 + - - +
269A ASN* 3.8 10.5 - - - +
271A THR* 1.3 75.1 - - - +
273A PHE* 1.3 60.7 + - + +
275A ASN* 3.1 6.1 + - - +
276A GLU* 2.9 59.9 + - + +
619A ILE* 4.0 21.0 - - - +
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 4.8 1.1 - - - +
232A VAL* 3.7 16.8 - - + -
237A PHE* 3.8 28.9 - + + -
240A GLN* 3.4 43.7 - - + -
259A TRP* 3.6 22.7 - + + -
269A ASN 3.0 19.8 + - - +
270A ASN 3.6 4.9 - - - +
272A TYR* 1.3 76.3 - - + +
274A ALA* 1.3 62.5 + - - +
277A SER* 2.8 41.7 + - - -
279A MET* 3.5 39.9 - - + -
281A LEU* 3.7 20.0 - - + -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASN 3.1 9.8 + - - +
271A THR 3.3 0.9 + - - +
273A PHE* 1.3 78.3 - - - +
275A ASN* 1.3 62.1 + - - +
276A GLU 3.7 0.2 + - - -
277A SER 4.8 0.5 + - - -
278A GLY 5.4 0.9 + - - -
279A MET 3.5 19.2 - - - +
280A SER* 5.2 1.7 - - - -
281A LEU* 3.7 22.4 - - + +
315A TYR* 3.6 37.5 - - + -
317A PHE* 4.2 13.0 - - - -
321A MET* 5.3 2.9 - - - -
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Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A THR* 3.1 28.2 + - - +
272A TYR* 3.1 5.7 + - - +
274A ALA* 1.3 82.0 - - - +
276A GLU* 1.3 70.9 + - + +
278A GLY 5.5 0.7 - - - -
314A ASP 3.1 22.6 + - - -
315A TYR* 3.7 5.1 - - - +
316A ASN* 2.8 49.5 + - - +
317A PHE* 4.1 16.2 + - - -
557A LYS* 4.4 7.6 + - - -
575A ASN 5.6 0.7 - - - +
577A ASN* 6.2 0.7 - - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 3.5 23.0 - - + -
241A LYS* 3.9 17.0 + - + +
272A TYR* 2.9 44.7 + - + +
275A ASN* 1.3 86.5 - - + +
277A SER* 1.3 65.1 + - - +
278A GLY 3.3 3.2 + - - -
508A MET* 4.3 4.9 - - - +
557A LYS* 2.7 39.7 + - - -
577A ASN* 4.5 12.9 + - - +
617A LYS* 5.2 5.7 + - - -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 3.5 17.9 - - - -
241A LYS* 3.6 18.0 - - - -
244A MET* 3.6 18.9 - - - +
273A PHE* 2.8 42.6 + - - -
274A ALA 4.8 0.2 - - - -
276A GLU* 1.3 78.3 - - - +
278A GLY* 1.3 56.4 + - - +
279A MET* 3.1 31.3 + - - +
508A MET* 3.8 4.8 - - - +
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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