Contacts of the helix formed by residues 269 - 280 (chain A) in PDB entry 1BJW
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 THR 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.4 24.0 - - + +
62A THR* 4.9 0.2 - - - -
63A LYS 2.7 28.4 + - - +
65A ALA* 4.0 10.3 + - + +
70A ILE* 4.0 11.7 - - + -
267A PRO 3.2 4.3 + - - -
268A ASP* 1.3 69.6 - - - +
270A ILE* 1.3 65.7 + - - +
272A GLN* 3.1 9.2 + - - +
273A TRP* 3.0 48.2 + - + +
240B GLY* 2.9 16.7 + - - -
242B ARG* 5.9 0.2 - - - -
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Residues in contact with ILE 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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53A ALA* 3.9 35.9 - - + +
56A ALA* 4.6 10.7 - - + +
57A LEU* 4.6 19.1 - - + +
61A LYS 3.8 18.4 - - - +
62A THR* 4.3 4.7 - - + -
241A TRP* 5.1 3.4 - - + -
268A ASP* 3.1 24.7 + - - +
269A THR* 1.3 76.9 - - - +
271A ALA* 1.3 57.3 + - - +
273A TRP* 3.3 2.8 + - - +
274A ALA* 3.0 26.6 + - - +
240B GLY 4.6 2.2 - - - +
241B TRP* 3.8 45.5 - - + +
270B ILE* 6.4 1.6 - - + -
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Residues in contact with ALA 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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238A MET* 4.8 0.5 - - - +
241A TRP* 3.5 42.4 - - + +
243A ILE* 3.7 12.6 - - + -
268A ASP* 2.9 28.4 + - + +
269A THR 3.2 0.6 - - - -
270A ILE* 1.3 73.3 - - - +
272A GLN* 1.3 62.7 + - - +
274A ALA* 3.4 2.0 + - - +
275A THR* 2.8 29.8 + - - -
268B ASP* 3.6 5.8 - - - +
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Residues in contact with GLN 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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65A ALA* 3.5 13.9 - - - +
69A GLY* 3.3 8.2 - - - -
70A ILE* 2.9 43.0 + - + +
73A LEU* 3.7 24.2 - - + +
96A VAL* 4.0 11.6 - - + +
243A ILE* 3.9 14.8 - - + -
266A SER* 3.3 18.0 + - - -
267A PRO* 2.9 25.8 + - + +
268A ASP 3.0 16.3 + - - +
269A THR 3.1 6.7 + - - +
271A ALA* 1.3 78.1 - - - +
273A TRP* 1.3 62.4 + - - +
275A THR* 3.3 4.0 + - - -
276A LEU* 3.1 18.4 + - - +
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Residues in contact with TRP 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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52A ALA* 4.2 7.0 - - - +
56A ALA* 3.9 15.3 - - + -
61A LYS* 3.4 52.6 - - + +
70A ILE* 4.0 20.0 - - + +
72A GLU* 3.6 38.6 - - + -
269A THR* 3.0 42.9 + - + +
270A ILE 3.8 6.3 - - - +
272A GLN* 1.3 72.8 - - - +
274A ALA* 1.3 67.3 + - - +
276A LEU* 3.4 43.2 + - + +
277A GLU* 3.5 7.1 + - - +
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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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49A VAL* 3.6 26.2 - - + +
52A ALA* 4.2 11.0 - - - -
53A ALA* 4.1 5.5 - - + +
238A MET* 4.6 0.7 - - + -
241A TRP* 3.5 30.7 - - + -
270A ILE 3.0 16.7 + - - +
271A ALA 3.5 4.7 - - - +
273A TRP* 1.3 77.6 - - - +
275A THR* 1.3 61.0 + - - +
277A GLU* 3.1 20.4 + - - +
278A ALA 3.4 4.2 + - - -
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Residues in contact with THR 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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73A LEU* 4.2 6.3 - - + -
232A ALA* 4.5 9.2 - - + -
238A MET* 3.6 14.5 - - - +
243A ILE* 3.5 34.4 - - + +
245A TYR* 3.9 18.8 - - + +
271A ALA 2.8 20.8 + - - -
272A GLN* 3.3 6.3 + - - -
274A ALA* 1.3 75.1 - - - +
276A LEU* 1.3 64.3 + - - +
278A ALA* 3.1 9.7 + - + +
279A LEU* 2.9 31.7 + - + +
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Residues in contact with LEU 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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70A ILE* 5.5 1.6 - - + -
72A GLU* 3.6 39.7 - - + +
73A LEU* 4.2 12.9 - - + +
76A ALA* 3.6 20.6 - - + -
272A GLN 3.1 12.8 + - - +
273A TRP* 3.5 42.4 - - + +
274A ALA 3.3 0.4 - - - -
275A THR* 1.3 74.4 - - - +
277A GLU* 1.3 52.9 + - - +
279A LEU* 3.1 3.0 + - - -
280A THR* 2.8 51.9 + - + +
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Residues in contact with GLU 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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48A HIS* 3.4 35.8 - - - +
49A VAL* 4.3 0.4 - - - -
52A ALA* 3.3 15.0 - - + -
55A ARG* 3.5 23.5 + - - +
273A TRP 3.5 2.1 + - - +
274A ALA 3.1 11.8 + - - +
275A THR 3.1 0.6 - - - -
276A LEU* 1.3 77.3 - - - +
278A ALA* 1.3 59.0 + - - +
280A THR* 3.8 7.7 + - - -
281A ASN* 2.8 66.8 + - - +
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Residues in contact with ALA 278 (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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48A HIS* 4.2 0.4 - - - -
49A VAL* 3.8 25.0 - - + +
236A PHE* 4.2 30.7 - - + -
238A MET* 4.6 4.0 - - - -
274A ALA 3.4 3.3 + - - +
275A THR* 3.1 15.6 + - + +
277A GLU* 1.3 79.0 - - - +
279A LEU* 1.3 62.0 + - + +
281A ASN 4.3 1.6 + - - -
282A GLN* 5.4 0.2 - - - -
285A SER* 2.6 34.9 + - - +
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Residues in contact with LEU 279 (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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73A LEU* 3.4 23.1 - - + -
76A ALA* 4.4 19.3 - - + +
77A LEU* 3.4 31.2 - - + -
80A LYS* 4.6 19.3 - - + -
83A ARG* 4.2 13.8 + - - +
236A PHE* 4.6 13.0 - - + -
245A TYR* 3.8 21.3 - - + +
275A THR* 2.9 21.4 + - + +
276A LEU 3.1 6.5 + - - +
278A ALA* 1.3 82.4 - - - +
280A THR* 1.3 59.3 + - - +
282A GLN* 4.2 14.8 + - - +
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Residues in contact with THR 280 (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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76A ALA* 4.1 12.1 - - + -
79A GLU* 5.8 3.6 - - - +
276A LEU* 2.8 50.5 + - + +
277A GLU* 3.8 9.4 + - - -
279A LEU* 1.3 76.1 - - - +
281A ASN* 1.3 58.0 + - - +
282A GLN* 2.9 22.7 + - - +
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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