Contacts of the helix formed by residues 269 - 279 (chain B) in PDB entry 3BWB
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 PRO 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B PRO* 4.2 14.3 - - + +
267B LEU 3.6 9.0 - - - +
268B ARG* 1.3 86.0 - - - +
270B VAL* 1.3 65.6 + - - +
271B GLU* 3.2 18.0 + - + +
272B ASP* 3.3 37.3 + - - +
273B MSE 3.7 6.8 - - - +
284B SER* 3.7 10.8 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS* 5.1 0.9 - - - +
91B CYS* 4.0 10.1 - - - -
268B ARG 3.3 4.3 + - - -
269B PRO* 1.3 71.8 - - - +
271B GLU* 1.3 81.0 + - - +
272B ASP 3.1 0.2 - - - -
273B MSE 3.0 20.4 + - + +
275B PHE* 3.6 35.0 - - + -
276B ALA* 3.0 24.3 - - + +
279B LEU* 3.8 15.9 - - + -
282B TYR* 3.8 28.9 + - + +
283B ASP* 4.0 11.7 - - + -
284B SER* 3.8 3.2 + - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PRO* 3.1 9.3 - - + +
270B VAL* 1.3 79.1 - - + +
272B ASP* 1.3 66.2 + - - +
273B MSE 3.8 5.0 - - - +
276B ALA* 3.9 11.4 - - + +
277B LYS* 6.5 1.1 - - - -
283B ASP* 3.7 12.6 - - - +
284B SER* 2.5 51.4 + - - -
285B GLU 4.7 0.5 + - - -
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PRO* 3.3 32.7 + - - +
270B VAL 3.1 0.6 - - - -
271B GLU* 1.3 82.9 - - - +
273B MSE 1.3 70.7 + - - +
274B PRO* 4.0 2.1 - - - +
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Residues in contact with MSE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B CYS* 5.9 0.4 - - - -
116B HIS* 5.4 5.4 - - + +
117B GLY* 5.6 8.1 - - - +
118B THR* 5.4 5.6 - - + -
268B ARG* 3.5 35.4 - - - +
269B PRO 3.7 12.8 - - - +
270B VAL* 3.0 30.5 + - - +
271B GLU 3.8 3.5 - - - +
272B ASP* 1.3 87.5 - - - +
274B PRO* 1.4 78.7 - - + +
275B PHE* 3.3 31.0 + - + -
276B ALA* 3.4 8.3 + - - +
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Residues in contact with PRO 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ASP 4.0 2.0 - - - +
273B MSE 1.4 88.3 - - + +
275B PHE* 1.3 65.4 + - + +
276B ALA* 3.2 1.8 + - - +
277B LYS* 4.4 5.9 + - - +
278B ASP* 4.5 3.6 - - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS* 3.4 23.3 - + - -
115B ARG* 3.4 55.4 - - + +
116B HIS* 3.8 33.2 - + - -
117B GLY 5.2 1.1 - - - -
270B VAL* 3.6 23.1 - - + -
273B MSE 3.6 22.4 - - + -
274B PRO* 1.3 80.2 - - + +
276B ALA* 1.3 65.0 + - - +
277B LYS 3.2 2.9 - - - -
278B ASP* 2.8 34.3 + - - +
279B LEU* 3.6 8.5 + - + +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 3.5 11.0 + - - -
270B VAL* 3.0 47.2 + - + +
271B GLU* 3.9 11.7 - - + +
273B MSE 3.4 8.1 + - - +
274B PRO 3.2 2.4 - - - -
275B PHE* 1.3 79.3 - - - +
277B LYS* 1.3 67.8 + - + +
279B LEU* 3.3 21.0 + - - +
282B TYR 5.0 0.2 - - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 3.3 41.4 + - - +
271B GLU* 6.5 0.9 - - - -
274B PRO 4.4 4.9 + - - +
275B PHE 3.2 1.0 - - - -
276B ALA* 1.3 80.6 - - + +
278B ASP* 1.3 65.0 + - - +
279B LEU 3.3 2.4 - - - +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 4.8 0.3 - - - +
115B ARG* 3.9 25.8 + - - +
274B PRO 4.5 2.7 - - - +
275B PHE* 2.8 28.3 + - - +
277B LYS* 1.3 82.3 - - - +
279B LEU* 1.3 64.2 + - - +
280B LYS* 3.7 14.0 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 2.9 22.5 + - - +
83B GLU* 3.7 12.3 - - - +
87B HIS* 3.4 37.5 - - + +
112B GLU* 3.6 11.9 - - - +
115B ARG* 3.8 18.4 - - - +
270B VAL* 3.8 28.9 - - + -
275B PHE* 4.0 7.2 - - + +
276B ALA 3.3 14.2 + - - +
277B LYS 3.9 2.6 - - - +
278B ASP* 1.3 79.7 - - - +
280B LYS* 1.3 60.6 + - - +
282B TYR* 3.6 31.4 - - + +
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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