Contacts of the helix formed by residues 270 - 279 (chain B) in PDB entry 2W8D
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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU* 4.5 4.3 - - + -
259B ILE* 3.6 38.2 + - + +
260B ILE* 3.7 1.4 - - - +
262B TYR 4.6 0.2 + - - -
269B VAL* 1.3 84.9 - - + +
271B PRO* 1.3 66.8 - - - +
272B PHE 3.3 2.0 - - - -
273B LEU* 3.1 14.2 + - + -
274B ASN* 2.7 46.5 + - - +
441B ALA* 3.8 13.2 - - + +
445B ASP* 3.3 24.7 - - + +
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Residues in contact with PRO 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.3 40.8 - - + +
269B VAL 3.4 9.6 - - - +
270B THR* 1.3 87.7 - - - +
272B PHE* 1.3 56.3 + - + +
274B ASN* 3.3 3.9 + - - +
275B LYS* 3.0 28.8 + - - +
442B HIS* 4.3 14.1 - - + +
445B ASP* 3.2 11.4 - - + +
446B GLN* 6.3 2.2 - - + -
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 1.3 74.9 - - + +
273B LEU* 1.3 63.5 + - + +
275B LYS* 3.4 32.5 + - - +
276B LEU* 3.2 44.6 + - + +
445B ASP* 2.8 27.0 + - - +
448B ILE* 3.7 26.5 - - + -
449B GLU* 3.6 45.3 - - + -
452B PHE* 3.5 33.9 - + + -
453B ASN* 5.1 2.9 - - - -
456B LYS* 5.0 10.5 - - - -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.7 3.4 - - + -
255B LEU* 3.8 28.7 - - + -
260B ILE* 5.0 4.3 - - + -
270B THR* 3.9 15.9 - - + +
272B PHE* 1.3 75.8 - - + +
274B ASN* 1.3 65.4 + - - +
276B LEU* 3.3 8.0 + - + -
277B ALA* 3.0 19.4 + - - +
444B LEU* 5.7 0.9 - - + -
445B ASP* 2.9 28.1 + - + +
448B ILE* 4.3 27.1 - - + -
468B MSE 3.6 31.4 - - + -
506B PHE* 3.4 33.7 - - + -
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Residues in contact with ASN 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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260B ILE* 3.2 6.7 - - - +
261B ASP* 2.8 48.7 + - - +
262B TYR 4.5 0.4 + - - +
268B GLU* 3.5 34.8 + - - +
270B THR* 2.7 47.7 + - - +
271B PRO 3.4 5.6 - - - +
272B PHE 3.3 0.2 - - - -
273B LEU* 1.3 70.4 - - - +
275B LYS* 1.3 66.0 + - - +
277B ALA* 3.2 11.6 + - - +
278B HIS* 3.0 25.8 - - + -
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Residues in contact with LYS 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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271B PRO 3.0 11.8 + - - +
272B PHE* 3.5 35.3 - - - +
273B LEU 3.3 0.2 - - - -
274B ASN* 1.3 74.9 - - - +
276B LEU* 1.3 60.8 + - + +
278B HIS* 2.7 28.1 + - - +
279B ASP* 3.0 16.7 + - + +
456B LYS* 6.2 0.2 - - - +
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Residues in contact with LEU 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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272B PHE* 3.2 45.0 + - + +
273B LEU* 3.5 13.7 - - + +
275B LYS* 1.3 82.9 - - + +
277B ALA* 1.3 55.9 + - - +
279B ASP* 3.3 20.9 - - + +
282B THR* 3.6 25.0 - - + +
284B TYR* 4.7 0.3 - - - +
452B PHE* 4.0 13.5 - - + -
461B TYR* 5.9 3.1 - - - +
468B MSE 3.9 25.6 - - + -
506B PHE* 4.0 12.9 - - + -
508B HIS* 6.2 1.1 - - + -
516B LYS* 3.1 20.3 + - - -
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Residues in contact with ALA 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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260B ILE* 4.1 16.8 - - + -
273B LEU 3.0 12.9 + - - +
274B ASN 3.4 9.6 - - - +
275B LYS 3.0 0.4 - - - -
276B LEU* 1.3 76.6 - - - +
278B HIS* 1.3 64.8 + - + +
284B TYR* 3.7 39.0 - - + -
506B PHE* 3.9 4.2 - - + -
516B LYS* 3.3 24.2 - - - +
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 5.0 0.4 - - + +
261B ASP* 2.8 37.7 + - - -
274B ASN* 3.0 23.5 + - + +
275B LYS* 2.7 16.2 + - - +
277B ALA* 1.3 80.0 + - + +
279B ASP* 1.3 64.0 + - - +
516B LYS* 4.7 1.6 - - - +
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Residues in contact with ASP 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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275B LYS* 3.0 13.7 + - + +
276B LEU* 3.6 18.1 - - + +
277B ALA 3.7 0.4 - - - -
278B HIS* 1.3 82.1 - - - +
280B ASN* 1.3 63.0 + - - +
281B GLU* 3.6 10.1 - - + +
282B THR* 2.7 48.9 + - - -
516B LYS* 2.8 35.3 + - - -
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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