Contacts of the helix formed by residues 270 - 279 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.7 3.8 - - + -
259A ILE* 3.3 38.0 + - + +
260A ILE* 3.7 7.6 - - - +
269A VAL* 1.3 87.0 - - + +
271A PRO* 1.4 59.3 - - - +
272A PHE 3.3 2.7 - - - -
273A LEU* 3.1 17.3 + - + -
274A ASN* 2.9 44.0 + - - +
441A ALA* 4.0 18.2 - - + +
445A ASP* 3.3 16.8 - - + -
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Residues in contact with PRO 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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268A GLU* 3.7 37.7 - - + +
269A VAL 3.3 9.9 - - - +
270A THR* 1.4 87.6 - - - +
272A PHE* 1.3 59.0 + - - +
274A ASN* 3.7 1.9 - - - +
275A LYS* 3.1 21.8 + - - +
442A HIS* 4.1 15.7 - - + +
445A ASP* 3.2 12.3 - - - +
446A GLN* 6.2 1.3 - - + -
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Residues in contact with PHE 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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271A PRO* 1.3 71.7 - - - +
273A LEU* 1.3 65.2 + - + +
275A LYS* 3.1 37.2 + - - +
276A LEU* 3.2 33.5 + - + +
445A ASP* 2.8 31.7 + - - +
448A ILE* 3.9 10.5 - - + -
449A GLU* 3.8 44.6 - - + +
452A PHE* 3.6 51.4 - + + -
453A ASN* 5.6 3.6 - - - -
456A LYS* 5.0 7.4 - - - -
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Residues in contact with LEU 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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252A LEU* 4.4 10.1 - - + -
255A LEU* 3.7 31.0 - - + -
260A ILE* 3.9 17.7 - - + -
270A THR* 3.1 13.7 + - + +
272A PHE* 1.3 75.6 - - - +
274A ASN* 1.3 57.6 + - - +
276A LEU* 3.2 10.8 + - + +
277A ALA* 2.9 28.7 + - - +
444A LEU* 5.6 1.6 - - + -
445A ASP* 2.9 27.4 + - + +
448A ILE* 4.1 22.7 - - + -
468A MSE 3.9 27.6 - - + -
506A PHE* 3.5 16.5 - - + -
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Residues in contact with ASN 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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260A ILE* 3.7 5.4 - - - +
261A ASP* 3.1 48.1 + - - +
262A TYR 4.9 0.4 + - - -
268A GLU* 3.0 34.9 + - - +
270A THR* 2.9 36.9 + - - +
271A PRO 3.7 5.6 - - - +
273A LEU* 1.3 72.9 - - - +
275A LYS* 1.3 65.4 + - - +
277A ALA* 3.1 7.3 + - - -
278A HIS* 2.9 31.6 + - + -
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Residues in contact with LYS 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 PRO 3.1 12.6 + - - +
272A PHE* 3.1 36.9 + - + +
274A ASN* 1.3 74.6 - - - +
276A LEU* 1.3 64.8 + - - +
278A HIS* 3.0 5.2 + - - +
279A ASP* 2.8 39.1 + - + +
456A LYS* 5.4 6.9 - - - +
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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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272A PHE* 3.2 35.3 + - + +
273A LEU* 3.2 16.6 + - + +
275A LYS* 1.3 83.4 - - - +
277A ALA* 1.3 58.2 - - - +
279A ASP* 3.2 22.8 - - - +
282A THR* 3.6 19.1 - - + +
284A TYR* 4.7 0.7 - - - +
452A PHE* 4.1 20.9 - - + -
461A TYR* 5.3 3.8 - - - +
468A MSE 3.6 32.1 - - + -
506A PHE* 3.8 14.6 - - + -
508A HIS* 6.3 0.2 - - + -
516A LYS* 3.0 22.2 + - - -
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Residues in contact with ALA 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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260A ILE* 4.1 16.8 - - + -
273A LEU 2.9 13.6 + - - +
274A ASN* 3.1 14.1 + - - +
276A LEU* 1.3 75.6 - - - +
278A HIS* 1.3 69.8 + - + +
284A TYR* 4.0 26.2 - - + +
506A PHE* 3.7 11.3 - - + -
516A LYS* 3.2 23.9 - - - +
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Residues in contact with HIS 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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261A ASP* 2.7 39.3 + - - -
274A ASN* 2.9 27.0 + - + +
275A LYS* 3.0 5.5 + - - +
277A ALA* 1.3 85.7 + - + +
279A ASP* 1.3 65.1 + - - +
516A LYS* 4.6 1.3 - - - +
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Residues in contact with ASP 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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275A LYS* 2.8 18.1 + - + +
276A LEU* 3.2 21.0 - - - +
278A HIS* 1.3 80.0 - - - +
280A ASN* 1.3 63.1 + - - +
281A GLU* 3.7 11.6 - - + +
282A THR* 2.6 47.3 + - - -
516A LYS* 2.8 32.2 + - - +
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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