Contacts of the helix formed by residues 277 - 285 (chain A) in PDB entry 2W8I
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 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A MET* 1.3 79.6 - - - +
278A LEU* 1.3 66.9 + - - +
279A ALA* 4.2 0.2 - - - +
280A GLU* 2.9 32.5 + - - +
281A ALA 3.0 10.4 + - - -
329A GLY 3.5 9.9 - - - -
330A THR* 3.4 24.0 - - - +
332A PHE 3.3 7.6 - - - +
333A GLN* 3.5 25.6 - - - +
334A LEU* 3.7 5.4 - - - +
258B PHE* 3.7 13.5 - - - -
337B TYR* 4.5 14.2 - - + -
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Residues in contact with LEU 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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55A MET* 3.6 38.8 - - + -
277A THR* 1.3 70.9 - - - +
279A ALA* 1.3 63.1 + - - +
281A ALA* 3.2 4.3 + - - +
282A LEU* 3.2 35.2 + - + +
298A ILE* 4.4 20.2 - - + -
300A VAL* 3.8 14.8 - - + -
318A LEU* 4.5 4.5 - - + -
326A MET* 4.9 0.2 - - + -
329A GLY* 3.1 23.6 + - - +
332A PHE* 3.1 16.2 + - + -
334A LEU* 3.8 7.6 - - + +
340A VAL* 3.5 34.5 - - + -
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Residues in contact with ALA 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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277A THR* 3.1 0.6 - - - +
278A LEU* 1.3 76.1 - - - +
280A GLU* 1.3 63.2 + - - +
282A LEU* 3.0 9.1 + - - +
283A GLY* 3.0 20.1 + - - -
326A MET* 5.1 2.5 - - + +
329A GLY* 2.8 19.5 + - - +
330A THR* 3.8 24.9 - - + -
258B PHE* 3.8 24.9 - - + -
260B MET* 3.6 15.7 - - + +
339B ILE* 4.9 3.6 - - + -
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Residues in contact with GLU 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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272A ASP* 3.8 8.1 - - - +
274A SER* 4.3 1.0 + - - -
275A GLY 4.0 3.6 - - - +
276A MET* 3.2 39.0 - - + +
277A THR* 2.9 24.2 + - - +
279A ALA* 1.3 76.0 - - - +
281A ALA* 1.3 57.1 + - - +
284A ASN* 2.9 55.6 + - - +
256B LYS* 2.9 39.0 + - - +
258B PHE* 3.3 15.3 - - + -
268B THR* 3.3 7.5 + - + -
337B TYR* 5.2 2.1 - - - -
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Residues in contact with ALA 281 (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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257A VAL* 4.7 0.7 - - + -
259A VAL* 3.7 31.8 - - + +
269A LEU* 4.5 2.7 - - - -
276A MET* 4.2 12.0 - - - +
277A THR 3.0 5.1 + - - -
278A LEU 3.3 9.9 - - - +
280A GLU* 1.3 78.3 - - - +
282A LEU* 1.3 62.7 + - - +
284A ASN* 3.3 2.6 + - - +
285A ALA* 3.2 17.2 + - - +
334A LEU* 3.6 26.0 - - + -
340A VAL* 4.1 11.0 - - + -
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Residues in contact with LEU 282 (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 VAL* 5.2 0.2 - - + -
263A VAL* 4.8 4.5 - - + -
278A LEU* 3.4 23.3 - - + +
279A ALA 3.0 6.3 + - - +
281A ALA* 1.3 75.7 - - - +
283A GLY* 1.3 59.7 + - - +
285A ALA* 3.1 12.5 + - - +
287A GLY* 2.9 26.5 + - - -
288A ILE* 4.0 32.3 - - + +
298A ILE* 4.4 7.4 - - + -
326A MET* 3.7 37.5 - - + -
340A VAL* 3.9 25.1 - - + -
342A VAL* 4.2 12.3 - - + -
260B MET* 3.5 12.1 - - + -
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Residues in contact with GLY 283 (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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279A ALA 3.0 10.4 + - - -
282A LEU* 1.3 77.7 - - - +
284A ASN* 1.3 61.2 + - - +
286A GLU* 3.2 9.7 + - - -
287A GLY* 4.2 5.6 - - - -
258B PHE* 5.5 0.7 - - - -
260B MET* 3.9 10.8 - - - +
266B GLN 3.6 0.9 - - - +
267B SER* 3.4 25.8 - - - -
268B THR* 3.3 25.9 + - - -
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Residues in contact with ASN 284 (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 SER* 5.0 2.6 + - - -
269A LEU* 3.5 30.0 - - + +
270A LYS 5.5 0.2 + - - -
276A MET* 3.7 18.4 - - - +
280A GLU* 2.9 43.9 + - - +
281A ALA 3.7 0.4 - - - +
283A GLY* 1.3 74.4 - - - +
285A ALA* 1.3 56.2 + - - +
286A GLU* 3.1 11.7 + - - +
268B THR* 3.0 22.4 - - - +
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Residues in contact with ALA 285 (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 VAL* 3.7 32.5 - - + -
263A VAL* 4.1 8.7 - - + -
264A GLY 3.4 2.9 + - - -
265A LYS* 2.8 46.1 + - - +
267A SER* 4.6 6.1 - - - +
269A LEU* 5.8 0.7 - - + -
281A ALA 3.2 5.0 + - - +
282A LEU 3.1 9.6 + - - +
284A ASN* 1.3 74.5 - - - +
286A GLU* 1.3 64.4 + - - +
287A GLY 3.2 1.4 + - - -
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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