Contacts of the helix formed by residues 274 - 285 (chain D) in PDB entry 1W8D
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 VAL 274 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLY* 4.1 11.2 - - - +
71D LEU* 3.8 29.6 - - + +
74D GLY* 3.4 34.1 - - - +
243D ILE* 3.6 11.6 - - + +
244D LYS 4.4 4.5 + - - +
245D THR* 4.2 15.0 - - - +
273D THR* 1.3 71.4 - - - +
275D GLU* 1.3 71.4 + - + +
277D LEU* 3.3 8.3 + - + +
278D ALA* 2.8 27.4 + - - +
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLN* 2.7 64.0 + - + +
78D LEU* 4.9 1.0 - - - +
273D THR* 3.9 5.7 - - - -
274D VAL* 1.3 86.2 + - + +
276D GLU* 1.3 64.7 + - - +
278D ALA* 3.8 5.9 - - - +
279D ASN* 3.1 30.1 + - - +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 5.8 0.5 - - - -
288C TYR 4.5 13.7 - - - +
290C SER* 3.4 12.3 + - - -
291C TRP* 3.6 13.4 + - - +
46D PRO* 3.5 13.2 - - + +
47D LEU 4.3 15.4 + - - +
270D ARG* 2.6 47.1 + - - -
272D GLY* 4.2 0.3 - - - -
273D THR* 2.9 29.0 + - - +
275D GLU* 1.3 78.1 - - - +
277D LEU* 1.3 62.0 + - - +
279D ASN* 3.3 13.1 - - - +
280D LEU* 3.3 16.1 + - - +
299D PHE* 3.5 21.9 - - + -
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.4 44.0 - - + +
75D MSE 4.7 16.6 - - + -
195D ILE* 5.1 6.3 - - + -
238D ILE* 3.7 35.9 - - + -
240D PRO* 4.7 6.7 - - + -
243D ILE* 4.4 4.3 - - + -
273D THR 3.1 7.8 + - - +
274D VAL* 3.6 9.2 - - - +
276D GLU* 1.3 75.7 - - - +
278D ALA* 1.3 65.6 + - - +
280D LEU* 3.0 6.6 + - + +
281D ALA* 2.9 19.8 + - - +
299D PHE* 3.4 32.8 - - + -
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLY 3.7 24.9 - - - +
75D MSE 3.9 23.4 - - + +
78D LEU* 3.4 21.1 - - + +
274D VAL 2.8 20.5 + - - +
275D GLU* 3.8 7.4 - - - +
276D GLU 3.4 0.2 - - - -
277D LEU* 1.3 71.7 - - - +
279D ASN* 1.3 54.0 + - - +
281D ALA* 3.2 2.3 + - - +
282D ALA* 2.8 31.2 + - - +
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Residues in contact with ASN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C PHE* 4.9 2.0 - - + -
288C TYR* 3.6 21.3 + - - +
47D LEU 3.8 9.1 + - - -
49D LYS 3.2 22.5 + - - +
50D ALA* 4.0 0.7 - - - -
51D MSE 3.2 44.7 + - + +
52D LEU 4.8 0.5 + - - -
78D LEU* 3.5 16.0 - - - +
275D GLU 3.1 18.9 + - - +
276D GLU* 3.3 11.7 - - - +
277D LEU 3.1 0.2 - - - -
278D ALA* 1.3 77.0 - - - +
280D LEU* 1.3 55.6 + - - +
282D ALA* 3.5 2.5 + - - +
283D PHE* 3.0 28.9 + - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C PHE* 3.7 34.3 - - + -
292C ILE* 4.4 5.4 - - + -
297C ILE* 5.9 0.2 - - + -
238D ILE* 3.8 36.8 - - + -
276D GLU 3.3 7.6 + - - +
277D LEU* 3.0 10.8 + - + +
279D ASN* 1.3 74.9 - - - +
281D ALA* 1.3 67.5 + - - +
283D PHE* 3.4 3.1 + - + +
284D LEU* 3.0 36.0 + - + +
297D ILE* 4.1 26.5 - - + -
299D PHE* 3.8 26.9 - - + -
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Residues in contact with ALA 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MSE 3.6 29.4 - - + -
79D LEU* 5.8 0.4 - - - -
142D ILE* 5.1 3.6 - - + -
193D LEU* 3.6 26.2 - - + -
238D ILE* 3.9 6.9 - - + +
277D LEU* 2.9 11.6 + - + +
278D ALA 3.4 7.4 - - - +
280D LEU* 1.3 77.0 - - - +
282D ALA* 1.3 56.5 + - - +
284D LEU* 3.2 3.0 + - - +
285D CYS* 2.9 35.5 + - - -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.9 16.4 - - + -
57D PHE* 3.4 14.4 - - + -
78D LEU* 3.8 18.6 - - + -
79D LEU* 4.2 19.1 - - + -
82D LEU* 5.0 1.6 - - + -
278D ALA 2.8 20.1 + - - +
279D ASN* 3.8 4.7 - - - +
281D ALA* 1.3 68.2 - - - +
283D PHE* 1.3 61.3 + - - +
285D CYS* 3.2 2.3 + - - -
286D SER* 2.8 31.2 + - - -
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Residues in contact with PHE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C MSE 3.4 38.6 - - + -
276C GLU 5.9 0.2 - - - -
279C ASN* 5.0 0.7 - - + -
280C LEU* 3.5 42.6 - - + -
283C PHE* 3.9 21.3 - + + -
51D MSE 3.7 11.0 - - + -
52D LEU* 4.0 5.9 - - - +
279D ASN 3.0 19.3 + - - +
280D LEU* 3.5 7.2 - - + +
282D ALA* 1.3 76.3 - - - +
284D LEU* 1.3 74.0 + - + +
286D SER* 2.8 25.5 + - - -
288D TYR* 4.3 12.3 - - + -
289D ALA* 3.2 14.5 - - + +
292D ILE* 3.7 27.4 - - + -
297D ILE* 5.6 0.9 - - + -
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ALA* 4.7 0.5 - - - +
193D LEU* 4.0 17.3 - - + -
234D ARG* 2.8 32.6 + - - -
236D ASN* 4.3 16.4 + - + +
237D VAL 4.7 0.7 - - - +
238D ILE* 3.7 30.5 - - + -
280D LEU* 3.0 19.4 + - + +
281D ALA 3.2 4.0 + - - +
283D PHE* 1.3 83.9 - - + +
285D CYS* 1.3 59.7 + - - +
289D ALA* 3.5 3.1 - - - +
292D ILE* 3.7 35.7 - - + -
297D ILE* 3.5 36.3 - - + -
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Residues in contact with CYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D PHE* 3.9 10.3 - - + -
79D LEU* 5.4 1.6 - - + -
139D ASN 5.2 0.2 - - - +
140D ILE* 3.7 44.3 - - + +
142D ILE* 4.2 4.9 - - - -
191D ALA* 4.0 17.9 - - + +
192D PHE 5.3 0.4 - - - -
193D LEU* 3.7 35.0 - - - -
234D ARG* 3.7 7.0 + - - +
281D ALA 2.9 22.1 + - - +
282D ALA* 3.5 4.9 - - - +
284D LEU* 1.3 75.2 - - - +
286D SER* 1.3 63.2 + - - +
287D ASP* 5.5 0.2 - - - +
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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