Contacts of the helix formed by residues 267 - 281 (chain D) in PDB entry 4RYD
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 ALA 267 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C ASP* 5.3 1.6 - - - +
233D ASP* 3.1 35.8 + - + +
265D GLY 3.6 3.0 + - - +
266D PRO* 1.3 74.6 - - - +
268D ARG* 1.3 75.4 + - - +
270D ALA* 3.2 2.8 + - - +
271D GLU* 3.0 21.0 + - - +
1K 2UE 3.7 14.4 + - - +
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Residues in contact with ARG 268 (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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268C ARG* 4.7 21.2 - - - +
271C GLU* 5.3 11.6 + - - +
490C ARG* 3.3 27.8 - - - +
529C ASN* 5.3 10.1 + - - +
530C ASP* 3.2 27.2 + - - +
233D ASP* 3.6 0.2 + - - -
267D ALA* 1.3 80.6 - - - +
269D LEU* 1.3 58.1 + - - +
271D GLU* 3.2 23.7 + - - +
272D GLU* 2.9 38.3 + - + +
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Residues in contact with LEU 269 (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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449C LYS* 4.1 11.3 + - - +
451C ILE* 4.0 22.6 - - + +
488C GLN* 5.6 0.7 - - - +
490C ARG* 4.0 28.0 - - - +
565C LYS* 5.9 2.0 - - - +
567C THR* 3.9 29.2 - - + +
569C VAL* 4.3 9.6 - - + -
233D ASP* 2.9 23.2 + - + +
234D ALA* 4.3 9.4 - - + +
237D ALA* 3.5 21.2 - - + +
268D ARG* 1.3 72.5 - - - +
270D ALA* 1.3 58.3 + - - +
272D GLU* 3.2 22.9 + - - +
273D ALA* 2.8 24.3 + - - +
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Residues in contact with ALA 270 (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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233D ASP* 2.9 18.8 + - - +
236D GLU* 3.7 26.5 - - + +
237D ALA* 3.8 8.9 - - - +
240D LEU* 4.1 8.9 - - + +
266D PRO* 3.6 21.5 - - + -
267D ALA 3.2 0.6 + - - +
269D LEU* 1.3 75.6 - - - +
271D GLU* 1.3 63.3 + - - +
273D ALA* 3.1 6.2 + - - +
274D PHE* 3.0 27.6 + - - -
308D TYR* 5.0 0.2 - - + -
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Residues in contact with GLU 271 (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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268C ARG* 5.0 12.7 - - - -
271C GLU* 5.4 4.3 - - - +
272C GLU* 5.7 0.9 - - - +
266D PRO* 3.9 25.2 - - + +
267D ALA 3.0 13.4 + - - +
268D ARG* 3.4 31.4 + - - +
270D ALA* 1.3 77.6 - - - +
272D GLU* 1.3 63.1 + - + +
274D PHE* 3.2 12.9 + - + +
275D PHE* 3.0 23.1 + - - +
313D TYR* 5.1 2.9 - - + -
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Residues in contact with GLU 272 (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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271C GLU* 5.4 3.1 - - - +
275C PHE* 4.2 15.0 - - + -
313C TYR* 4.5 5.0 + - - -
449C LYS* 2.6 37.4 + - - +
488C GLN* 5.4 2.6 + - - -
490C ARG* 4.5 11.4 + - - -
571C TYR* 4.0 5.4 + - - -
603C FMT 3.8 20.0 - - - +
268D ARG* 2.9 22.1 + - + +
269D LEU* 3.5 17.1 - - - +
271D GLU* 1.3 78.0 - - + +
273D ALA* 1.3 58.0 + - - +
275D PHE* 3.7 0.5 - - - +
276D ARG* 2.8 37.5 + - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C LYS* 5.1 0.6 - - - +
237D ALA* 3.7 27.1 - - + +
240D LEU* 3.9 18.1 - - + +
241D GLY* 4.3 8.1 - - - +
269D LEU 2.8 13.8 + - - +
270D ALA 3.1 9.6 + - - +
272D GLU* 1.3 77.7 - - - +
274D PHE* 1.3 56.8 + - - +
276D ARG* 3.8 7.8 - - - +
277D GLY* 2.8 27.9 + - - -
289D PHE* 4.3 4.4 - - - -
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D LEU* 3.8 28.7 - - + -
266D PRO* 4.2 15.3 - - + -
270D ALA 3.0 22.9 + - - -
271D GLU* 3.2 11.9 + - + +
273D ALA* 1.3 76.1 - - - +
275D PHE* 1.3 62.7 + - - +
277D GLY* 3.1 2.1 + - - -
278D VAL* 3.0 28.8 + - - +
289D PHE* 3.6 28.8 - + - -
291D TRP* 3.5 28.3 - + - -
308D TYR* 4.1 19.7 - + + -
311D SER* 5.0 5.2 - - - -
313D TYR* 3.7 25.6 - + + -
314D THR* 3.7 26.2 - - + -
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Residues in contact with PHE 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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272C GLU* 5.1 4.9 - - + -
275C PHE* 3.3 65.5 - + + -
276C ARG* 4.0 20.4 - - + -
279C SER* 3.7 10.1 - - - -
280C GLN* 4.8 2.5 - - - -
271D GLU 3.0 15.0 + - - +
272D GLU 3.8 0.2 - - - +
274D PHE* 1.3 75.5 - - - +
276D ARG* 1.3 61.4 + - - +
278D VAL* 3.5 5.3 - - - +
279D SER* 2.6 49.4 + - - -
313D TYR* 3.3 24.0 - + + +
601D FMT 4.0 11.9 - - - -
602D FMT 3.6 25.6 - - - -
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Residues in contact with ARG 276 (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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275C PHE* 3.9 9.4 - - + -
447C GLN* 2.9 48.7 + - - -
449C LYS* 3.9 37.2 - - - +
571C TYR* 4.3 1.0 - - - -
602C FMT 3.5 13.9 + - - -
603C FMT 2.9 29.9 + - - +
272D GLU 2.8 29.7 + - - +
273D ALA* 3.9 6.3 - - - +
275D PHE* 1.3 73.2 - - - +
277D GLY* 1.3 55.8 + - - +
279D SER* 4.4 0.4 - - - -
280D GLN* 2.7 61.2 + - + +
281D GLY 3.5 1.0 + - - -
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Residues in contact with GLY 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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240D LEU 5.9 1.1 - - - -
244D PRO* 5.6 4.7 - - - -
273D ALA 2.8 15.7 + - - -
274D PHE 3.1 4.9 + - - -
276D ARG* 1.3 77.7 - - - +
278D VAL* 1.3 57.6 + - - +
281D GLY* 2.8 25.0 + - - -
287D SER* 2.8 32.8 + - - -
289D PHE* 4.3 4.7 - - - -
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Residues in contact with VAL 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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274D PHE 3.0 17.8 + - - +
275D PHE* 3.5 12.3 - - + +
277D GLY* 1.3 73.4 - - - +
279D SER* 1.3 65.9 + - - +
284D GLY 4.4 1.6 - - - +
285D LEU 4.3 0.9 - - - +
286D GLY* 3.2 23.0 + - - -
287D SER 4.0 12.1 - - - +
289D PHE* 4.2 4.9 - - + -
313D TYR* 3.8 47.6 - - + +
390D TRP* 3.3 45.5 + - + -
601D FMT 4.3 6.3 - - - -
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Residues in contact with SER 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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279C SER* 4.9 11.2 - - - -
280C GLN* 5.0 3.2 + - - -
275D PHE* 2.6 45.3 + - - -
276D ARG* 3.8 3.6 - - - -
278D VAL* 1.3 83.9 - - - +
280D GLN* 1.3 73.2 + - - +
284D GLY* 3.6 20.4 - - - +
601D FMT 4.7 4.7 - - - -
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Residues in contact with GLN 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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275C PHE* 5.1 3.0 - - - -
279C SER* 5.1 4.0 + - - -
447C GLN* 4.8 8.0 + - - +
602C FMT 3.3 27.8 + - - +
244D PRO* 5.5 0.9 - - + -
245D ASN* 3.9 7.1 + - - +
276D ARG* 2.7 48.8 + - + +
279D SER* 1.3 84.3 - - - +
281D GLY* 1.3 68.6 + - - +
283D GLY* 3.6 3.6 + - - -
284D GLY* 3.0 14.1 + - - -
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Residues in contact with GLY 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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244D PRO* 3.7 18.1 - - - +
245D ASN* 4.4 0.7 - - - -
276D ARG 3.5 3.0 + - - -
277D GLY 2.8 24.0 + - - -
280D GLN* 1.3 75.5 - - - +
282D ARG* 1.3 69.1 + - - -
284D GLY 2.9 3.1 + - - -
286D GLY* 2.8 21.9 + - - -
287D SER* 3.7 11.9 - - - -
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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