Contacts of the helix formed by residues 266 - 283 (chain A) in PDB entry 3DGI
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 HIS 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 4.0 13.9 - - + -
149A THR* 2.8 53.9 + - - +
150A LEU* 3.5 23.6 - - + +
153A ILE* 4.2 1.3 - - + -
173A PHE* 5.0 1.8 - + - -
174A ILE* 4.1 11.7 - - + +
177A MET* 3.6 20.2 - - + +
262A LEU 2.7 25.5 + - - +
263A ILE* 3.3 4.7 + - - -
265A GLY* 1.3 80.4 - - - +
267A GLU* 1.3 104.4 + - + +
268A ALA 3.6 1.6 - - - -
269A THR* 3.5 3.0 + - - -
270A SER* 3.1 11.4 + - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 4.2 10.2 + - - +
174A ILE* 4.7 4.3 - - - +
177A MET* 3.2 28.3 - - + +
178A VAL* 4.8 2.7 - - - +
181A LEU* 5.8 2.0 - - + -
263A ILE* 3.2 15.4 + - + +
264A ALA 4.1 1.0 + - - -
266A HIS* 1.3 112.2 + - + +
268A ALA* 1.3 64.3 + - - +
270A SER* 3.1 3.3 + - - -
271A GLY* 3.1 18.0 + - - -
436A THR* 5.4 3.9 + - - +
437A LEU* 6.1 2.0 - - + -
438A THR* 4.1 21.5 + - + +
440A LYS* 2.3 39.3 + - - -
503A DMS 5.2 1.6 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA 4.7 0.8 + - - -
267A GLU* 1.3 77.4 - - - +
269A THR* 1.3 58.0 + - - +
271A GLY 3.5 0.9 + - - -
272A LEU* 2.9 20.3 + - - +
327A THR* 2.8 41.0 + - - +
438A THR* 4.4 5.6 - - + +
501A HEM 3.4 32.0 - - + +
503A DMS 3.7 23.5 - - + +
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Residues in contact with THR 269 (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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149A THR* 3.8 18.6 - - + -
264A ALA 5.4 0.2 + - - -
265A GLY 4.2 4.3 + - - -
266A HIS 3.5 8.4 + - - -
267A GLU 3.2 0.8 - - - -
268A ALA* 1.3 77.0 - - - +
270A SER* 1.3 64.4 + - - +
272A LEU* 3.2 3.3 + - + +
273A LEU* 3.0 30.9 + - + +
406A ALA* 3.6 37.1 - - + +
409A GLU* 4.1 17.8 + - + +
410A ALA* 4.6 5.4 - - + -
501A HEM 3.7 23.6 - - + +
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Residues in contact with SER 270 (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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142A PRO 3.4 3.3 + - - -
145A MET* 3.1 12.1 - - - +
146A THR* 2.7 40.8 + - - -
149A THR* 3.4 26.6 - - - +
266A HIS 3.1 7.7 + - - -
267A GLU* 3.1 8.7 + - - -
269A THR* 1.3 71.6 - - - +
271A GLY* 1.3 61.9 + - - +
273A LEU 3.3 1.0 + - - -
274A SER* 2.8 31.9 + - - -
440A LYS* 3.8 6.2 - - - +
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Residues in contact with GLY 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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267A GLU 3.1 12.1 + - - -
268A ALA 3.5 3.8 + - - -
270A SER* 1.3 76.2 - - - +
272A LEU* 1.3 56.2 + - - +
274A SER* 3.1 2.6 + - - -
275A PHE* 2.9 33.8 + - - -
327A THR* 3.6 7.6 - - - -
439A LEU 3.7 17.3 - - - -
440A LYS* 3.6 20.2 - - - +
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Residues in contact with LEU 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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268A ALA 2.9 18.3 + - - +
269A THR* 3.2 10.0 + - + +
271A GLY* 1.3 71.3 - - - +
273A LEU* 1.3 63.9 + - - +
274A SER 3.2 0.2 + - - -
275A PHE* 3.3 1.9 + - - -
276A ALA* 2.9 25.5 + - - +
318A LEU* 3.5 38.4 - - + +
321A ALA* 3.9 14.1 - - + -
322A LEU* 3.6 27.1 - - + +
325A TRP 6.0 0.2 - - - +
327A THR* 3.6 7.3 - - + +
406A ALA 5.2 1.6 - - - +
407A LEU* 4.4 10.3 - - + -
410A ALA* 4.2 20.0 - - + -
501A HEM 3.7 23.3 - - + -
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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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145A MET* 3.6 29.9 - - + +
148A LEU* 4.0 27.4 - - + -
149A THR* 4.2 10.1 - - + -
269A THR* 3.0 20.7 + - + +
270A SER 3.9 0.4 - - - +
272A LEU* 1.3 76.8 - - - +
274A SER* 1.3 60.5 + - - +
276A ALA* 3.5 5.1 + - - +
277A LEU* 3.2 23.2 + - - +
318A LEU* 4.7 3.6 - - + -
409A GLU* 5.2 0.7 - - + -
410A ALA* 3.5 42.4 - - + +
413A VAL* 4.2 11.0 - - + -
414A LEU* 4.2 21.5 - - + +
417A MET* 5.0 4.8 - - - +
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Residues in contact with SER 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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141A VAL* 3.9 17.0 - - - -
142A PRO* 3.4 26.6 - - - +
145A MET* 3.5 5.5 - - - +
270A SER 2.8 22.6 + - - -
271A GLY 3.5 3.8 - - - -
273A LEU* 1.3 74.5 - - - +
275A PHE* 1.3 65.3 + - - +
277A LEU 3.4 0.9 + - - -
278A TYR* 3.0 23.0 + - - +
440A LYS* 4.2 0.8 - - - +
441A PRO* 3.6 24.7 - - - -
444A PHE* 3.7 6.8 - - - -
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Residues in contact with PHE 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 GLY 2.9 25.6 + - - +
272A LEU* 3.9 3.6 - - - +
274A SER* 1.3 76.3 - - - +
276A ALA* 1.3 57.4 + - - +
278A TYR* 3.3 6.5 + + - +
279A PHE* 2.8 43.5 + + + -
321A ALA* 4.4 12.3 - - + +
325A TRP* 3.7 48.0 - + + -
327A THR* 3.8 13.9 - - + -
431A LEU* 4.1 11.2 - - + -
433A ILE* 4.0 25.1 - - + -
439A LEU* 3.7 25.4 - - + -
440A LYS* 3.9 7.4 - - - -
441A PRO* 3.8 26.7 - - + -
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Residues in contact with ALA 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 LEU 2.9 18.7 + - - +
273A LEU* 3.7 5.8 - - - +
274A SER 3.2 0.2 - - - -
275A PHE* 1.3 77.7 - - - +
277A LEU* 1.3 58.1 + - - +
279A PHE* 3.3 3.6 + - - +
280A LEU* 2.9 34.8 + - - +
317A VAL* 4.5 8.0 - - + +
318A LEU* 3.8 25.6 - - + -
321A ALA* 4.0 16.0 - - + +
414A LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 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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130A TRP* 5.0 3.8 - - + -
141A VAL* 3.9 33.0 - - + -
145A MET* 6.5 0.2 - - - -
273A LEU 3.2 16.5 + - - +
274A SER 3.9 3.4 - - - +
275A PHE 3.3 0.2 - - - -
276A ALA* 1.3 72.5 - - - +
278A TYR* 1.3 64.6 + - - +
280A LEU* 3.2 10.9 + - + +
281A VAL* 2.9 39.4 + - + +
287A LEU* 6.0 0.7 - - + -
414A LEU* 4.7 9.6 - - + +
417A MET* 3.9 31.9 - - + -
418A LEU* 5.4 0.9 - - + -
423A PHE* 4.1 29.4 - - + -
444A PHE* 4.0 5.4 - - + -
446A VAL* 4.2 14.4 - - + -
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Residues in contact with TYR 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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274A SER 3.0 14.5 + - - +
275A PHE* 3.4 13.5 - + - +
277A LEU* 1.3 76.2 - - - +
279A PHE* 1.3 96.0 + + - +
281A VAL* 3.3 2.0 - - + +
282A LYS* 3.0 65.8 + - + +
429A TYR* 3.8 30.5 + + - -
431A LEU* 3.6 47.1 + - + +
441A PRO* 4.8 3.6 - - + -
444A PHE* 3.4 21.6 - + + -
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Residues in contact with PHE 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 PHE* 2.8 37.6 + - + +
276A ALA 3.8 1.8 - - - +
278A TYR* 1.3 96.4 - + - +
280A LEU* 1.3 62.1 + - - +
282A LYS* 3.3 1.7 + - + -
283A ASN* 2.8 36.4 + - - +
321A ALA* 4.2 11.7 - - + -
324A LEU* 3.6 33.7 - - + -
325A TRP* 3.7 31.6 - + - -
372A GLU 5.6 1.1 - - - -
374A PHE* 3.2 52.3 - + + -
431A LEU* 5.3 0.7 - - + -
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Residues in contact with LEU 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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276A ALA 2.9 21.8 + - - +
277A LEU* 3.2 10.1 + - + +
279A PHE* 1.3 77.1 - - - +
281A VAL* 1.3 58.3 + - - +
283A ASN 3.0 28.5 + - - +
284A PRO 3.8 0.3 - - - -
286A VAL* 3.5 31.0 - - + +
287A LEU* 3.5 30.5 - - + +
290A ALA* 4.5 1.3 - - + -
317A VAL* 3.9 25.6 - - + -
374A PHE* 4.7 0.9 - - + -
414A LEU* 4.0 19.3 - - + -
418A LEU* 4.0 33.7 - - + -
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Residues in contact with VAL 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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277A LEU* 2.9 24.0 + - + +
278A TYR* 3.3 11.4 - - - +
280A LEU* 1.3 75.9 - - - +
282A LYS* 1.3 68.1 + - + +
283A ASN 3.5 0.5 + - - -
284A PRO* 4.3 10.9 - - - +
287A LEU* 4.1 10.3 - - + -
423A PHE* 4.0 31.6 - - + +
425A ASP* 3.9 34.5 - - + +
444A PHE* 4.0 17.5 - - + -
446A VAL* 4.3 14.1 - - + -
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Residues in contact with LYS 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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278A TYR* 3.0 54.7 + - + +
279A PHE* 4.4 2.0 - - + -
280A LEU 3.2 0.2 - - - -
281A VAL* 1.3 78.7 - - + +
283A ASN* 1.3 72.2 + - - +
284A PRO* 3.7 7.9 - - - +
425A ASP* 2.6 31.3 + - - +
428A ASN* 3.7 8.3 - - - +
429A TYR* 2.7 32.8 + - - +
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Residues in contact with ASN 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 PHE* 2.8 32.2 + - - +
280A LEU 3.0 10.2 + - - +
282A LYS* 1.3 90.6 + - - +
284A PRO* 1.3 68.2 - - - +
285A HIS* 3.2 2.9 - - - -
286A VAL* 3.0 30.9 + - + +
287A LEU 3.1 4.9 + - - -
374A PHE* 3.8 34.1 + - + +
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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