Contacts of the helix formed by residues 282 - 295 (chain D) in PDB entry 3IAD
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 ARG 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B ARG* 4.3 5.7 - - - +
515B GLU* 2.9 43.2 + - - +
516B ARG* 6.1 0.2 - - - +
279D SER* 3.0 29.1 + - - +
280D GLY 4.1 4.7 - - - +
281D ASN* 1.3 81.7 + - - +
283D PRO* 1.4 65.2 - - - +
284D LEU 3.3 2.5 - - - -
285D THR* 3.3 17.2 + - + -
286D VAL* 3.2 26.2 + - + +
313D MET* 3.7 23.0 + - - +
316D GLU* 3.4 39.3 + - - +
317D ASP* 2.8 37.6 + - - -
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Residues in contact with PRO 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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272D VAL* 4.6 5.6 - - + +
275D ILE* 4.4 7.2 - - + -
276D ALA* 4.0 30.1 - - + +
279D SER* 3.6 4.2 - - - +
281D ASN* 3.2 11.2 - - - +
282D ARG* 1.4 90.7 - - - +
284D LEU* 1.3 62.4 + - - +
286D VAL* 3.8 5.6 - - + +
287D ILE* 3.0 32.7 + - + +
316D GLU* 3.2 9.6 - - - +
328D ASN* 3.5 11.9 - - - +
329D ILE* 4.2 17.3 - - + -
332D ALA* 3.7 13.9 - - + -
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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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283D PRO* 1.3 78.5 - - - +
285D THR* 1.3 59.0 + - - +
287D ILE* 4.8 0.9 - - + -
288D MET* 2.8 57.3 + - + +
312D LEU* 4.8 3.6 - - + +
315D LEU* 3.8 26.5 - - + -
316D GLU* 3.0 38.6 + - + +
319D TYR* 4.1 6.3 - - + -
328D ASN* 4.3 7.2 - - + +
331D ALA* 3.9 22.4 - - + -
332D ALA* 3.8 24.2 - - - +
335D VAL* 4.1 11.0 - - + -
364D ALA* 4.2 4.3 - - - +
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Residues in contact with THR 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ARG* 3.3 14.1 + - - -
284D LEU* 1.3 78.8 - - - +
286D VAL* 1.3 64.2 + - + +
289D HIS* 3.0 29.7 + - + +
309D ILE* 4.6 15.5 - - + -
312D LEU* 3.4 42.7 - - + +
313D MET* 3.4 22.5 + - + -
316D GLU* 2.8 21.0 + - - -
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Residues in contact with VAL 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 4.7 10.8 - - + -
262D LEU* 4.3 16.9 - - + +
275D ILE* 4.0 24.0 - - + -
279D SER* 4.2 18.6 - - - -
282D ARG* 3.2 21.4 + - + +
283D PRO 3.8 4.3 - - - +
285D THR* 1.3 80.2 - - + +
287D ILE* 1.3 61.8 + - - +
289D HIS* 4.0 5.9 - - - +
290D THR* 2.8 31.4 + - - -
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Residues in contact with ILE 287 (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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262D LEU* 4.4 11.2 - - + -
265D VAL* 4.6 5.4 - - + -
270D LEU* 4.0 23.6 - - + -
272D VAL* 4.0 11.4 - - + -
275D ILE* 4.2 20.6 - - + -
283D PRO 3.0 22.7 + - - +
284D LEU* 4.1 2.0 - - - +
286D VAL* 1.3 76.8 - - - +
288D MET* 1.3 63.9 + - + +
290D THR* 3.6 4.3 + - - -
291D ILE* 3.1 42.2 + - + +
332D ALA* 3.9 25.4 - - + +
335D VAL* 4.6 4.0 - - + -
336D GLN* 4.2 17.3 - - + -
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Residues in contact with MET 288 (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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284D LEU* 2.8 38.7 + - + +
287D ILE* 1.3 69.7 - - - +
289D HIS* 1.3 61.3 + - - +
291D ILE* 3.3 3.4 + - - +
292D PHE* 2.8 63.8 + - + -
311D TYR* 6.0 0.7 - - + -
312D LEU* 3.4 38.1 - - + -
315D LEU* 5.6 0.2 - - + -
335D VAL* 3.6 24.5 - - + -
360D ILE* 3.8 15.7 - - + +
361D PHE* 5.0 7.9 - - + -
364D ALA* 3.8 23.6 - - + -
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Residues in contact with HIS 289 (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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285D THR* 3.0 21.5 + - + +
286D VAL* 4.0 6.8 - - - +
288D MET* 1.3 78.1 - - - +
290D THR* 1.3 58.4 + - - +
292D PHE* 3.2 4.9 + - - +
293D GLN* 2.9 62.4 + - + +
298D LEU* 5.1 0.4 - - + -
305D VAL* 3.9 18.6 - - + +
308D LEU* 4.4 16.8 - - + -
309D ILE* 4.9 18.8 - - + +
312D LEU* 3.9 8.7 - - + +
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Residues in contact with THR 290 (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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262D LEU* 3.8 31.5 - - + +
265D VAL* 4.1 28.0 - - + -
286D VAL 2.8 21.3 + - - -
287D ILE* 3.9 5.8 - - - -
289D HIS* 1.3 78.4 + - - +
291D ILE* 1.3 58.7 + - - +
293D GLN* 3.2 7.2 + - - +
294D GLU* 2.9 33.1 + - + +
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Residues in contact with ILE 291 (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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265D VAL* 4.0 10.3 - - + -
287D ILE* 3.1 33.3 + - + +
288D MET* 3.6 4.7 - - - +
290D THR* 1.3 77.1 - - - +
292D PHE* 1.3 68.3 + - + +
294D GLU* 4.1 6.8 - - - +
295D ARG* 3.1 26.9 + - - +
335D VAL* 3.7 23.3 - - + -
336D GLN* 4.1 4.0 - - - -
339D HIS* 3.6 48.2 - - + +
360D ILE* 3.8 32.5 - - + -
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Residues in contact with PHE 292 (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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288D MET* 2.8 62.0 + - + +
289D HIS 3.7 3.6 - - - +
291D ILE* 1.3 77.7 - - + +
293D GLN* 1.3 59.6 + - - +
296D ASP 3.2 1.9 + - - -
297D LEU* 2.8 53.4 + - + +
298D LEU* 3.7 14.7 - - + +
303D ILE* 4.0 15.9 - - + -
308D LEU* 3.7 30.5 - - + -
357D LEU* 3.6 32.5 - - + -
360D ILE* 3.7 18.6 - - + -
361D PHE* 5.5 4.0 - - + -
414D ILE* 5.1 7.9 - - + -
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Residues in contact with GLN 293 (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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289D HIS* 2.9 51.3 + - + +
290D THR* 3.5 7.0 - - - +
291D ILE 3.2 0.2 - - - -
292D PHE* 1.3 75.2 - - - +
294D GLU* 1.3 61.4 + - - +
296D ASP* 2.8 27.0 + - - +
298D LEU* 4.2 23.3 - - + +
299D LYS* 6.1 3.4 - - - +
305D VAL* 4.4 4.3 - - - +
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Residues in contact with GLU 294 (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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265D VAL* 4.7 9.2 - - + +
266D ASN* 2.8 42.7 + - - +
290D THR* 2.9 23.4 + - + +
291D ILE* 4.1 8.5 - - - +
293D GLN* 1.3 73.6 - - - +
295D ARG* 1.3 61.8 + - + +
296D ASP* 3.3 1.4 + - - +
339D HIS* 3.7 13.3 + - + +
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Residues in contact with ARG 295 (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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291D ILE* 3.1 20.4 + - - +
294D GLU* 1.3 76.8 - - + +
296D ASP* 1.3 69.5 + - - +
297D LEU* 3.4 17.8 + - + +
300D THR* 4.8 1.6 + - - -
339D HIS* 3.1 39.2 + - + -
342D LEU* 3.4 19.6 + - - +
343D SER* 3.0 28.8 + - - +
356D ILE* 3.8 35.7 - - - +
360D ILE* 3.8 24.7 - - - +
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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