Contacts of the helix formed by residues 304 - 318 (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 PRO 304 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302D LYS 3.4 10.1 - - - +
303D ILE* 1.3 88.3 - - + +
305D VAL* 1.3 66.3 + - - +
306D ASP* 3.7 12.3 - - - +
307D THR* 3.1 26.5 + - + +
308D LEU 3.1 18.7 + - - -
413D ASP 5.6 0.2 - - - +
414D ILE 5.3 1.6 - - - +
416D GLN* 4.2 24.0 - - + +
417D ASN* 4.3 6.5 - - - +
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 3.9 26.7 - - + +
293D GLN* 4.4 4.0 - - - +
298D LEU* 3.7 23.3 - - + +
303D ILE 3.3 2.4 + - - -
304D PRO* 1.3 71.2 - - - +
306D ASP* 1.3 71.9 + - + +
308D LEU* 3.3 3.8 + - + +
309D ILE* 3.1 34.1 + - + +
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Residues in contact with ASP 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D PRO* 3.7 15.3 - - - +
305D VAL* 1.3 82.6 + - + +
307D THR* 1.3 57.8 + - - +
309D ILE* 3.5 8.7 + - - +
310D THR* 2.7 38.5 + - - +
411D ASN* 3.2 23.2 + - - +
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Residues in contact with THR 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ILE* 5.2 0.2 - - - -
304D PRO* 3.1 33.3 + - + +
306D ASP* 1.3 77.3 + - - +
308D LEU* 1.3 59.7 + - - +
311D TYR* 3.0 28.1 + - - +
411D ASN* 2.7 49.0 + - - +
412D CYS 3.9 0.2 - - - -
413D ASP 3.8 30.1 - - - +
414D ILE* 4.0 3.8 - - - +
416D GLN* 4.2 7.6 + - - +
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 4.4 14.4 - - + -
292D PHE* 3.7 45.1 - - + -
298D LEU* 3.8 25.4 - - + -
303D ILE* 4.0 10.0 - - + +
304D PRO 3.1 11.6 + - - +
305D VAL* 3.6 9.4 - - - +
307D THR* 1.3 77.2 - - - +
309D ILE* 1.3 57.8 + - + +
311D TYR* 3.2 1.8 + - + +
312D LEU* 2.9 58.1 + - + +
414D ILE* 3.7 25.7 - - + +
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Residues in contact with ILE 309 (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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515B GLU 5.7 1.3 - - - +
285D THR* 4.6 9.0 - - + -
289D HIS* 4.9 22.7 - - + -
305D VAL* 3.1 34.4 + - + +
306D ASP* 3.9 7.2 - - - +
308D LEU* 1.3 72.5 - - + +
310D THR* 1.3 67.3 + - - +
312D LEU* 3.2 8.7 + - + +
313D MET* 2.9 54.1 + - + +
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Residues in contact with THR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ARG* 4.1 27.7 + - + +
306D ASP* 2.7 24.1 + - - +
309D ILE* 1.3 79.0 - - - +
311D TYR* 1.3 56.7 + - - +
313D MET* 3.5 7.3 + - - +
314D THR* 2.8 32.4 + - - -
410D GLU 3.6 23.8 - - - +
411D ASN* 3.5 21.2 + - + +
412D CYS* 3.9 6.5 - - - -
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Residues in contact with TYR 311 (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* 6.0 0.7 - - + -
307D THR 3.0 18.6 + - - +
308D LEU 3.7 1.1 - - - +
310D THR* 1.3 76.5 - - - +
312D LEU* 1.3 66.9 + - + +
314D THR* 3.2 1.7 + - - -
315D LEU* 2.8 55.8 + - + +
361D PHE* 3.2 34.2 - + - -
364D ALA* 6.0 0.2 - - + -
365D ILE* 3.6 9.2 - - - +
403D GLY 2.9 20.9 + - - -
406D LEU* 4.0 9.2 - - + -
407D LEU* 3.4 28.7 - - + -
412D CYS* 3.3 40.8 - - + +
414D ILE* 3.6 20.2 - - + -
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Residues in contact with LEU 312 (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* 4.8 4.9 - - + +
285D THR* 3.4 32.2 + - + +
288D MET* 3.4 58.6 - - + -
289D HIS* 3.9 9.6 - - + +
308D LEU* 2.9 43.4 + - + +
309D ILE* 3.7 5.6 - - + +
311D TYR* 1.3 87.1 - - + +
313D MET* 1.3 60.2 + - - +
315D LEU* 3.5 9.2 + - + +
316D GLU* 2.9 31.4 + - - +
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Residues in contact with MET 313 (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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515B GLU* 3.8 53.2 - - + +
516B ARG* 4.5 18.2 - - - +
282D ARG* 3.7 28.9 - - - +
285D THR* 3.6 16.2 - - + +
309D ILE* 2.9 41.8 + - + +
310D THR* 3.8 4.9 - - - +
312D LEU* 1.3 75.4 - - - +
314D THR* 1.3 56.9 + - - +
316D GLU* 3.4 0.9 + - - +
317D ASP* 2.9 38.0 + - - +
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Residues in contact with THR 314 (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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516B ARG* 3.3 29.6 + - - +
310D THR 2.8 24.9 + - - -
311D TYR* 3.5 4.3 - - - -
313D MET* 1.3 75.7 - - - +
315D LEU* 1.3 60.6 + - - +
317D ASP* 3.3 8.6 + - - +
318D HIS* 3.0 28.5 + - + +
406D LEU* 3.9 25.6 - - + -
409D GLU* 3.4 24.6 + - - +
412D CYS* 3.5 18.2 - - - -
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LEU* 3.8 15.5 - - + -
311D TYR* 2.8 47.3 + - + +
312D LEU* 3.9 7.4 - - + +
314D THR* 1.3 73.8 - - - +
316D GLU* 1.3 62.8 + - - +
318D HIS* 3.2 13.0 + - - +
319D TYR* 3.5 12.5 + - + -
364D ALA* 3.7 36.1 - - + +
365D ILE* 3.5 27.8 - - + -
368D VAL* 3.8 26.0 - - + +
403D GLY* 4.7 1.3 - - - -
406D LEU* 4.0 14.8 - - + +
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Residues in contact with GLU 316 (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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281D ASN 4.8 0.2 - - - +
282D ARG* 3.5 28.0 + - - +
283D PRO* 3.2 4.7 - - - +
284D LEU* 3.0 41.3 + - + +
285D THR* 2.8 34.8 + - - -
312D LEU 2.9 17.2 + - - +
313D MET 3.7 3.4 - - - +
314D THR 3.3 0.2 - - - -
315D LEU* 1.3 75.6 - - - +
317D ASP* 1.3 57.9 + - - +
319D TYR* 3.0 29.0 + - - +
328D ASN* 2.9 37.3 + - + +
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Residues in contact with ASP 317 (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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512B ARG* 2.9 45.3 + - - +
516B ARG* 3.5 13.7 + - - +
282D ARG* 2.8 34.2 + - - -
313D MET 2.9 21.2 + - - +
314D THR* 3.6 6.7 - - - +
316D GLU* 1.3 74.9 - - - +
318D HIS* 1.3 63.5 + - + +
319D TYR 3.3 8.6 + - - +
320D HIS* 6.0 0.2 - - - -
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Residues in contact with HIS 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B ARG* 6.1 1.1 - - - -
314D THR* 3.0 24.3 + - + +
315D LEU 3.2 10.6 + - - +
316D GLU 3.1 1.4 - - - -
317D ASP* 1.3 81.8 - - + +
319D TYR* 1.3 60.0 + - - +
320D HIS* 3.7 5.8 - - - -
368D VAL* 3.7 15.0 - - + -
369D ASP* 3.0 35.4 + - + +
402D VAL* 4.7 7.9 - - + -
406D LEU* 3.6 33.3 - - + +
409D GLU* 4.3 9.9 + - - -
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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