Contacts of the helix formed by residues 304 - 318 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B LEU* 4.5 0.2 - - - -
302B LYS 3.4 10.5 - - - +
303B ILE* 1.3 87.8 - - + +
305B VAL* 1.3 65.2 + - - +
306B ASP* 3.4 18.6 - - - +
307B THR* 3.5 21.5 - - + +
308B LEU* 3.0 21.3 + - - +
413B ASP 5.8 0.2 - - - +
414B ILE 5.7 0.2 - - - +
416B GLN* 4.2 13.0 - - + +
417B ASN* 4.3 7.2 - - - +
801B EPE 4.0 20.2 - - - +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B HIS* 4.3 16.6 - - + +
293B GLN* 4.9 7.0 - - - +
298B LEU* 3.9 21.8 - - + -
303B ILE 3.5 1.8 + - - +
304B PRO* 1.3 70.9 - - - +
306B ASP* 1.3 64.0 + - - +
308B LEU* 3.2 3.6 + - - +
309B ILE* 3.1 46.5 + - + +
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B PRO* 3.4 12.0 - - - +
305B VAL* 1.3 81.7 + - - +
307B THR* 1.3 54.6 + - - -
309B ILE* 4.1 7.9 - - - +
310B THR* 2.7 35.3 + - - +
411B ASN* 2.8 24.2 + - - +
801B EPE 3.2 27.9 + - - -
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B PRO* 3.2 19.0 + - - +
306B ASP* 1.3 76.6 - - - +
308B LEU* 1.3 64.5 + - - +
311B TYR* 3.2 17.5 + - - +
411B ASN* 2.6 38.7 + - - +
412B CYS 3.7 3.4 - - - -
413B ASP 3.5 34.8 - - - +
414B ILE* 3.5 10.9 - - - +
416B GLN* 3.6 8.8 + - - +
801B EPE 3.5 14.0 - - - -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B HIS* 4.4 15.5 - - + -
292B PHE* 3.8 49.8 - - + -
298B LEU* 3.8 24.5 - - + -
303B ILE* 4.1 9.0 - - + -
304B PRO 3.0 12.0 + - - +
305B VAL* 3.2 9.6 + - - +
307B THR* 1.3 78.4 - - - +
309B ILE* 1.3 57.3 + - + +
311B TYR* 3.3 3.5 + - + +
312B LEU* 3.0 51.9 + - + +
414B ILE* 3.6 26.0 - - + +
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B THR* 4.3 10.3 - - + -
289B HIS* 4.8 25.4 - - + +
305B VAL* 3.1 42.7 + - + +
306B ASP* 4.1 5.6 - - - +
308B LEU* 1.3 76.3 - - + +
310B THR* 1.3 59.0 + - - +
312B LEU* 3.4 7.8 + - + +
313B MET* 2.8 56.9 + - + +
515D GLU 5.5 3.1 - - - +
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ASP* 2.7 23.4 + - - +
309B ILE* 1.3 78.2 - - - +
311B TYR* 1.3 56.1 + - - +
313B MET* 3.7 7.7 - - - +
314B THR* 2.8 34.1 + - - -
410B GLU 3.7 23.8 - - - +
411B ASN* 3.5 20.4 + - + +
412B CYS* 3.9 3.8 - - - -
516D ARG* 3.7 40.3 + - + +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B MET* 5.9 0.4 - - + -
307B THR 3.2 13.3 + - - +
308B LEU 3.3 2.7 + - - +
310B THR* 1.3 75.5 - - - +
312B LEU* 1.3 68.5 + - + +
314B THR* 3.2 1.9 + - - -
315B LEU* 2.7 58.7 + - + +
361B PHE* 3.2 36.0 - + - -
365B ILE* 3.5 11.3 - - - +
403B GLY* 2.8 26.3 + - - -
406B LEU* 3.8 20.4 - - + -
407B LEU* 3.5 22.0 - - + -
412B CYS* 3.4 36.5 - - + +
414B ILE* 3.8 15.3 - - + -
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU* 4.7 5.1 - - + +
285B THR* 3.6 41.0 + - + +
288B MET* 3.3 50.5 - - + -
289B HIS* 4.0 9.6 - - + +
292B PHE* 6.1 0.2 - - + -
308B LEU* 3.0 41.9 + - + +
309B ILE* 3.8 5.2 - - + +
311B TYR* 1.3 86.8 - - + +
313B MET* 1.3 54.0 + - - +
315B LEU* 3.3 8.8 + - + +
316B GLU* 2.7 36.6 + - - +
414B ILE* 6.4 0.4 - - + -
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ARG* 3.6 24.2 + - - +
285B THR* 3.7 21.1 - - + +
309B ILE* 2.8 42.3 + - + +
310B THR* 3.8 5.2 - - - +
312B LEU* 1.3 74.1 - - - +
314B THR* 1.3 58.5 + - - +
316B GLU 3.5 0.2 + - - -
317B ASP* 3.0 34.8 + - - +
515D GLU* 3.4 59.5 - - + +
516D ARG* 5.0 12.3 - - + +
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Residues in contact with THR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B THR 2.8 25.6 + - - -
311B TYR* 3.2 7.6 + - + -
313B MET* 1.3 71.8 - - - +
315B LEU* 1.3 62.8 + - - +
317B ASP* 3.4 9.7 + - - +
318B HIS* 3.0 29.9 + - + +
406B LEU* 3.8 27.4 - - + +
409B GLU* 3.4 22.6 + - - +
412B CYS* 3.6 14.5 - - - -
516D ARG* 2.8 29.2 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU* 4.1 13.7 - - + -
311B TYR* 2.7 49.8 + - + +
312B LEU* 3.6 10.1 - - + +
314B THR* 1.3 73.4 - - - +
316B GLU* 1.3 62.8 + - - +
318B HIS* 3.3 11.3 + - - +
319B TYR* 3.4 14.9 + - + -
364B ALA* 4.0 21.3 - - + +
365B ILE* 3.8 26.2 - - + -
368B VAL* 3.6 29.6 - - + -
403B GLY* 4.8 1.1 - - - -
406B LEU* 4.0 11.9 - - + -
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ASN 3.9 0.9 - - - +
282B ARG* 3.3 31.7 + - - +
283B PRO* 3.2 5.0 - - - +
284B LEU* 3.0 40.8 + - + +
285B THR* 2.6 33.5 + - - +
312B LEU 2.7 20.1 + - - +
315B LEU* 1.3 74.2 - - - +
317B ASP* 1.3 57.1 - - - +
319B TYR* 3.1 28.7 + - - +
328B ASN* 2.7 37.2 + - + +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ARG* 2.9 31.1 + - - -
313B MET* 3.0 20.7 + - - +
314B THR* 3.8 8.3 - - - +
315B LEU 3.3 0.4 - - - -
316B GLU* 1.3 74.5 - - - +
318B HIS* 1.3 64.4 + - + +
319B TYR 3.3 10.8 - - - +
508D ARG* 5.4 5.4 + - - -
512D ARG* 3.3 45.4 + - - +
516D ARG* 4.7 7.6 + - - -
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Residues in contact with HIS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B THR* 3.0 25.9 + - + +
315B LEU 3.3 4.3 + - - +
316B GLU 3.1 1.4 - - - -
317B ASP* 1.3 82.0 - - + +
319B TYR* 1.3 60.1 + - - +
320B HIS* 4.0 5.4 - - - -
368B VAL* 3.8 21.3 - - + -
369B ASP* 2.9 38.3 + - + +
402B VAL* 4.6 8.1 - - + -
406B LEU* 3.6 35.0 - - + +
409B GLU* 4.5 6.8 + - - -
512D ARG* 6.0 1.8 - - - -
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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