Contacts of the helix formed by residues 304 - 318 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LYS 3.4 10.3 - - - +
303A ILE* 1.3 87.1 - - + +
305A VAL* 1.3 59.7 + - - +
306A ASP* 3.5 17.9 - - - +
307A THR* 3.2 19.8 + - + +
308A LEU* 3.0 26.3 + - - +
413A ASP 5.5 0.4 - - - +
414A ILE 5.6 0.4 - - - +
416A GLN* 4.3 26.7 - - + +
417A ASN* 4.6 4.5 - - - +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A HIS* 4.2 24.7 - - + -
293A GLN* 5.1 3.6 - - - +
298A LEU* 3.8 20.4 - - + +
303A ILE 3.4 3.0 + - - -
304A PRO* 1.3 72.2 - - - +
306A ASP* 1.3 65.9 + - + +
308A LEU* 3.2 3.5 + - + +
309A ILE* 2.9 35.7 + - + +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 3.5 17.5 - - - +
305A VAL* 1.3 85.1 + - + +
307A THR* 1.3 56.7 + - - +
309A ILE* 3.5 5.8 + - - +
310A THR* 2.8 37.9 + - - +
411A ASN* 2.7 28.5 + - - +
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Residues in contact with THR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO* 3.2 28.6 + - - +
306A ASP* 1.3 80.7 + - - +
308A LEU* 1.3 56.9 + - - +
310A THR 3.4 0.2 + - - -
311A TYR* 3.0 27.5 + - - +
411A ASN* 2.7 49.4 + - - +
412A CYS 3.7 6.5 - - - -
413A ASP 3.6 25.4 - - - +
414A ILE* 4.1 4.5 - - - +
416A GLN* 3.7 10.1 + - - +
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Residues in contact with LEU 308 (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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289A HIS* 4.4 15.0 - - + +
292A PHE* 3.9 36.1 - - + -
298A LEU* 3.7 36.8 - - + -
303A ILE* 4.0 10.3 - - + +
304A PRO 3.0 12.9 + - - +
305A VAL* 3.5 8.3 - - - +
307A THR* 1.3 77.8 - - - +
309A ILE* 1.3 61.9 + - + +
311A TYR* 3.4 1.0 + - - +
312A LEU* 3.1 50.3 + - + +
414A ILE* 3.8 26.4 - - + +
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Residues in contact with ILE 309 (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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285A THR* 4.4 14.1 - - + -
289A HIS* 3.8 35.9 - - + +
305A VAL* 2.9 30.7 + - + +
306A ASP* 3.9 6.1 - - - +
308A LEU* 1.3 76.0 - - + +
310A THR* 1.3 62.6 + - - +
312A LEU* 3.6 5.9 + - + +
313A MET* 3.1 49.2 + - + +
515C GLU 5.1 3.8 - - - +
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 2.8 22.1 + - - +
309A ILE* 1.3 78.0 - - - +
311A TYR* 1.3 55.8 + - - +
313A MET* 3.7 11.8 + - - +
314A THR* 2.7 33.3 + - - -
410A GLU 3.6 23.6 - - - +
411A ASN* 3.5 21.8 + - + +
412A CYS* 3.8 8.1 - - - -
516C ARG* 4.0 30.8 + - + +
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Residues in contact with TYR 311 (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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288A MET* 6.1 0.4 - - + -
307A THR 3.0 7.7 + - - +
308A LEU* 3.8 1.6 - - + +
309A ILE 3.3 0.2 - - - -
310A THR* 1.3 74.1 - - - +
312A LEU* 1.3 72.0 + - + +
314A THR* 3.1 3.4 + - - -
315A LEU* 2.8 50.8 + - + +
361A PHE* 3.4 34.6 - + - -
365A ILE* 3.6 9.4 - - - +
403A GLY* 2.8 22.4 + - - -
406A LEU* 3.9 21.3 - - + -
407A LEU* 3.5 27.4 - - + -
412A CYS* 3.5 26.2 - - + +
414A ILE* 3.4 35.7 - - + -
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Residues in contact with LEU 312 (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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284A LEU* 4.9 5.1 - - + +
285A THR* 3.3 31.8 + - + +
288A MET* 3.5 57.2 - - + -
289A HIS* 3.9 9.4 - - + +
292A PHE* 6.2 0.4 - - + -
308A LEU* 3.1 39.3 + - + +
309A ILE* 3.9 5.6 - - + +
311A TYR* 1.3 90.9 - - + +
313A MET* 1.3 57.9 + - - +
315A LEU* 3.5 9.7 + - + +
316A GLU* 2.9 30.8 + - - +
414A ILE* 6.1 0.2 - - + -
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Residues in contact with MET 313 (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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282A ARG* 4.0 22.6 + - - +
285A THR* 3.6 19.7 - - + +
309A ILE* 3.1 42.0 + - + +
310A THR* 4.0 10.3 - - - +
312A LEU* 1.3 75.1 - - - +
314A THR* 1.3 58.4 + - - +
316A GLU* 3.4 1.6 + - - +
317A ASP* 2.8 37.1 + - - +
515C GLU* 3.5 49.1 - - - +
516C ARG* 4.0 26.5 - - + +
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Residues in contact with THR 314 (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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310A THR 2.7 23.3 + - - -
311A TYR* 3.4 4.5 - - - -
313A MET* 1.3 73.6 - - - +
315A LEU* 1.3 64.5 + - - +
317A ASP* 3.4 2.9 + - - +
318A HIS* 2.9 36.6 + - + -
406A LEU* 3.8 27.8 - - + -
409A GLU* 3.5 23.5 + - - +
412A CYS* 3.7 13.9 - - - -
516C ARG* 3.3 28.8 + - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.1 12.6 - - + -
311A TYR* 2.8 44.4 + - + +
312A LEU* 3.7 10.1 - - + +
314A THR* 1.3 69.5 - - - +
316A GLU* 1.3 66.7 + - - +
318A HIS* 3.0 15.4 + - - +
319A TYR* 3.5 12.7 + - + -
364A ALA* 3.9 24.7 - - + +
365A ILE* 3.8 34.5 - - + -
368A VAL* 3.7 26.5 - - + -
403A GLY* 4.5 2.0 - - - -
406A LEU* 3.9 15.1 - - + +
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Residues in contact with GLU 316 (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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281A ASN 4.5 0.7 - - - +
282A ARG* 3.0 38.7 + - - +
283A PRO 3.2 4.7 - - - -
284A LEU* 3.0 39.9 + - + +
285A THR* 3.0 21.8 + - - -
312A LEU 2.9 16.6 + - - +
313A MET 3.7 0.2 - - - +
315A LEU* 1.3 76.1 - - - +
317A ASP* 1.3 57.8 + - - +
319A TYR* 2.9 30.7 + - - +
328A ASN* 2.8 37.1 + - + +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 2.7 25.8 + - - -
313A MET 2.8 19.1 + - - +
314A THR* 3.5 8.7 - - - +
315A LEU 3.2 0.2 - - - -
316A GLU* 1.3 75.6 - - - +
318A HIS* 1.3 63.8 + - + +
319A TYR 3.3 10.3 - - - +
512C ARG* 3.0 42.0 + - - +
515C GLU* 5.0 0.2 - - - +
516C ARG* 3.3 20.0 + - - +
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Residues in contact with HIS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A THR* 2.9 28.3 + - + +
315A LEU 3.0 11.7 + - - +
317A ASP* 1.3 79.9 - - + +
319A TYR* 1.3 62.2 + - - +
320A HIS* 3.6 6.4 - - - -
368A VAL* 3.7 15.5 - - + -
369A ASP* 3.0 35.9 + - - +
402A VAL* 4.6 9.0 - - + -
406A LEU* 3.7 33.3 - - + +
409A GLU* 4.3 8.5 + - - -
512C ARG* 6.3 0.2 - - - -
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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