Contacts of the helix formed by residues 304 - 318 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C LYS 3.1 12.1 - - - +
303C ILE* 1.3 90.7 - - + +
305C VAL* 1.3 59.5 + - - +
306C ASP* 3.3 18.2 - - - +
307C THR* 3.4 18.7 + - + +
308C LEU* 3.1 22.5 + - - +
413C ASP 5.7 0.2 - - - +
414C ILE 5.5 1.1 - - - +
416C GLN* 4.5 19.7 - - + +
417C ASN* 4.3 8.1 - - - +
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C HIS* 4.0 16.8 - - + +
298C LEU* 4.1 21.3 - - + +
303C ILE 3.4 1.8 + - - -
304C PRO* 1.3 70.8 - - - +
306C ASP* 1.3 72.6 + - + +
308C LEU* 3.8 3.4 - - + +
309C ILE* 3.0 44.0 + - + +
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Residues in contact with ASP 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ARG 6.2 0.2 - - - +
304C PRO* 3.3 19.1 - - - +
305C VAL* 1.3 81.5 + - + +
307C THR* 1.3 57.3 + - - -
309C ILE* 3.9 6.3 - - - +
310C THR* 2.7 38.9 + - - +
411C ASN* 3.2 24.6 + - - +
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Residues in contact with THR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C PRO* 3.4 29.6 + - - +
305C VAL 3.2 0.6 - - - -
306C ASP* 1.3 78.4 + - - +
308C LEU* 1.3 59.3 + - - +
310C THR 3.3 0.3 + - - -
311C TYR* 2.9 28.1 + - - +
411C ASN* 2.8 38.6 + - - +
412C CYS 3.9 0.7 - - - -
413C ASP 3.6 36.3 - - - +
414C ILE* 4.1 5.2 - - - +
416C GLN* 3.7 10.4 + - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C HIS* 4.7 13.0 - - + +
292C PHE* 3.9 43.7 - - + -
298C LEU* 4.0 28.0 - - + -
303C ILE* 3.8 8.5 - - + -
304C PRO 3.1 16.5 + - - +
305C VAL* 3.8 6.1 - - + +
307C THR* 1.3 76.8 - - - +
309C ILE* 1.3 57.1 + - + +
311C TYR* 3.3 1.3 + - + +
312C LEU* 2.8 59.0 + - + +
414C ILE* 3.7 24.6 - - + +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A GLU 5.0 8.7 - - - +
285C THR* 5.2 4.9 - - + -
289C HIS* 4.1 25.4 - - + +
305C VAL* 3.0 37.3 + - + +
306C ASP* 3.9 6.5 - - - +
308C LEU* 1.3 77.1 - - + +
310C THR* 1.3 61.5 + - - +
312C LEU* 3.5 6.8 + - + +
313C MET* 3.0 59.9 + - + +
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Residues in contact with THR 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLU 5.2 1.2 + - - -
516A ARG* 3.8 47.0 + - + +
306C ASP* 2.7 24.1 + - - +
309C ILE* 1.3 77.2 - - - +
311C TYR* 1.3 63.7 + - - +
313C MET* 3.5 6.6 + - - +
314C THR* 2.9 29.1 + - - -
410C GLU 3.8 4.0 - - - +
411C ASN* 3.4 28.7 + - + +
412C CYS* 3.6 12.6 - - - -
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Residues in contact with TYR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C MET* 5.6 1.1 - - + -
307C THR 2.9 8.6 + - - +
308C LEU* 3.8 1.1 - - + +
310C THR* 1.3 77.4 - - - +
312C LEU* 1.3 68.7 + - + +
314C THR* 3.1 3.8 + - - -
315C LEU* 2.9 53.2 + - + +
361C PHE* 3.4 32.0 - + - -
365C ILE* 3.5 10.6 - - - +
403C GLY 2.8 21.3 + - - -
406C LEU* 3.9 32.1 - - + -
407C LEU* 3.6 13.0 - - + -
412C CYS* 3.6 26.4 - - + +
414C ILE* 3.6 36.3 - - + -
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 4.5 6.3 - - + +
285C THR* 3.3 45.8 + - + +
288C MET* 3.3 49.8 - - + -
289C HIS* 3.8 11.4 - - + +
308C LEU* 2.8 41.7 + - + +
309C ILE* 3.9 5.6 - - - +
311C TYR* 1.3 87.0 - - + +
313C MET* 1.3 57.1 + - - +
315C LEU* 3.5 10.3 + - + +
316C GLU* 3.0 24.3 + - - +
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLU* 3.2 50.5 - - + +
516A ARG* 6.3 1.1 - - + -
282C ARG* 3.7 26.4 + - - +
285C THR* 3.9 21.1 - - + +
309C ILE* 3.0 43.3 + - + +
310C THR* 4.0 6.5 - - - +
312C LEU* 1.3 74.1 - - - +
314C THR* 1.3 65.3 + - - +
316C GLU 3.6 0.2 + - - -
317C ASP* 3.2 31.5 + - - +
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Residues in contact with THR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ARG* 3.3 21.8 + - - +
310C THR 2.9 17.2 + - - -
311C TYR* 3.1 5.4 + - - -
313C MET* 1.3 73.8 - - - +
315C LEU* 1.3 64.4 + - - +
317C ASP* 3.4 7.3 + - - +
318C HIS* 3.1 35.8 + - + +
406C LEU* 3.6 26.9 - - + -
409C GLU* 3.2 24.2 - - - +
412C CYS* 3.7 8.5 - - - -
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 4.0 15.5 - - + -
311C TYR* 2.9 49.6 + - + +
312C LEU* 3.7 10.3 - - + +
314C THR* 1.3 75.5 - - - +
316C GLU* 1.3 64.7 + - - +
318C HIS* 3.2 11.3 + - - +
319C TYR* 3.3 18.5 + - + -
364C ALA* 3.8 33.9 - - + +
365C ILE* 4.1 11.4 - - + -
368C VAL* 3.8 28.0 - - + -
403C GLY* 4.9 1.1 - - - -
406C LEU* 4.0 13.6 - - + +
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ASN 4.5 1.6 - - - +
282C ARG* 3.5 34.4 - - - +
283C PRO 3.2 4.0 - - - -
284C LEU* 2.9 36.1 + - + +
285C THR* 2.7 36.6 + - - -
312C LEU 3.0 14.9 + - - +
313C MET 3.9 0.7 - - - +
314C THR 3.3 0.2 - - - -
315C LEU* 1.3 76.7 - - - +
317C ASP* 1.3 57.2 + - - +
319C TYR* 3.1 32.5 + - - +
328C ASN* 3.0 34.0 + - + +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ARG* 3.1 43.0 - - - +
282C ARG* 3.2 25.9 + - - -
313C MET* 3.2 18.5 + - - +
314C THR* 3.8 7.6 - - - +
315C LEU 3.3 0.4 - - - -
316C GLU* 1.3 75.7 - - - +
318C HIS* 1.3 61.8 + - + +
319C TYR 3.3 10.5 - - - +
320C HIS* 5.7 0.7 - - - -
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Residues in contact with HIS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C THR* 3.1 26.4 + - + +
315C LEU 3.2 4.7 + - - +
316C GLU 3.2 1.0 - - - -
317C ASP* 1.3 80.3 - - + +
319C TYR* 1.3 58.9 + - - +
320C HIS* 3.8 5.2 - - - -
368C VAL* 3.6 21.8 - - + -
369C ASP* 2.8 40.5 + - + +
402C VAL* 4.6 10.5 - - + -
406C LEU* 3.5 33.3 - - + +
409C GLU* 4.6 6.9 + - - -
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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
------------------------------------------------------------
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