Contacts of the helix formed by residues 409 - 416 (chain A) in PDB entry 2IBI
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 SER 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A HIS* 2.5 35.3 + - - -
373A VAL* 3.5 27.6 - - - -
374A ASN* 3.7 6.1 - - - -
375A ARG* 3.5 10.8 - - - +
408A ASP* 1.3 75.5 + - - +
410A ARG* 1.3 58.9 + - - +
411A ILE* 3.3 14.5 + - - +
412A GLY* 3.1 5.6 + - - +
413A ASP* 2.9 30.1 + - - +
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Residues in contact with ARG 410 (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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290A GLU* 3.1 42.1 + - - +
291A LEU* 6.1 0.7 - - + -
294A TYR* 3.3 60.0 - - + +
299A LEU* 5.9 2.4 - - - +
303A ASP* 4.4 2.8 + - - +
373A VAL* 4.8 1.6 + - - +
375A ARG* 3.5 14.0 - - - +
409A SER* 1.3 71.7 - - - +
411A ILE* 1.3 66.6 + - + +
413A ASP* 3.3 45.9 + - - +
414A LEU* 3.4 37.9 - - + +
496A LYS* 4.9 5.7 - - - +
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Residues in contact with ILE 411 (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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291A LEU* 4.3 21.1 - - + -
294A TYR* 4.6 10.3 - - + -
315A VAL* 6.3 0.2 - - + -
318A PHE* 6.3 0.4 - - + -
366A LEU* 4.0 28.9 - - + +
369A LEU* 4.0 21.1 - - + -
370A HIS* 3.6 19.7 - - + -
373A VAL* 3.9 15.5 - - + -
409A SER* 3.2 12.3 - - - +
410A ARG* 1.3 76.3 - - - +
412A GLY* 1.3 63.6 + - - +
414A LEU* 3.0 15.5 + - - -
415A PHE* 3.1 28.9 + - + +
439A TRP* 3.7 18.6 - - + -
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Residues in contact with GLY 412 (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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370A HIS* 4.8 1.8 - - - -
409A SER* 3.1 14.7 + - - -
411A ILE* 1.3 75.2 - - - +
413A ASP* 1.3 65.3 + - - +
414A LEU 2.9 3.4 + - - -
416A VAL* 3.1 46.5 + - - +
439A TRP* 3.7 9.8 - - - -
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Residues in contact with ASP 413 (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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375A ARG* 2.8 41.2 + - - -
408A ASP* 4.5 1.9 - - - +
409A SER 2.9 18.5 + - - +
410A ARG* 3.3 34.7 + - - +
412A GLY* 1.3 73.7 - - - +
414A LEU* 1.3 61.4 + - - +
416A VAL 5.1 1.9 + - - +
496A LYS* 3.7 27.8 + - - +
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Residues in contact with LEU 414 (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 THR* 4.6 6.7 - - + -
290A GLU* 3.5 30.5 - - + +
291A LEU* 3.5 48.2 - - + +
410A ARG* 3.4 41.5 - - + +
411A ILE* 3.0 7.4 + - - +
412A GLY 2.9 2.4 + - - -
413A ASP* 1.3 78.7 - - - +
415A PHE* 1.3 66.1 + - + +
416A VAL 3.7 0.4 - - - -
496A LYS* 3.3 15.8 + - + -
497A ILE* 2.8 40.6 + - + -
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Residues in contact with PHE 415 (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 LEU* 3.7 27.4 - - + -
288A THR* 4.5 10.8 - - + -
291A LEU* 4.4 10.3 - - + -
362A LEU* 5.2 0.4 - - + -
366A LEU* 3.8 33.2 - - + -
411A ILE* 3.1 25.2 + - + +
414A LEU* 1.3 88.3 - - + +
416A VAL* 1.3 62.7 + - - +
417A GLY 3.6 1.7 + - - -
438A PHE* 3.6 0.5 - - - +
439A TRP* 3.5 42.7 - - + +
495A PRO* 3.4 12.5 - - - +
497A ILE* 3.6 31.9 - - + +
499A VAL* 3.7 26.5 - - + -
595A PHE* 4.9 2.9 - + - -
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Residues in contact with VAL 416 (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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400A TRP* 3.7 27.8 - - + -
403A TYR* 3.8 22.4 - - + -
412A GLY* 3.1 26.6 + - - +
413A ASP 5.3 1.9 - - - +
414A LEU 3.7 0.6 - - - -
415A PHE* 1.3 74.8 - - - +
417A GLY* 1.3 71.4 + - - +
437A PRO* 4.2 4.3 - - + -
438A PHE 3.4 8.7 - - - +
439A TRP* 3.2 42.6 - - + +
493A ARG* 5.8 0.2 - - - +
494A PHE 4.7 0.5 - - - +
495A PRO* 3.5 13.7 - - - +
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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