Contacts of the helix formed by residues 375 - 379 (chain B) in PDB entry 1IAS
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 THR 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B SO4 4.2 20.2 - - - +
215B ARG* 4.2 8.2 + - - +
333B ASP* 3.0 11.6 + - - -
335B LYS* 2.5 44.3 + - + +
374B GLY* 1.3 69.2 - - - -
376B LYS* 1.3 69.9 + - + +
377B ARG* 4.0 8.7 - - + +
378B TYR* 3.1 30.2 + - + +
379B MET* 3.2 11.3 + - - +
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 6.1 0.7 - - - +
374B GLY 3.9 11.0 - - - +
375B THR* 1.3 72.2 - - - +
377B ARG* 1.3 66.7 + - - +
379B MET* 2.8 41.9 + - - +
436B PRO* 3.6 27.6 + - + +
437B SER* 5.1 1.6 - - - +
438B VAL* 3.5 34.6 - - + +
441B MET* 4.0 20.5 - - + +
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Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SO4 2.7 52.7 + - - +
375B THR* 3.3 3.6 + - + +
376B LYS* 1.3 78.7 - - - +
378B TYR* 1.3 73.7 + - + +
379B MET 4.8 0.3 - - - +
406B LEU* 4.0 2.3 - - - +
426B LEU* 3.6 28.0 - - - +
427B PRO* 2.7 36.1 + - + +
428B TYR* 3.7 23.7 + - + +
429B TYR* 4.2 7.5 - - - +
432B VAL* 3.8 20.3 + - - -
433B PRO 4.0 8.3 + - - -
434B SER* 4.7 2.0 - - - +
436B PRO* 3.3 23.0 - - + +
441B MET* 3.3 25.8 - - + +
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Residues in contact with TYR 378 (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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12B SO4 6.1 0.9 - - - -
333B ASP* 6.1 0.2 - - - +
334B LEU 3.7 19.5 - - - +
335B LYS* 3.5 32.4 - - + +
336B SER* 3.3 13.9 + - - -
337B LYS* 6.0 0.2 - - - +
375B THR* 3.1 19.4 + - + +
376B LYS 2.8 2.0 + - - -
377B ARG* 1.3 96.8 - - + +
379B MET* 1.3 67.8 + - - +
380B ALA 3.3 1.2 + - - -
399B ALA 5.2 0.3 - - - +
402B TYR* 3.3 16.9 - - - -
403B ALA* 3.9 17.4 - - + +
406B LEU* 3.8 27.8 - - + -
407B VAL* 4.0 6.1 - - + -
410B GLU* 2.6 36.1 + - - -
426B LEU* 3.8 7.2 - - + +
427B PRO* 3.7 8.8 - - + +
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Residues in contact with MET 379 (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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372B ARG* 3.5 34.5 - - + +
373B VAL 3.2 32.3 - - - +
374B GLY 4.0 4.5 - - - +
375B THR 3.2 12.7 + - - +
376B LYS* 2.8 44.2 + - + +
377B ARG 4.8 1.0 - - - +
378B TYR* 1.3 78.6 - - - +
380B ALA* 1.3 65.1 + - - +
383B VAL* 3.6 20.0 - - + -
384B LEU* 3.7 34.6 - - + +
402B TYR* 3.3 10.9 + - - -
438B VAL* 5.0 2.0 - - - -
441B MET* 5.3 0.5 - - - +
445B VAL* 5.3 0.3 - - - +
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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