Contacts of the strand formed by residues 412 - 416 (chain C) in PDB entry 1AX4
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 PHE 412 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ALA 6.1 0.4 - - - -
157C SER* 3.7 25.1 - - - -
195C SER 6.0 2.0 - - - -
196C ALA 6.4 1.3 - - - -
347C GLN* 4.5 17.7 - - + -
356C PHE* 4.0 37.9 - + + -
357C VAL 3.3 15.9 - - - -
358C ASP* 3.9 17.5 - - + -
373C ALA* 3.5 11.3 - - - +
390C GLU* 3.7 1.0 - - - -
391C ILE* 2.9 56.3 + - + +
410C MET* 3.8 32.3 - - + -
411C GLU* 1.3 76.5 - - - +
413C MET* 1.3 59.5 + - - +
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Residues in contact with MET 413 (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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355C VAL 3.6 1.0 - - - +
356C PHE* 3.4 4.6 - - - -
357C VAL* 2.9 48.6 + - + +
359C CYS* 3.8 12.5 - - - -
376C VAL* 3.9 15.7 - - + -
377C ILE* 3.5 34.3 - - + -
380C LEU* 4.0 20.0 - - + -
388C ALA* 3.9 11.9 - - + -
389C VAL 3.7 3.8 - - - -
411C GLU 4.0 0.2 + - - -
412C PHE* 1.3 74.3 - - - +
414C ARG* 1.3 62.2 + - - +
415C LEU* 3.8 10.0 + - + -
434C LEU* 3.6 42.0 - - + -
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Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU 3.9 1.0 - - - +
49C LEU 3.0 23.2 + - - -
50C THR* 4.2 9.9 + - - +
132C PHE* 5.3 5.5 - - - -
194C ASN* 4.6 19.4 + - - +
226C ARG* 5.9 1.6 - - - +
353C HIS* 4.8 2.6 + - - -
354C ALA* 3.8 10.8 - - + -
355C VAL 3.7 2.2 - - - +
356C PHE* 3.5 33.7 - - + +
388C ALA* 3.5 5.5 - - - +
389C VAL* 2.8 53.5 + - + +
391C ILE* 3.8 26.2 - - + +
412C PHE 4.0 1.0 - - - -
413C MET* 1.3 73.8 - - - +
415C LEU* 1.3 62.2 + - - +
416C THR* 2.8 35.2 + - - +
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Residues in contact with LEU 415 (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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48C LEU* 4.0 22.7 - - + -
335C LEU* 4.0 22.0 - - + -
339C LEU* 3.8 29.2 - - + -
354C ALA* 3.2 4.5 - - - -
355C VAL* 2.8 37.1 + - + +
357C VAL* 4.2 13.2 - - + -
380C LEU* 4.3 8.3 - - + -
388C ALA* 3.8 24.0 - - + -
413C MET* 4.1 16.8 - - + -
414C ARG* 1.3 71.8 - - - +
416C THR* 1.3 59.2 + - - +
417C ILE* 3.8 7.7 - - - +
430C ILE* 4.2 11.0 - - + -
434C LEU* 4.5 5.2 - - + -
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Residues in contact with THR 416 (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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47C ASP 4.4 0.3 - - - +
48C LEU* 2.7 44.2 + - - +
49C LEU 3.3 4.0 + - - -
50C THR* 3.5 15.4 - - - +
51C ASP* 3.5 19.5 - - - +
226C ARG* 5.7 0.2 - - - +
353C HIS* 3.7 28.9 - - + +
354C ALA* 4.0 0.4 - - + -
389C VAL* 4.1 0.2 - - - +
414C ARG* 2.8 40.1 + - - +
415C LEU* 1.3 72.8 - - - +
417C ILE* 1.3 60.9 - - - +
418C ALA 4.0 1.2 + - - -
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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