Contacts of the strand formed by residues 412 - 416 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A SER* 3.7 23.8 - - - -
195A SER 5.9 2.9 - - - -
196A ALA 5.9 3.6 - - - -
197A GLY* 6.2 0.4 - - - -
346A ILE 5.5 0.4 - - - -
347A GLN* 4.3 22.7 - - + -
356A PHE* 3.8 36.6 - + + -
357A VAL 3.1 21.1 - - - -
358A ASP* 4.2 11.0 - - + -
373A ALA* 3.9 3.5 - - - +
390A GLU* 3.7 2.3 - - - -
391A ILE* 2.7 55.9 + - + +
410A MET* 4.1 34.3 - - + -
411A GLU* 1.3 75.6 - - - +
413A MET* 1.3 57.9 + - - +
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Residues in contact with MET 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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355A VAL 3.6 1.6 - - - +
356A PHE* 3.3 4.0 - - - -
357A VAL* 2.9 52.5 + - + +
359A CYS* 3.7 14.4 - - - -
373A ALA* 4.7 0.4 - - + -
376A VAL* 4.3 8.1 - - + -
377A ILE* 3.7 39.3 - - + -
380A LEU* 3.7 22.2 - - + -
388A ALA* 4.0 11.7 - - + -
389A VAL 3.8 3.1 - - - -
411A GLU 4.0 0.8 + - - -
412A PHE* 1.3 71.7 - - - +
414A ARG* 1.3 59.3 + - - +
415A LEU* 3.9 10.9 + - + -
434A LEU* 3.6 37.9 - - + -
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Residues in contact with ARG 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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48A LEU 3.9 0.5 - - - +
49A LEU 2.8 27.7 + - - -
50A THR* 4.0 10.9 + - - +
132A PHE* 5.5 4.4 - - - -
194A ASN* 4.9 14.1 + - - +
353A HIS* 4.7 4.7 - - - -
354A ALA* 4.0 7.0 - - + -
355A VAL 3.6 1.8 - - - -
356A PHE* 3.3 46.8 - - + -
388A ALA* 3.4 18.4 - - - +
389A VAL* 2.9 39.4 + - + +
391A ILE* 4.1 21.0 - - + +
412A PHE 4.0 1.2 - - - -
413A MET* 1.3 71.9 - - - +
415A LEU* 1.3 63.8 + - - +
416A THR* 2.9 29.5 + - - +
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Residues in contact with LEU 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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48A LEU* 3.9 27.4 - - + -
335A LEU* 4.1 21.5 - - + -
339A LEU* 3.8 28.5 - - + -
354A ALA* 3.2 4.0 - - - -
355A VAL* 2.7 41.5 + - + +
357A VAL* 4.1 12.1 - - + -
380A LEU* 4.2 9.4 - - + -
388A ALA* 3.9 18.6 - - + -
413A MET* 4.2 20.0 - - + -
414A ARG* 1.3 70.5 - - - +
416A THR* 1.3 62.6 + - - +
417A ILE* 3.9 7.5 + - - +
430A ILE* 4.4 10.1 - - + -
434A LEU* 4.7 4.7 - - + -
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Residues in contact with THR 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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47A ASP 4.3 0.9 - - - +
48A LEU* 2.6 50.3 + - - +
49A LEU 3.1 5.4 + - - -
50A THR* 3.5 12.3 - - - +
51A ASP* 3.4 22.2 - - - +
353A HIS* 3.7 28.3 - - + -
354A ALA* 3.9 2.2 - - + -
414A ARG* 2.9 35.6 + - - +
415A LEU* 1.3 71.6 - - - +
417A ILE* 1.3 62.9 - - - +
418A ALA 3.9 1.7 + - - -
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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