Contacts of the strand formed by residues 388 - 393 (chain A) in PDB entry 1IGR
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 TYR 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TYR* 3.8 1.2 - - - +
383A GLN* 3.3 9.3 - - - +
384A LEU* 3.0 36.8 + - + +
385A GLU 3.7 16.8 - - - -
386A GLY* 3.8 14.8 - - - -
387A ASN* 1.3 74.6 - - - +
389A SER* 1.3 62.4 - - - +
390A PHE 4.6 2.9 - - - +
391A TYR* 4.0 31.4 - + + -
415A LYS* 3.2 50.7 + - + +
416A MET 3.5 22.7 - - - -
417A TYR* 3.8 14.4 - + + +
443A SER* 5.0 0.5 - - - -
446A ASP* 2.7 21.6 + - - -
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Residues in contact with SER 389 (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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357A TYR* 3.1 11.2 - - - +
358A VAL* 2.8 27.7 + - - +
378A ILE* 4.3 13.1 - - - +
380A GLY* 3.5 10.9 - - - -
383A GLN* 3.9 2.7 + - - -
384A LEU* 5.4 0.4 - - - -
388A TYR* 1.3 73.6 - - - +
390A PHE* 1.3 57.0 + - - +
391A TYR 4.3 0.2 - - - -
411A ILE* 3.4 26.7 - - - -
413A ALA 2.4 25.3 + - - -
414A GLY* 3.3 6.4 - - - -
415A LYS 2.7 13.0 + - - +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 3.4 32.8 - - + -
360A ILE* 4.5 2.5 - - + -
369A LEU* 3.7 18.2 - - + -
378A ILE* 4.1 11.2 - - + -
388A TYR* 4.7 0.6 - - - +
389A SER* 1.3 79.3 - - - +
391A TYR* 1.3 59.6 + - - +
392A VAL* 3.3 25.1 - - + -
401A LEU* 4.7 0.9 - - + -
402A TRP* 3.6 36.1 - + - -
411A ILE* 3.9 18.6 - - + -
415A LYS 3.4 2.7 + - - +
416A MET* 3.1 17.2 - - + +
417A TYR 3.0 24.4 + - - +
418A PHE* 3.6 19.7 - + - -
432A MET* 3.7 18.4 - - + -
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Residues in contact with TYR 391 (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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358A VAL 3.0 7.7 + - - +
359A LYS* 3.2 32.8 - - + -
360A ILE* 2.6 34.9 + - - +
361A ARG* 5.9 0.7 - - + -
384A LEU* 3.5 31.4 - - + -
385A GLU 5.6 0.9 - - - -
388A TYR* 4.0 21.8 - + + -
390A PHE* 1.3 74.2 - - - +
392A VAL* 1.3 58.5 + - - +
393A LEU* 4.1 25.2 - - + +
417A TYR* 3.3 51.8 - + + -
500A SO4 5.0 2.2 - - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 3.1 14.1 - - + +
390A PHE* 3.3 30.1 - - + -
391A TYR* 1.3 79.6 - - - +
393A LEU* 1.3 59.0 + - - +
395A ASN* 3.2 20.9 - - - +
398A LEU* 3.9 19.5 - - + -
401A LEU* 5.2 1.1 - - + -
417A TYR* 3.0 10.0 + - - +
418A PHE* 3.2 35.7 - - + -
419A ALA 3.1 22.3 + - - -
421A ASN* 3.5 10.9 + - - +
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Residues in contact with LEU 393 (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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360A ILE 2.9 9.7 + - - +
361A ARG* 3.2 22.2 - - + +
362A HIS* 3.1 16.0 + - - +
391A TYR* 4.1 23.9 - - + +
392A VAL* 1.3 75.1 - - - +
394A ASP* 1.4 81.8 + - + +
395A ASN* 3.5 4.3 + - - +
417A TYR* 4.5 10.1 - - + +
419A ALA* 3.0 27.4 - - + +
420A PHE* 3.5 26.2 - - + -
500A SO4 4.4 16.2 - - - +
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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