Contacts of the strand formed by residues 456 - 462 (chain A) in PDB entry 1M2O
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 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A CYS 3.7 0.9 - - - +
36A LEU* 3.4 4.1 - - - -
37A TYR* 2.7 34.9 + - - +
39A PRO* 3.7 28.7 - - + -
404A MET* 3.5 19.1 - - + -
417A LEU* 3.9 31.4 - - + -
418A ILE 3.9 3.6 - - - -
420A HIS* 3.7 30.2 + - - -
421A ALA* 4.5 0.2 - - + -
447A MET* 3.5 32.8 - - + +
450A LEU* 3.5 20.5 - - + +
454A HIS* 3.4 33.7 - + + +
455A SER* 1.3 78.4 - - - +
457A ALA* 1.3 60.9 + - - +
458A ILE* 3.9 4.6 + - + +
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Residues in contact with ALA 457 (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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35A CYS 3.2 5.4 - - - -
36A LEU* 4.0 6.9 - - + +
416A GLY 3.8 0.2 - - - +
417A LEU* 3.1 7.4 - - - +
418A ILE* 2.9 40.2 + - + +
456A TYR* 1.3 73.6 - - - +
458A ILE* 1.3 62.3 + - - +
459A PHE* 3.8 21.5 - - + -
531A LEU* 3.8 24.5 - - + -
534A ARG* 4.4 7.9 - - + +
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Residues in contact with ILE 458 (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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34A GLY* 3.2 2.4 - - - -
35A CYS* 2.8 36.0 + - - +
37A TYR* 4.5 10.3 - - + -
404A MET* 4.1 15.0 - - - -
406A VAL* 3.8 20.0 - - + -
414A VAL* 4.2 19.1 - - + -
416A GLY 3.4 9.0 - - - +
417A LEU* 4.5 13.5 - - + -
445A TRP* 4.5 3.4 - - + -
456A TYR 4.4 3.8 - - - +
457A ALA* 1.3 79.7 - - - +
459A PHE* 1.3 65.3 + - - +
460A PHE* 3.6 23.8 - - + -
489A PHE* 3.3 32.8 - - + -
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Residues in contact with PHE 459 (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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15A THR* 6.0 0.4 - - + -
32A PRO* 4.4 13.9 - - + -
33A VAL 3.7 7.2 - - - +
34A GLY* 4.6 0.7 - - - -
414A VAL* 3.6 2.8 - - - +
415A GLN* 2.6 36.1 + - + +
416A GLY 3.1 18.8 + - - +
418A ILE* 3.4 30.7 - - + -
437A ILE* 3.7 36.3 - - + -
457A ALA* 3.8 24.9 - - + -
458A ILE* 1.3 76.2 - - - +
460A PHE* 1.3 57.5 + - - +
531A LEU* 3.9 29.2 - - + -
534A ARG* 5.1 0.2 - - + -
535A ILE* 3.4 39.0 - - + -
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Residues in contact with PHE 460 (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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14A PHE* 3.9 16.4 - + - -
32A PRO* 5.2 0.9 - - - +
33A VAL* 2.9 35.8 + - + +
34A GLY* 3.7 13.9 - - - -
35A CYS* 3.9 21.5 - - - -
406A VAL* 3.9 13.0 - - + -
408A THR* 3.9 7.2 - - + -
412A LEU* 4.1 24.2 - - + -
413A LYS 3.2 13.9 - - - +
414A VAL* 4.3 5.8 - - + -
415A GLN* 3.0 14.8 - - - +
458A ILE* 3.6 30.3 - - + -
459A PHE* 1.3 74.8 - - - +
461A GLU* 1.3 62.3 + - - +
462A ILE 4.3 0.2 - - - -
487A THR* 3.7 33.0 - - + -
489A PHE* 4.3 3.1 - + - -
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Residues in contact with GLU 461 (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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23A ARG* 3.3 44.8 + - + +
33A VAL* 5.7 0.7 - - - -
412A LEU* 3.8 5.2 - - - -
413A LYS* 2.7 45.6 + - + +
415A GLN* 3.9 22.5 + - + +
433A SER* 2.8 23.0 + - - +
434A GLU* 3.2 13.2 - - - +
435A SER* 4.2 11.1 + - - -
460A PHE* 1.3 75.9 - - - +
462A ILE* 1.3 61.9 + - - +
463A ALA 2.9 6.8 + - - -
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Residues in contact with ILE 462 (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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19A PHE* 3.7 19.5 - - + -
20A PRO* 3.6 19.7 - - + +
21A SER* 3.8 4.3 - - - +
22A THR* 3.4 45.1 - - - +
23A ARG* 2.7 37.0 + - - +
26A ALA* 4.0 16.6 - - + +
33A VAL* 4.3 12.5 - - + +
411A ASP 4.2 4.5 - - - +
412A LEU* 3.6 22.4 - - + -
461A GLU* 1.3 68.2 - - - +
463A ALA* 1.3 59.4 + - - +
464A ASN* 4.3 6.5 - - + +
511A LEU* 4.2 8.5 - - + -
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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