Contacts of the helix formed by residues 482 - 495 (chain A) in PDB entry 1M7X
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 ASN 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A LYS 3.5 1.2 + - - -
481A TRP* 1.3 69.1 - - - +
483A LEU* 1.3 63.7 + - - +
484A GLY 3.6 2.3 + - - -
485A TRP* 2.9 47.7 + - + +
486A MET 3.3 8.5 + - - -
510A GLY* 5.3 4.2 + - - -
513A TYR* 3.2 17.6 + - - -
514A ASN* 5.2 2.8 - - - +
519A PHE* 3.4 43.8 - - + +
520A VAL 2.8 19.6 + - - +
521A LEU* 3.7 15.6 - - + +
522A PRO* 3.4 12.4 - - + +
560A PHE* 5.7 1.2 - - - -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 3.7 31.6 - - + +
459A GLU 4.5 5.4 - - - +
460A SER* 4.4 17.3 - - - +
481A TRP* 3.0 38.5 + - + +
482A ASN* 1.3 72.3 - - - +
484A GLY* 1.3 57.1 + - - +
486A MET* 3.2 25.1 + - + +
487A HIS* 2.8 47.8 + - + +
522A PRO* 4.6 6.1 - - + -
524A SER* 5.9 0.9 - - - +
527A GLU* 4.8 4.7 - - - +
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Residues in contact with GLY 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASN* 3.2 2.4 + - - -
483A LEU* 1.3 80.2 - - - +
485A TRP* 1.3 56.1 + - - +
487A HIS* 3.2 9.3 + - - +
488A ASP* 2.9 35.2 + - - +
513A TYR* 3.6 13.0 - - - -
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Residues in contact with TRP 485 (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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482A ASN* 2.9 33.6 + - - +
484A GLY* 1.3 75.2 - - - +
486A MET* 1.3 79.2 + - + +
488A ASP* 3.2 5.5 + - + -
489A THR* 2.8 66.3 + - + +
506A LYS 5.9 0.4 - - - -
507A LEU 6.0 0.2 - - - -
510A GLY* 4.9 7.6 - - - -
513A TYR* 3.3 7.0 + - - +
521A LEU* 3.7 39.9 - - + -
522A PRO 4.3 11.4 - - - -
523A LEU* 4.4 0.9 - - + -
553A TYR* 3.3 29.2 - + - -
556A TRP* 4.3 5.8 - + - +
557A MET* 3.7 40.2 - - + -
560A PHE* 3.4 39.0 - + - -
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Residues in contact with MET 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASN 3.3 7.5 + - - +
483A LEU* 3.2 22.4 + - + +
485A TRP* 1.3 90.8 - - + +
487A HIS* 1.3 87.2 + - + +
489A THR* 3.6 2.6 + - - -
490A LEU* 3.0 57.4 + - + +
522A PRO* 3.4 27.4 - - + +
523A LEU* 4.1 4.7 - - + -
527A GLU* 3.1 43.7 - - + +
553A TYR* 4.7 0.2 - - - -
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Residues in contact with HIS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 2.8 40.4 + - + +
484A GLY* 3.6 9.1 + - - +
486A MET* 1.3 101.3 - - + +
488A ASP* 1.3 61.4 + - - +
490A LEU* 4.4 1.7 - - - +
491A ASP* 2.9 42.1 + - - +
527A GLU* 4.6 4.9 + - - -
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Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLY* 2.9 22.8 + - - +
485A TRP* 3.7 5.4 - - - +
487A HIS* 1.3 80.1 - - - +
489A THR* 1.3 58.9 + - + +
491A ASP* 3.3 8.2 + - - +
492A TYR* 3.0 21.7 + - - +
506A LYS* 3.2 48.8 + - - +
509A PHE* 3.9 25.0 - - - +
510A GLY 5.1 2.2 + - - +
513A TYR* 4.2 4.9 + - - -
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Residues in contact with THR 489 (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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485A TRP* 2.8 63.1 + - + +
486A MET 3.6 2.8 + - - -
488A ASP* 1.3 70.6 - - + +
490A LEU* 1.3 61.9 + - - +
492A TYR* 3.3 2.1 + - - +
493A MET* 2.9 33.1 + - - +
506A LYS 4.3 4.9 - - - +
507A LEU* 4.1 24.2 - - + +
553A TYR* 2.7 35.1 + - - -
556A TRP* 4.3 8.3 - - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A MET* 3.0 47.6 + - + +
487A HIS* 4.4 2.2 - - - +
489A THR* 1.3 73.8 + - - +
491A ASP* 1.3 66.1 + - - +
493A MET* 3.4 3.2 + - + +
494A LYS* 2.9 34.2 + - - +
523A LEU* 4.1 9.0 - - + -
527A GLU* 5.0 2.5 - - + -
535A ILE* 4.5 14.6 - - + -
538A ARG* 4.2 37.9 - - + +
539A MET* 5.1 5.3 - - + +
553A TYR* 3.2 39.7 - - + +
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Residues in contact with ASP 491 (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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487A HIS* 2.9 31.7 + - - +
488A ASP* 3.5 6.7 - - - +
490A LEU* 1.3 79.0 - - - +
492A TYR* 1.3 60.3 - - - +
494A LYS* 3.5 24.5 + - - +
495A LEU* 3.5 23.0 + - - +
506A LYS* 3.9 27.5 + - + +
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Residues in contact with TYR 492 (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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488A ASP 3.0 16.0 + - - +
489A THR 3.5 4.9 - - - +
490A LEU 3.1 0.2 - - - -
491A ASP* 1.3 74.5 - - - +
493A MET* 1.3 76.5 + - - +
494A LYS 3.2 1.8 - - - -
495A LEU* 3.1 31.8 + - + +
500A ARG* 3.2 57.2 + - + +
503A HIS 3.4 23.3 - - - -
504A HIS* 4.3 6.9 - - - -
506A LYS* 3.9 4.5 - - + +
507A LEU* 3.4 43.0 - - + +
637A SER* 3.7 11.4 + - - -
639A LEU* 4.5 2.8 - - - +
657A PHE* 3.5 33.7 - + - +
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Residues in contact with MET 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A THR 2.9 20.3 + - - +
490A LEU* 3.4 4.5 + - - +
492A TYR* 1.3 88.3 - - - +
494A LYS* 1.3 59.1 + - - +
500A ARG* 2.8 22.9 + - - +
507A LEU* 5.8 1.1 - - + -
538A ARG 4.6 1.3 - - - -
539A MET* 3.7 20.8 - - + +
540A PRO* 3.1 13.4 - - - +
549A ASN* 3.2 55.2 - - + +
553A TYR* 3.7 31.6 - - + -
657A PHE* 3.8 29.8 - - + -
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Residues in contact with LYS 494 (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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490A LEU* 2.9 25.6 + - - +
491A ASP* 3.5 29.3 + - - +
492A TYR 3.2 0.2 - - - -
493A MET* 1.3 73.0 - - - +
495A LEU* 1.3 71.3 + - - +
496A ASP 3.6 0.3 + - - -
538A ARG* 3.4 50.5 - - + +
540A PRO* 3.8 12.6 - - - +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ASP 3.5 13.7 + - - +
492A TYR* 3.1 21.8 + - + +
494A LYS* 1.3 88.0 - - - +
496A ASP* 1.3 67.1 + - - +
497A PRO 3.3 2.9 - - - -
499A TYR* 4.5 9.2 - - + -
500A ARG* 3.4 32.9 + - + -
503A HIS* 3.2 52.9 - - + +
506A LYS* 4.9 2.7 - - + -
540A PRO* 3.4 11.6 - - - +
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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