Contacts of the helix formed by residues 543 - 561 (chain A) in PDB entry 4FM9
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 ASP 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A GLU* 3.8 2.6 - - - +
541A ASP* 2.4 40.1 + - + +
542A GLN* 1.3 74.9 - - - +
544A GLN* 1.3 64.2 + - - +
545A ASP* 4.3 7.0 - - - +
546A GLY* 2.6 35.8 + - - -
547A SER* 3.2 6.0 + - - -
550A LYS* 5.7 0.5 + - - -
614A LYS* 3.9 8.0 - - - +
1201A MG 2.0 35.0 - - - -
1202A GOL 4.7 5.4 + - - -
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Residues in contact with GLN 544 (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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543A ASP* 1.3 74.7 - - - +
545A ASP* 1.3 71.4 + - - +
547A SER* 2.8 24.9 + - - -
548A HIS 2.8 9.7 + - - -
592A LEU* 6.0 3.6 - - - +
705A LEU* 4.9 8.1 - - + -
706A PHE* 3.6 33.5 - - + +
709A SER* 4.3 22.6 + - - +
759A HIS* 5.7 5.4 - - - -
1202A GOL 4.3 14.9 + - - +
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Residues in contact with ASP 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LYS* 3.2 27.9 + - - -
543A ASP* 3.2 8.2 - - - +
544A GLN* 1.3 82.1 - - - +
546A GLY* 1.3 49.9 + - - +
548A HIS* 2.8 7.0 + - - +
549A ILE* 2.7 37.5 + - - +
706A PHE* 3.9 10.2 - - - -
713A ARG* 3.2 31.9 + - - -
759A HIS* 4.7 6.4 - - - -
12C T 3.9 3.8 - - - +
13C G 3.4 38.2 + - - +
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Residues in contact with GLY 546 (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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461A GLU* 4.1 3.7 + - - -
540A THR* 3.0 30.9 + - - -
543A ASP* 2.6 28.6 + - - -
545A ASP* 1.3 70.7 - - - +
547A SER* 1.3 61.1 + - - -
549A ILE* 2.9 6.5 + - - +
550A LYS* 2.9 28.3 + - - +
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Residues in contact with SER 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ASP 3.2 2.7 + - - -
544A GLN* 2.8 23.1 + - - +
546A GLY* 1.3 70.6 - - - +
548A HIS* 1.3 56.2 + - - +
550A LYS* 4.0 7.6 - - - +
551A GLY* 2.9 26.2 + - - -
698A PHE* 3.3 11.6 - - - -
702A GLU* 2.6 56.3 + - - +
703A LEU* 4.2 6.4 - - - +
706A PHE* 4.7 2.0 - - - -
1202A GOL 3.3 9.7 + - - -
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Residues in contact with HIS 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LYS* 3.3 23.7 + - - +
544A GLN 2.8 4.4 + - - -
545A ASP* 2.8 17.4 + - - +
547A SER* 1.3 76.8 - - - +
549A ILE* 1.3 54.7 + - - +
551A GLY* 3.2 1.2 + - - -
552A LEU* 2.9 44.3 + - + +
653A PHE* 4.0 15.7 - + - -
703A LEU* 4.1 9.1 - - + +
706A PHE* 3.2 47.8 - + + -
7D T 3.1 41.8 + - - -
8D C 3.2 11.5 + - - -
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Residues in contact with ILE 549 (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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461A GLU* 3.2 41.7 - - + +
486A LEU* 3.8 27.8 - - + -
488A GLY* 3.4 28.5 - - - +
489A LYS* 4.3 13.0 - - + -
490A ILE* 3.9 4.1 - - + +
538A ILE* 3.9 8.1 - - + -
540A THR* 4.2 5.6 - - + -
545A ASP 2.7 19.8 + - - +
546A GLY* 2.9 8.3 + - - +
548A HIS* 1.3 68.2 - - - +
550A LYS* 1.3 66.9 + - - +
552A LEU* 3.3 9.2 + - - +
553A LEU* 3.0 22.0 + - - +
13C G 3.8 8.3 - - - +
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Residues in contact with LYS 550 (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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538A ILE* 3.3 34.1 - - + -
540A THR* 3.4 29.7 + - + +
541A ASP 5.2 1.2 + - - -
542A GLN* 3.8 20.2 + - - -
543A ASP 5.7 0.4 + - - -
546A GLY 2.9 14.7 + - - +
547A SER* 3.5 7.9 - - - +
549A ILE* 1.3 72.2 - - - +
551A GLY* 1.3 67.9 + - - +
553A LEU* 3.1 4.3 + - - +
554A ILE* 2.9 31.9 + - + +
572A GLU* 2.5 39.3 + - + +
573A PHE 5.7 0.7 - - - -
574A ILE* 4.5 0.6 - - - +
638A PHE* 5.1 2.0 - - + -
686A TYR* 4.3 1.0 + - - -
698A PHE* 3.7 21.3 - - + -
702A GLU* 3.1 16.2 + - - -
1202A GOL 4.5 1.4 + - - -
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Residues in contact with GLY 551 (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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547A SER 2.9 14.5 + - - -
548A HIS* 3.2 4.7 + - - -
550A LYS* 1.3 75.5 - - - +
552A LEU* 1.3 50.6 + - - +
554A ILE* 3.0 7.4 + - - +
555A ASN* 2.7 34.7 + - - +
653A PHE* 3.4 23.0 - - - -
698A PHE* 3.7 17.2 - - - -
699A ILE* 5.5 0.4 - - - -
703A LEU* 5.0 0.7 - - - -
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Residues in contact with LEU 552 (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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489A LYS* 4.0 9.0 - - + -
490A ILE* 3.3 45.3 - - + +
491A LEU 4.6 5.2 - - - +
492A ASN* 4.6 7.6 - - + -
548A HIS* 2.9 35.5 + - + +
549A ILE* 3.7 6.3 - - - +
550A LYS 3.3 0.4 - - - -
551A GLY* 1.3 74.3 - - - +
553A LEU* 1.3 57.8 + - - +
555A ASN* 3.3 7.1 + - - +
556A PHE* 2.8 29.3 + - - +
653A PHE* 3.4 26.9 - - + -
7D T 3.7 34.1 - - - +
8D C 4.4 0.9 - - - +
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Residues in contact with LEU 553 (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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459A LEU* 4.0 27.4 - - + -
486A LEU* 5.4 0.2 - - + -
490A ILE* 3.8 20.7 - - + +
510A ILE* 5.2 7.4 - - + -
536A ILE* 4.6 10.3 - - + +
538A ILE* 3.8 33.2 - - + -
549A ILE 3.0 13.8 + - - +
550A LYS 3.3 9.2 - - - +
552A LEU* 1.3 73.3 - - - +
554A ILE* 1.3 69.3 + - + +
556A PHE* 2.9 23.6 + - + +
557A ILE* 2.9 32.1 + - + +
570A LEU* 5.1 9.0 - - + -
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Residues in contact with ILE 554 (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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550A LYS* 2.9 22.7 + - + +
551A GLY* 3.4 6.7 - - - +
553A LEU* 1.3 75.3 - - + +
555A ASN* 1.3 52.7 + - - +
557A ILE* 3.2 5.2 + - - +
558A HIS* 2.8 37.0 + - - +
565A LEU* 4.3 2.5 - - + +
570A LEU* 4.5 12.1 - - + -
638A PHE* 4.2 28.5 - - + -
649A ILE* 3.7 21.1 - - + -
653A PHE* 6.4 0.2 - - + -
695A TYR* 3.6 41.5 - - + -
698A PHE* 4.3 23.3 - - + -
699A ILE* 5.7 4.3 - - + -
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Residues in contact with ASN 555 (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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491A LEU 4.7 0.2 + - - -
492A ASN* 3.3 40.2 + - - +
493A VAL 3.9 4.8 - - - +
494A ARG* 2.7 45.9 + - - +
551A GLY 2.7 16.1 + - - +
552A LEU* 3.4 11.2 + - - +
554A ILE* 1.3 72.1 - - - +
556A PHE* 1.3 66.0 + - - +
559A HIS* 2.8 24.3 + - - +
649A ILE* 4.2 4.3 - - - -
653A PHE* 3.5 29.7 - - + +
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Residues in contact with PHE 556 (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 ILE* 5.1 6.7 - - + -
491A LEU 5.2 0.4 - - - +
493A VAL* 3.6 26.2 - - + -
507A ILE* 3.2 40.2 - - + -
510A ILE* 4.6 18.6 - - + -
511A ILE* 4.0 11.2 - - + -
516A LEU* 4.8 1.3 - - + -
552A LEU 2.8 17.2 + - - +
553A LEU* 2.9 21.3 + - + +
555A ASN* 1.3 75.2 - - - +
557A ILE* 1.3 101.6 + - + +
559A HIS* 3.3 1.2 + - - +
560A ASN* 2.9 50.3 + - - +
561A TRP* 3.6 20.4 - + - -
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Residues in contact with ILE 557 (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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510A ILE* 5.8 1.8 - - + -
516A LEU* 4.6 6.3 - - + -
553A LEU* 2.9 23.5 + - + +
554A ILE 3.8 5.6 - - - +
556A PHE* 1.3 102.8 - - + +
558A HIS* 1.3 53.9 + - - +
561A TRP* 2.6 45.6 + - + +
564A LEU* 4.1 23.6 - - + -
565A LEU* 3.7 17.7 - - + -
569A PHE* 4.2 16.6 - - + -
570A LEU* 3.6 30.1 - - + -
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Residues in contact with HIS 558 (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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494A ARG* 2.8 34.9 + - - +
554A ILE 2.8 18.6 + - - +
555A ASN 3.6 3.4 - - - +
557A ILE* 1.3 76.9 - - - +
559A HIS* 1.3 68.5 + - - +
560A ASN 3.1 0.7 + - - -
561A TRP 3.2 5.7 + - - -
562A PRO* 3.2 25.8 - - + +
565A LEU* 3.5 35.0 - - + +
646A ASP* 3.0 52.2 + - + +
649A ILE* 3.6 16.2 - - + +
650A SER* 5.3 0.7 - - - -
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Residues in contact with HIS 559 (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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493A VAL* 3.4 34.8 + - + -
494A ARG* 3.1 56.8 + - + +
555A ASN* 2.8 21.7 + - - +
558A HIS* 1.3 75.6 - - - +
560A ASN* 1.3 71.4 + - - +
562A PRO* 4.4 4.9 - - - +
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Residues in contact with ASN 560 (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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493A VAL* 4.2 9.3 - - - +
501A ILE* 5.7 0.7 - - - +
518A TYR* 3.5 38.3 - - + +
556A PHE* 2.9 46.2 + - - +
559A HIS* 1.3 92.5 - - - +
561A TRP* 1.3 97.0 + - + +
562A PRO* 4.0 2.7 - - - +
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Residues in contact with TRP 561 (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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511A ILE* 4.0 14.8 - - + -
516A LEU* 3.6 37.9 - - + -
517A GLN 3.1 17.6 + - - -
518A TYR* 3.6 28.5 + + - -
520A LYS 3.4 17.9 + - - -
521A ASN* 4.9 2.5 - - - -
522A TYR* 3.6 18.3 - + - -
556A PHE* 3.6 22.4 - + - -
557A ILE* 2.6 28.4 + - + +
558A HIS 3.2 0.4 + - - -
560A ASN* 1.3 111.8 + - + +
562A PRO* 1.3 73.0 - - - +
563A SER* 3.0 7.7 + - - +
564A LEU* 3.1 40.3 + - + +
565A LEU* 3.4 5.9 - - - +
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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
------------------------------------------------------------
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