Contacts of the helix formed by residues 544 - 564 (chain A) in PDB entry 6DMY
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 THR 544 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 3.7 27.6 - - + -
518A LEU* 3.3 16.4 - - - +
520A HIS* 6.0 1.3 - - - +
521A ALA* 3.7 21.7 - - + +
540A CYS 3.1 18.2 + - - -
541A LEU 3.3 0.4 + - - -
543A ARG* 1.3 87.5 - - + +
545A GLY* 1.3 64.9 + - - +
546A ALA 3.4 2.2 - - - -
547A SER* 3.3 12.6 + - - -
548A VAL* 3.1 22.6 + - - +
1122A MET* 5.5 9.9 - - + -
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Residues in contact with GLY 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.5 13.9 - - - -
518A LEU* 5.7 2.0 - - - -
541A LEU* 2.9 18.6 + - - -
542A LYS 4.1 3.6 + - - -
544A THR* 1.3 77.7 - - - +
546A ALA* 1.3 57.5 + - - +
548A VAL* 3.2 8.6 + - - +
549A ALA* 2.9 28.6 + - - +
589A LEU* 4.3 13.4 - - - +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 5.2 20.9 - - + -
87A LEU* 5.8 0.4 - - - +
542A LYS 5.5 0.8 + - - -
544A THR 3.4 0.6 - - - -
545A GLY* 1.3 72.8 - - - +
547A SER* 1.3 58.9 - - - +
549A ALA* 3.9 6.0 - - - +
550A LEU* 2.9 31.1 + - - +
1046A PHE* 4.5 24.2 - - + +
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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
----------------------------------------------------------
517A LEU* 4.7 4.2 - - - +
544A THR* 3.3 15.6 + - - -
546A ALA* 1.3 78.8 - - - +
548A VAL* 1.3 64.4 + - - +
550A LEU* 3.0 10.5 + - - +
551A THR* 3.0 28.3 + - - +
1098A VAL* 4.3 7.5 - - - +
1099A HIS* 3.1 33.6 + - - -
1102A LEU* 5.3 15.8 - - - +
1122A MET* 6.4 1.6 - - - -
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Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 4.1 28.2 - - + +
517A LEU* 3.7 23.8 - - + -
518A LEU* 4.1 24.5 - - + -
544A THR 3.1 14.5 + - - +
545A GLY* 3.2 7.6 + - - +
547A SER* 1.3 75.3 - - - +
549A ALA* 1.3 60.9 + - - +
551A THR* 3.2 16.6 + - - -
552A SER* 3.6 11.8 + - - -
585A PHE* 3.8 9.4 - - + -
588A VAL* 5.2 3.6 - - + -
589A LEU* 4.1 23.3 - - + -
1099A HIS* 6.1 0.4 - - + -
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLY 2.9 16.1 + - - +
546A ALA* 4.1 5.8 - - - +
548A VAL* 1.3 77.2 - - - +
550A LEU* 1.3 59.0 + - - +
552A SER* 3.3 1.6 + - - -
553A ILE* 3.0 35.9 + - + +
585A PHE* 3.6 27.1 - - + -
589A LEU* 5.3 0.9 - - + -
1046A PHE* 4.2 15.5 - - + -
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Residues in contact with LEU 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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546A ALA 2.9 19.8 + - - +
547A SER* 3.0 7.6 + - - +
549A ALA* 1.3 74.1 - - - +
551A THR* 1.3 65.9 + - - +
553A ILE* 4.0 1.0 - - - +
554A SER* 3.0 26.0 + - - -
1042A VAL* 3.7 17.7 - - + +
1043A CYS* 3.7 19.7 - - - -
1046A PHE* 3.6 40.1 - - + +
1047A LEU* 4.1 22.7 - - + -
1098A VAL* 3.7 32.5 - - + -
1102A LEU* 6.4 0.7 - - + -
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Residues in contact with THR 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 3.4 21.6 + - - +
547A SER 3.0 12.6 + - - +
548A VAL* 3.2 12.0 + - - -
550A LEU* 1.3 76.6 - - - +
552A SER* 1.3 60.6 + - - +
554A SER* 2.5 23.2 + - - -
555A ASN* 3.0 23.6 + - - -
1095A GLU* 3.9 32.3 - - + +
1098A VAL* 4.3 13.5 - - + -
1099A HIS* 3.9 18.2 - - + +
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Residues in contact with SER 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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514A ASP* 5.1 5.6 - - - -
548A VAL 3.6 14.6 + - - -
549A ALA 3.3 4.3 + - - -
550A LEU 3.3 0.6 - - - -
551A THR* 1.3 79.1 + - - +
553A ILE* 1.3 63.4 + - - +
555A ASN* 3.0 12.5 + - - +
556A VAL* 2.9 32.5 + - - +
581A VAL* 4.0 12.8 + - - +
582A VAL* 5.0 0.3 - - - -
585A PHE* 3.3 38.1 - - - +
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Residues in contact with ILE 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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549A ALA* 3.0 24.1 + - + +
550A LEU 4.1 1.1 - - - +
552A SER* 1.3 77.3 - - - +
554A SER* 1.3 63.1 + - - +
556A VAL* 3.1 13.7 + - + +
557A THR* 3.1 31.1 + - + +
585A PHE* 6.1 6.7 - - + -
1042A VAL* 3.8 28.5 - - + -
1046A PHE* 3.7 24.9 - - + -
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Residues in contact with SER 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LEU* 3.0 14.2 + - - -
551A THR* 2.5 29.6 + - - -
553A ILE* 1.3 77.1 - - - +
555A ASN* 1.3 61.3 + - - +
557A THR* 3.5 14.5 + - - -
558A ALA* 3.8 2.9 + - - +
1035A VAL* 6.1 0.2 - - - +
1039A THR* 4.5 8.9 - - - +
1042A VAL* 4.6 8.9 - - - +
1043A CYS* 5.7 0.2 - - - -
1091A GLY* 3.8 17.9 + - - -
1094A VAL* 3.7 38.1 - - - +
1095A GLU* 5.4 0.7 + - - +
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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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510A VAL* 4.3 16.2 - - - +
551A THR* 3.0 27.3 + - - +
552A SER* 3.0 11.3 + - - +
554A SER* 1.3 77.9 - - - +
556A VAL* 1.3 63.9 + - - +
558A ALA* 3.2 8.1 + - - +
559A PHE* 3.0 31.6 + - + -
581A VAL* 3.9 19.4 - - + +
1091A GLY* 2.9 28.2 - - - +
1092A ILE* 3.5 15.5 - - - +
1095A GLU* 6.1 2.3 - - - +
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Residues in contact with VAL 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A SER* 2.9 24.5 + - - +
553A ILE* 3.1 16.3 + - + +
555A ASN* 1.3 76.2 - - - +
557A THR* 1.3 64.3 + - + +
559A PHE* 3.2 7.4 + - - +
560A PHE* 3.0 49.3 + - + +
578A ALA* 4.8 4.0 - - + +
581A VAL* 3.7 16.4 - - + -
582A VAL* 3.6 32.5 - - + -
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Residues in contact with THR 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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553A ILE* 3.1 23.1 + - + +
554A SER* 3.5 14.6 + - - -
556A VAL* 1.3 79.0 - - + +
558A ALA* 1.3 58.7 + - - +
560A PHE* 3.5 5.5 + - - +
561A MET* 3.0 38.4 + - - +
1035A VAL* 5.2 2.5 - - - +
1038A CYS* 3.7 31.5 - - + -
1039A THR* 5.3 3.5 + - - -
1042A VAL* 4.7 9.8 - - + +
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Residues in contact with ALA 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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554A SER 3.9 2.9 - - - +
555A ASN* 3.2 10.4 + - - +
557A THR* 1.3 82.7 + - - +
559A PHE* 1.3 60.5 + - + +
562A ALA* 2.9 29.6 + - - +
1035A VAL* 4.7 10.3 - - + -
1087A ILE* 3.3 34.5 - - + +
1088A ALA* 4.5 3.8 - - - -
1091A GLY* 3.7 21.8 - - - +
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Residues in contact with PHE 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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506A LEU* 4.4 17.9 - - + -
510A VAL* 5.9 2.2 - - + -
555A ASN* 3.0 25.7 + - + +
556A VAL* 3.2 2.6 + - - +
558A ALA* 1.3 81.1 - - + +
560A PHE* 1.3 62.0 + - - +
562A ALA* 3.7 7.6 - - + +
563A ALA* 2.9 28.1 + - - +
573A PHE* 6.4 2.0 - + - -
574A SER* 3.8 16.0 - - - +
577A ALA* 3.6 36.1 - - + -
578A ALA* 3.6 20.2 - - + -
581A VAL* 3.6 27.6 - - + -
1084A VAL* 6.3 1.1 - - + -
1088A ALA* 3.6 32.3 - - + -
1092A ILE* 5.4 9.6 - - + -
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Residues in contact with PHE 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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556A VAL* 3.0 36.0 + - + +
557A THR* 4.0 5.6 - - - +
559A PHE* 1.3 77.1 - - - +
561A MET* 1.3 62.7 + - + +
563A ALA* 2.8 20.9 + - - +
564A LEU* 3.1 21.4 + - + +
575A LEU* 4.2 20.6 - - + -
578A ALA* 3.6 27.1 - - + -
579A VAL* 6.3 0.9 - - + -
582A VAL* 5.7 3.6 - - + -
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Residues in contact with MET 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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557A THR* 3.0 24.3 + - - +
558A ALA 4.5 0.2 - - - +
560A PHE* 1.3 78.6 - - + +
562A ALA* 1.3 60.3 + - - +
564A LEU* 3.6 29.1 + - + +
565A ILE* 4.9 1.2 + - - +
1031A PHE* 4.0 29.0 - - + +
1034A VAL* 4.4 26.2 - - + -
1035A VAL* 3.6 26.2 - - + -
1038A CYS* 5.2 13.0 - - + -
1087A ILE* 4.4 2.2 - - - -
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Residues in contact with ALA 562 (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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558A ALA 2.9 21.4 + - - +
559A PHE* 3.7 10.3 - - + +
560A PHE 3.2 0.2 - - - -
561A MET* 1.3 79.2 - - - +
563A ALA* 1.3 60.2 + - - +
564A LEU 3.3 1.0 + - - -
565A ILE* 3.4 26.9 + - - +
570A LEU 5.2 0.5 - - - +
574A SER* 4.1 6.8 + - - -
1084A VAL* 4.4 24.8 - - + +
1087A ILE* 3.9 24.4 - - + +
1088A ALA 5.1 0.4 - - - +
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Residues in contact with ALA 563 (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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559A PHE 2.9 15.0 + - - +
560A PHE* 2.8 9.2 + - - +
562A ALA* 1.3 72.7 - - - +
564A LEU* 1.3 64.4 + - + +
565A ILE* 3.2 4.9 + - - +
571A ARG* 3.4 28.7 + - - +
574A SER* 3.3 20.9 - - - +
575A LEU* 3.8 31.2 - - + -
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Residues in contact with LEU 564 (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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560A PHE* 3.1 29.2 + - + +
561A MET* 3.7 24.0 - - - +
562A ALA 3.2 1.4 - - - -
563A ALA* 1.3 78.1 - - - +
565A ILE* 1.3 62.5 + - - +
566A PRO* 4.4 1.6 - - - +
571A ARG* 3.4 10.7 + - - +
1031A PHE* 3.9 25.3 - - + -
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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