Contacts of the helix formed by residues 545 - 560 (chain A) in PDB entry 3CMM
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 545 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A LYS* 5.7 5.8 - - - +
543A LEU* 4.5 2.6 - - - +
544A ASP* 1.3 88.7 + - - +
546A VAL* 1.3 60.7 - - + +
547A ASP* 3.5 32.1 - - - +
548A ALA* 3.2 23.4 - - - +
549A ARG* 3.3 29.0 + - - +
74B ARG* 4.9 7.0 - - - +
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Residues in contact with VAL 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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545A ASN* 1.3 72.3 - - + +
547A ASP* 1.3 70.6 + - - +
548A ALA 3.2 1.6 - - - -
549A ARG* 3.1 9.5 + - - +
550A THR* 2.8 37.7 + - - +
586A TYR* 4.3 19.5 - - + +
591A ASP* 5.8 1.8 - - - +
74B ARG* 5.0 18.3 - - + +
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ASN* 3.5 13.5 - - - +
546A VAL* 1.3 85.7 - - - +
548A ALA* 1.3 56.7 + - - +
550A THR* 3.4 7.9 + - - +
551A TYR* 2.9 26.3 + - - +
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Residues in contact with ALA 548 (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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440A VAL* 6.1 0.2 - - + -
519A LYS* 5.4 12.1 - - - -
520A VAL* 5.0 8.9 - - + +
543A LEU* 3.8 22.0 - - + -
545A ASN* 3.2 23.3 - - - +
546A VAL 3.2 0.6 - - - -
547A ASP* 1.3 75.5 - - - +
549A ARG* 1.3 64.4 + - - +
551A TYR* 3.3 7.5 + - - +
552A VAL* 3.1 29.2 + - + +
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Residues in contact with ARG 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASN* 3.6 14.9 - - - +
543A LEU* 2.8 32.8 + - + +
545A ASN 3.3 35.9 + - - +
546A VAL* 3.1 7.8 + - - +
548A ALA* 1.3 77.6 - - - +
550A THR* 1.3 56.8 + - - +
552A VAL* 3.3 2.6 + - - +
553A ASP* 3.0 30.3 + - - +
563A LEU* 5.3 0.2 - - - +
565A GLU* 2.9 30.5 + - - +
566A SER 2.9 22.2 + - - -
567A GLY* 3.5 9.9 - - - -
586A TYR* 3.3 38.8 + - + +
73B LEU 4.3 1.7 + - - -
74B ARG* 3.6 11.1 - - - +
75B GLY 3.3 27.8 + - - +
76B GLY* 5.3 0.2 - - - -
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Residues in contact with THR 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A VAL* 2.8 27.8 + - - +
547A ASP* 3.5 11.4 - - - -
549A ARG* 1.3 70.9 - - - +
551A TYR* 1.3 66.3 + - - +
553A ASP* 3.4 6.8 + - - +
554A ARG* 3.0 31.9 + - + +
586A TYR* 4.2 9.6 - - - -
587A SER* 3.9 17.6 + - - +
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Residues in contact with TYR 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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520A VAL* 3.4 34.3 - - + +
521A GLY* 3.5 19.6 + - - -
522A PRO* 3.5 26.7 - - + -
525A GLU* 2.5 41.9 + - - +
533A TRP* 5.4 0.4 - + - -
547A ASP 2.9 14.1 + - - +
548A ALA* 3.3 9.6 + - - +
550A THR* 1.3 76.1 - - - +
552A VAL* 1.3 65.2 + - + +
554A ARG* 3.2 12.7 + - + +
555A ARG* 3.2 52.6 + - + +
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Residues in contact with VAL 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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440A VAL* 4.2 20.2 - - + -
520A VAL* 3.9 27.8 - - + +
533A TRP* 4.2 7.6 - - + -
539A VAL* 4.0 22.4 - - + -
541A ASN* 3.5 25.8 - - - +
543A LEU* 4.5 1.1 - - + -
548A ALA* 3.1 16.9 + - + +
549A ARG 4.0 1.6 - - - +
551A TYR* 1.3 77.4 - - + +
553A ASP* 1.3 64.6 + - - +
555A ARG* 3.0 7.9 + - - +
556A CYS* 2.9 28.9 + - - -
563A LEU* 4.1 2.7 - - + -
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Residues in contact with ASP 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 ARG 3.0 17.5 + - - +
550A THR* 3.7 4.7 - - - +
551A TYR 3.3 0.2 - - - -
552A VAL* 1.3 76.9 - - - +
554A ARG* 1.3 61.2 + - - +
556A CYS* 3.4 2.6 + - - +
557A VAL* 3.2 28.9 + - - +
563A LEU* 3.7 21.0 - - + +
578A ILE* 4.1 3.3 - - - +
585A SER* 3.0 28.0 + - - -
586A TYR* 2.8 36.6 + - + +
587A SER* 2.8 23.2 + - - +
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Residues in contact with ARG 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 THR* 3.0 24.7 + - + +
551A TYR* 3.4 16.8 - - + +
553A ASP* 1.3 75.5 + - - +
555A ARG* 1.3 77.3 + - + +
557A VAL* 3.3 14.6 + - + +
558A PHE* 3.0 23.8 + - - +
587A SER* 5.4 3.1 - - - +
1002A ILE* 4.2 30.7 - - - +
1004A GLU* 4.7 11.7 + - - -
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Residues in contact with ARG 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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525A GLU* 2.7 39.0 + - - +
528A PHE 5.2 3.6 + - - -
533A TRP* 3.6 38.1 - - + +
551A TYR* 3.2 45.7 + - + +
552A VAL 3.0 7.2 + - - +
554A ARG* 1.3 90.1 - - - +
556A CYS* 1.3 58.1 + - - +
558A PHE* 3.1 8.4 + - - +
559A TYR* 2.8 62.9 + - + +
1002A ILE* 6.2 1.4 - - - +
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Residues in contact with CYS 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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533A TRP* 4.2 4.0 - - - -
539A VAL* 3.6 37.5 - - - -
552A VAL* 2.9 26.5 + - - +
553A ASP* 3.7 6.7 - - - +
555A ARG* 1.3 76.0 - - - +
557A VAL* 1.3 60.2 + - + +
559A TYR* 4.6 1.3 - - - +
560A ARG* 2.8 23.0 + - - -
561A LYS* 2.9 29.5 + - - +
563A LEU* 3.9 22.4 - - + -
578A ILE* 5.8 0.7 - - + -
928A TRP* 3.5 5.6 - - + -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASP* 3.2 18.6 + - - +
554A ARG* 3.3 15.5 + - + +
556A CYS* 1.3 74.4 - - + +
558A PHE* 1.3 62.1 + - + +
560A ARG 3.6 3.3 + - - -
585A SER* 4.1 22.4 - - - +
927A ILE* 4.2 23.3 - - + +
928A TRP* 3.4 29.7 - - + -
930A ARG* 2.5 34.2 + - - +
1019A PHE* 5.3 6.7 - - + -
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Residues in contact with PHE 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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530A ASP* 4.3 0.4 - - - -
554A ARG* 3.0 18.3 + - - +
555A ARG* 3.1 10.1 + - - +
557A VAL* 1.3 80.9 - - + +
559A TYR* 1.3 100.9 + + - +
560A ARG* 4.5 0.5 - - - +
930A ARG* 2.4 29.6 + - - +
1000A THR* 2.8 39.9 - - + -
1002A ILE* 3.6 33.9 - - + -
1019A PHE* 4.1 8.5 - + + -
1021A THR* 3.4 25.8 - - + -
1023A HIS* 6.1 0.7 - + - -
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Residues in contact with TYR 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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528A PHE 4.8 0.5 + - - -
529A ASN* 3.9 2.9 - - - -
530A ASP* 2.3 54.0 + - + -
533A TRP* 3.3 48.3 - + + -
534A GLU* 4.4 16.3 - - + +
555A ARG* 2.8 47.9 + - - +
558A PHE* 1.3 101.7 - + - +
560A ARG* 1.3 72.7 + - - +
561A LYS* 3.6 28.6 - - + -
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Residues in contact with ARG 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 CYS 2.8 10.9 + - - -
557A VAL 3.6 0.8 + - - +
558A PHE 3.3 1.0 - - - -
559A TYR* 1.3 82.2 - - - +
561A LYS* 1.3 63.9 + - - +
562A PRO* 4.4 1.4 - - - +
580A PRO* 3.6 19.9 - - + +
581A ARG* 4.2 39.5 - - - +
928A TRP* 4.0 21.9 + - + +
929A ASP* 5.1 4.8 + - - -
930A ARG* 3.5 63.9 + - - +
932A ASP* 4.1 10.1 + - - -
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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