Contacts of the helix formed by residues 545 - 559 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543C LEU* 4.4 1.3 - - - +
544C ASP* 1.3 88.5 - - - +
546C VAL* 1.3 63.7 + - - +
547C ASP* 3.4 30.5 + - - +
548C ALA* 2.9 38.6 + - - +
549C ARG* 3.2 29.5 + - - +
74D ARG* 4.5 6.3 - - - +
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Residues in contact with VAL 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C ASN* 1.3 74.5 - - - +
547C ASP* 1.3 78.4 + - - +
549C ARG* 3.3 9.7 + - - +
550C THR* 3.0 26.0 + - - +
586C TYR* 4.1 22.9 - - + +
591C ASP* 5.7 5.4 - - + +
74D ARG* 4.4 16.6 - - + +
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Residues in contact with ASP 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C ASN* 3.4 14.7 + - - +
546C VAL* 1.3 87.6 - - - +
548C ALA* 1.3 57.7 + - - +
550C THR* 3.4 9.7 + - - +
551C TYR* 3.0 27.3 + - - +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C VAL* 6.2 0.2 - - + -
520C VAL 5.2 9.0 - - - +
543C LEU* 3.8 26.5 - - + -
545C ASN* 2.9 25.8 + - - +
547C ASP* 1.3 70.1 - - - +
549C ARG* 1.3 66.0 + - - +
551C TYR* 3.2 7.8 + - - +
552C VAL* 3.0 29.1 + - + +
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Residues in contact with ARG 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ILE* 4.9 0.2 - - - +
541C ASN* 3.9 10.9 - - - +
543C LEU* 2.8 44.8 + - + +
545C ASN 3.2 34.6 + - - +
546C VAL* 3.3 9.5 + - - +
548C ALA* 1.3 77.8 - - - +
550C THR* 1.3 58.3 + - - +
552C VAL* 3.5 2.3 + - - +
553C ASP* 3.0 28.4 + - - +
563C LEU* 5.1 0.7 - - - +
565C GLU* 2.7 31.4 + - - +
566C SER 2.8 21.8 + - - -
567C GLY* 3.4 15.4 - - - -
586C TYR* 3.3 36.2 + - + +
73D LEU 3.8 1.7 + - - -
74D ARG* 3.5 11.2 - - - +
75D GLY 3.4 15.8 + - - +
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Residues in contact with THR 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C VAL* 3.0 18.7 + - - +
547C ASP* 3.5 11.9 - - - +
549C ARG* 1.3 74.0 - - - +
551C TYR* 1.3 65.3 + - - +
553C ASP* 3.3 7.4 + - - +
554C ARG* 3.0 42.3 + - + +
586C TYR* 4.2 13.3 - - - -
587C SER* 4.0 17.1 + - - +
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Residues in contact with TYR 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C VAL* 3.6 24.9 - - + +
521C GLY* 3.1 39.5 + - - -
522C PRO* 3.5 23.6 - - + -
525C GLU* 2.5 36.4 + - - +
533C TRP* 5.3 0.2 - + - -
547C ASP 3.0 14.4 + - - +
548C ALA* 3.2 11.2 + - - +
550C THR* 1.3 75.3 - - - +
552C VAL* 1.3 65.7 + - + +
554C ARG* 3.2 36.8 + - - +
555C ARG* 3.1 46.0 + - + +
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Residues in contact with VAL 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C VAL* 4.3 20.6 - - + -
520C VAL* 3.9 27.6 - - + +
533C TRP* 4.3 6.3 - - + -
539C VAL* 4.0 21.5 - - + -
541C ASN* 3.6 24.9 - - - +
543C LEU* 4.4 2.0 - - + -
548C ALA* 3.0 16.7 + - + +
549C ARG 4.0 3.6 - - - +
551C TYR* 1.3 75.8 - - + +
553C ASP* 1.3 58.6 + - - +
555C ARG* 3.3 7.6 + - - +
556C CYS* 2.9 33.8 + - - -
563C LEU* 4.3 4.3 - - + -
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Residues in contact with ASP 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C ARG 3.0 18.3 + - - +
550C THR 3.4 6.1 - - - +
552C VAL* 1.3 72.9 - - - +
554C ARG* 1.3 65.9 + - - +
556C CYS* 3.1 5.2 + - - +
557C VAL* 3.0 26.7 + - - +
563C LEU* 3.9 18.6 - - + +
578C ILE* 4.3 5.4 - - - +
585C SER* 3.0 23.6 + - - -
586C TYR* 2.9 34.2 + - + +
587C SER* 2.6 29.8 + - - +
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Residues in contact with ARG 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522C PRO* 6.2 0.4 - - - +
550C THR* 3.0 32.2 + - + +
551C TYR* 3.2 44.4 + - - +
553C ASP* 1.3 74.4 - - - +
555C ARG* 1.3 63.8 + - + +
557C VAL* 3.4 11.5 + - - +
558C PHE* 3.0 24.0 + - - +
587C SER* 4.4 11.4 - - - +
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Residues in contact with ARG 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C GLU* 3.5 36.5 + - - +
528C PHE 4.5 2.6 + - - -
529C ASN* 6.0 0.4 - - - +
533C TRP* 3.7 40.7 - - + +
551C TYR* 3.1 42.6 + - + +
552C VAL 3.4 8.3 - - - +
553C ASP 3.1 0.2 - - - -
554C ARG* 1.3 77.8 - - + +
556C CYS* 1.3 57.4 + - - +
558C PHE* 3.2 20.4 + - - +
559C TYR* 2.8 62.4 + - - -
1000C THR* 6.1 2.2 - - - +
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Residues in contact with CYS 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C TRP* 4.2 4.0 - - - -
539C VAL* 3.8 32.3 - - - -
552C VAL* 2.9 21.2 + - - +
553C ASP* 3.1 9.4 + - - +
555C ARG* 1.3 73.6 - - - +
557C VAL* 1.3 64.6 + - + +
559C TYR* 3.5 1.3 + - - +
560C ARG* 3.0 4.5 + - - -
561C LYS* 2.9 47.6 + - - +
562C PRO 4.5 0.2 - - - -
563C LEU* 3.8 29.8 - - + -
578C ILE* 5.6 1.3 - - + -
928C TRP* 3.8 3.2 - - + -
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Residues in contact with VAL 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C ASP* 3.0 23.3 + - - +
554C ARG* 4.0 8.1 - - - +
556C CYS* 1.3 71.8 - - + +
558C PHE* 1.3 71.6 + - + +
560C ARG* 3.2 8.3 + - - +
578C ILE* 5.9 0.2 - - + -
585C SER* 4.2 24.7 - - - +
927C ILE* 4.0 27.4 - - + +
928C TRP* 3.4 24.8 - - + -
930C ARG* 3.0 21.9 + - - +
1019C PHE* 5.5 5.6 - - + -
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Residues in contact with PHE 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C ASP* 4.4 1.1 - - - -
554C ARG 3.0 14.5 + - - +
555C ARG* 3.3 24.0 - - - +
557C VAL* 1.3 80.1 - - - +
559C TYR* 1.3 99.0 + + - +
560C ARG* 3.3 3.6 + - - -
930C ARG* 2.8 32.7 + - - +
1000C THR* 3.6 36.8 - - + -
1002C ILE* 3.8 39.3 - - + -
1019C PHE* 5.1 5.6 - + - -
1021C THR* 4.1 17.7 - - + -
1023C HIS* 6.2 0.4 - + - -
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Residues in contact with TYR 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ASN* 4.1 1.9 - - - -
530C ASP* 3.0 48.4 + - + -
533C TRP* 3.4 47.6 - + + -
534C GLU* 4.3 16.6 - - + +
555C ARG* 2.8 55.3 + - - +
556C CYS 3.5 0.4 - - - +
557C VAL 3.3 0.2 - - - -
558C PHE* 1.3 97.4 - + - +
560C ARG* 1.3 70.4 + - - +
561C LYS* 3.0 31.7 + - + +
1000C THR* 5.4 0.9 - - - +
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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
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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