Contacts of the helix formed by residues 554 - 566 (chain C) in PDB entry 6M6A
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 554 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553C ASP* 1.3 72.4 - - - +
555C ALA* 1.3 60.6 + - - +
556C ASN* 2.8 43.2 + - - +
557C ARG* 3.3 6.0 + - - +
558C ALA* 2.9 27.2 + - - +
879C ARG 3.2 22.1 - - - +
880C MET* 2.5 40.3 + - + +
881C ASN* 3.0 7.1 + - - +
1042D ARG* 4.2 15.2 + - - -
1061D PHE* 4.2 7.5 - - - -
1070D TYR* 4.2 0.2 - - - -
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Residues in contact with ALA 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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441C VAL* 3.4 18.3 - - + +
553C ASP 3.7 1.6 + - - -
554C ASP* 1.3 74.6 + - - +
556C ASN* 1.3 60.9 + - - +
558C ALA* 3.2 4.0 + - - +
559C LEU* 2.9 23.9 + - - +
1042D ARG* 5.7 4.1 - - - +
1061D PHE* 5.5 0.4 - - - -
1070D TYR* 3.3 32.4 - - + +
1073D SER* 5.8 2.5 - - - +
1074D SER* 5.1 11.7 - - - +
1077D ALA* 4.5 17.3 - - + -
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Residues in contact with ASN 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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554C ASP* 2.8 29.2 + - - +
555C ALA* 1.3 73.6 - - - +
557C ARG* 1.3 61.8 + - - +
559C LEU* 3.2 16.4 + - + +
560C MET* 3.0 43.2 + - + +
880C MET* 5.6 0.4 - - - +
1042D ARG* 5.7 1.4 - - - +
1077D ALA* 3.3 43.3 - - - +
1081D GLY* 5.1 2.4 + - - -
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Residues in contact with ARG 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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554C ASP* 3.3 4.7 + - - +
556C ASN* 1.3 76.0 - - - +
558C ALA* 1.3 59.3 + - - +
560C MET* 3.2 38.1 + - - +
561C GLY 2.9 24.3 + - - -
564C MET* 6.2 0.2 - - - +
843C HIS 4.4 1.3 - - - -
844C GLY* 3.2 44.7 + - - -
845C ASN* 4.3 1.3 - - - +
846C LYS* 6.2 3.0 - - - +
878C SER 5.6 0.4 + - - -
879C ARG* 3.2 59.2 + - + +
881C ASN* 3.2 36.3 - - - +
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Residues in contact with ALA 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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441C VAL* 4.4 7.9 - - + -
547C ILE* 5.6 2.4 - - - +
550C LEU* 5.5 12.8 - - + -
553C ASP* 5.5 5.8 - - + +
554C ASP 2.9 16.9 + - - +
555C ALA* 3.3 14.1 - - - +
556C ASN 3.1 0.4 - - - -
557C ARG* 1.3 74.1 - - - +
559C LEU* 1.3 59.1 + - - +
561C GLY* 3.4 1.5 + - - -
562C SER* 2.9 29.7 + - - -
565C GLN* 5.3 0.3 + - - -
842C ARG 5.1 2.0 - - - +
843C HIS 5.0 5.4 - - - -
881C ASN* 4.8 0.4 - - - +
1070D TYR* 4.1 9.4 - - - +
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Residues in contact with LEU 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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441C VAL* 3.3 30.1 - - + +
442C GLU* 3.7 3.8 - - - -
443C THR 3.3 36.3 - - - +
445C GLU* 5.4 13.0 - - + +
449C ILE* 6.0 3.4 - - + -
555C ALA 2.9 11.7 + - - +
556C ASN* 3.2 16.8 - - + +
558C ALA* 1.3 75.9 - - - +
560C MET* 1.3 67.1 + - + +
562C SER* 2.4 23.2 + - - +
563C ASN* 3.0 22.2 + - - +
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Residues in contact with MET 560 (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 GLU* 6.3 3.1 - - + -
556C ASN* 3.0 36.9 + - + +
557C ARG* 3.2 55.6 + - - +
559C LEU* 1.3 82.6 - - + +
561C GLY* 1.3 56.8 + - - +
563C ASN* 3.4 4.6 + - - +
564C MET* 2.9 49.8 + - + +
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Residues in contact with GLY 561 (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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557C ARG 2.9 11.9 + - - -
558C ALA 3.8 1.8 - - - -
560C MET* 1.3 75.5 - - - +
562C SER* 1.3 57.4 + - - +
564C MET* 3.0 11.0 + - - +
565C GLN* 3.0 39.8 + - - +
841C ASN 4.6 0.6 - - - +
842C ARG 3.6 10.8 - - - -
844C GLY* 3.6 21.2 - - - -
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Residues in contact with SER 562 (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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441C VAL* 6.0 1.8 - - - -
442C GLU* 3.5 24.1 - - - +
543C ASN* 2.5 33.2 + - - -
544C THR* 5.4 4.3 - - - -
547C ILE* 5.1 6.3 - - - -
558C ALA 2.9 15.2 + - - -
559C LEU* 2.4 27.2 + - - -
561C GLY* 1.3 75.0 - - - +
563C ASN* 1.3 65.1 + - - +
565C GLN* 3.3 25.0 + - - +
566C THR* 3.8 3.1 - - - +
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Residues in contact with ASN 563 (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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409C ARG* 4.2 8.7 + - - -
442C GLU* 3.4 18.2 - - - +
443C THR 4.0 0.4 - - - -
444C PRO* 3.5 42.9 - - - +
445C GLU 5.0 0.4 - - - +
559C LEU* 3.0 28.0 + - - +
560C MET* 4.0 4.0 - - - +
562C SER* 1.3 81.2 + - - +
564C MET* 1.3 60.5 + - - +
566C THR* 2.8 28.8 + - - +
567C GLN* 4.3 3.6 + - - +
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Residues in contact with MET 564 (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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560C MET* 2.9 39.2 + - + +
561C GLY* 3.0 16.4 + - - +
563C ASN* 1.3 78.1 - - - +
565C GLN* 1.3 61.5 + - - +
567C GLN* 3.1 21.9 + - - +
568C ALA 4.1 0.5 + - - -
840C ALA* 4.0 18.8 - - + -
841C ASN 4.2 8.1 - - - +
844C GLY 3.3 24.5 - - - +
846C LYS* 3.7 41.5 - - + -
995C MET* 4.3 7.1 - - + +
997C LEU* 4.1 16.4 - - + +
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Residues in contact with GLN 565 (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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399C ASN* 3.6 7.8 + - - -
401C LEU* 3.3 17.6 - - + +
543C ASN* 2.8 33.8 - - - +
546C LEU* 4.7 5.0 - - + +
547C ILE* 3.3 22.1 - - - +
561C GLY 3.0 25.1 + - - +
562C SER* 3.3 13.9 - - - +
563C ASN 3.2 0.8 - - - -
564C MET* 1.3 76.6 - - - +
566C THR* 1.3 60.4 + - - +
567C GLN 3.4 0.3 + - - -
568C ALA* 3.7 8.2 + - - +
668C LEU* 4.4 5.8 - - + +
842C ARG* 3.0 38.0 + - + +
995C MET* 3.9 21.8 - - + -
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Residues in contact with THR 566 (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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398C THR* 3.9 2.6 - - - -
399C ASN* 2.6 28.4 + - - +
401C LEU* 4.2 8.1 - - + -
402C SER* 3.4 12.5 - - - +
405C ARG* 3.4 47.6 + - + +
442C GLU* 4.4 1.3 - - - +
543C ASN* 4.3 9.2 - - - +
562C SER 3.8 15.0 - - - +
563C ASN* 2.8 24.3 + - - +
565C GLN* 1.3 77.6 - - - +
567C GLN* 1.3 64.9 + - - +
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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