Contacts of the helix formed by residues 549 - 553 (chain C) in PDB entry 6M6C
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 PHE 549 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C ILE 3.8 0.2 + - - -
548C PRO* 1.3 80.8 - - + +
550C LEU* 1.3 65.2 + - - +
551C GLU* 3.2 17.8 + - - -
552C HIS* 3.4 19.6 + + + -
553C ASP* 3.6 9.7 - - - +
579C VAL* 4.0 20.2 - - + -
883C GLY* 3.9 20.6 - - - -
886C LEU* 4.1 22.0 - - + -
887C GLU* 4.0 29.4 - - + -
890C LEU* 3.9 22.2 - - + -
903C SER* 4.2 15.6 + - - -
904C PRO 5.5 1.8 + - - -
905C ILE* 4.9 2.6 - - - +
908C GLY* 5.6 0.7 - - - -
909C ALA* 3.4 30.5 - - + -
914C ILE* 4.3 12.6 - - + -
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Residues in contact with LEU 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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540C PHE* 4.1 20.2 - - + -
544C THR* 3.6 34.3 - - + +
547C ILE* 3.7 21.1 - - + +
548C PRO 3.3 2.3 - - - -
549C PHE* 1.3 73.1 - - - +
551C GLU* 1.3 61.0 + - - +
552C HIS 2.9 11.7 + - - -
553C ASP* 3.1 20.6 + - + +
558C ALA* 3.7 30.3 - - + -
905C ILE* 3.8 27.4 - - + +
906C PHE* 4.8 4.0 - - + -
1070D TYR* 3.7 22.2 - - + +
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Residues in contact with GLU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 3.2 11.1 + - - -
550C LEU* 1.3 84.4 + - - +
552C HIS* 1.3 80.6 + - + +
553C ASP 3.6 1.3 - - - -
904C PRO 5.0 1.6 - - - +
905C ILE* 4.9 0.7 - - - -
906C PHE* 3.4 63.6 + - + -
907C ASP 4.5 0.5 + - - -
908C GLY* 4.6 8.5 + - - -
1061D PHE* 4.3 7.0 - - - -
1064D GLY* 3.4 9.1 - - - -
1065D LEU* 3.1 33.9 + - - +
1070D TYR* 4.9 3.3 - - - -
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Residues in contact with HIS 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 4.0 15.7 - + + +
550C LEU 2.9 1.6 + - - -
551C GLU* 1.3 104.1 + - + +
553C ASP* 1.3 60.1 + - - +
880C MET 4.0 0.9 - - - +
882C LEU* 3.0 28.5 + - + +
883C GLY 3.9 15.0 - - - +
886C LEU* 3.5 30.8 - - + +
911C GLU* 5.3 3.8 - - + -
951D ILE* 5.5 0.8 - - - +
1061D PHE* 2.6 40.5 + - - +
1062D ARG 3.8 7.9 + - - -
1063D GLU 3.8 7.4 - - - -
1064D GLY* 3.6 21.9 + - - -
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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
----------------------------------------------------------
547C ILE* 4.2 10.2 - - - +
549C PHE 3.6 9.9 - - - +
550C LEU* 3.1 17.0 + - + +
551C GLU 3.6 0.4 - - - -
552C HIS* 1.3 78.8 - - - +
554C ASP* 1.3 65.3 + - - +
558C ALA* 4.6 6.6 - - + +
843C HIS* 3.0 31.4 + - - +
880C MET 4.0 2.0 - - - -
881C ASN* 3.2 19.8 - - + +
883C GLY* 2.9 26.6 + - - -
1061D PHE* 3.7 6.5 - - - -
1070D TYR* 3.0 29.8 + - - -
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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