Contacts of the helix formed by residues 645 - 653 (chain C) in PDB entry 5MKE
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 645 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625C ASP* 4.8 18.7 + - - +
638C ARG* 4.7 11.4 + - - +
643C ASP 3.3 12.8 - - - +
644C ILE* 1.3 73.0 - - - +
646C PHE* 1.3 62.3 + - - +
647C ALA* 3.4 3.3 + - + +
648C GLU* 3.9 21.0 + - + +
649C ILE* 4.4 8.5 + - - +
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Residues in contact with PHE 646 (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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634B PHE* 4.7 17.3 - + + -
638B ARG* 4.9 25.8 - - + +
643B ASP* 4.8 6.5 + - - +
644C ILE* 3.4 35.5 + - + +
645C ASN* 1.3 71.4 - - - +
647C ALA* 1.3 67.0 + - - +
648C GLU 3.0 4.0 + - - -
649C ILE* 3.3 30.5 + - + +
650C GLU* 3.5 27.1 + - + +
658C PRO* 4.7 7.6 - - + -
661C PHE* 3.2 52.5 - + + -
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Residues in contact with ALA 647 (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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271B LYS* 6.1 2.2 - - - +
638B ARG* 5.7 6.5 - - - +
645C ASN* 3.4 1.6 - - + -
646C PHE* 1.3 79.8 - - - +
648C GLU* 1.3 68.7 + - + +
650C GLU* 4.0 5.4 - - - +
651C GLU* 3.1 33.7 + - - +
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Residues in contact with GLU 648 (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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271B LYS* 5.2 5.4 - - - -
455B TRP* 3.2 31.2 - - - -
622C GLN* 5.5 5.6 + - - +
623C VAL* 4.9 20.4 - - + +
624C ASP 6.3 0.2 - - - +
645C ASN* 4.2 18.8 - - + +
646C PHE 3.0 0.8 - - - -
647C ALA* 1.3 89.6 - - + +
649C ILE* 1.3 66.3 + - + +
651C GLU* 3.1 3.3 + - - +
652C ALA* 2.9 23.4 + - - +
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Residues in contact with ILE 649 (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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619C PHE* 4.0 26.0 - - + -
623C VAL* 5.0 8.1 - - + -
626C PHE* 4.4 26.7 - - + -
639C ILE* 4.6 17.7 - - + -
644C ILE* 5.2 3.8 - - + -
645C ASN 4.5 10.5 - - - +
646C PHE* 3.3 36.6 + - + +
648C GLU* 1.3 77.2 - - - +
650C GLU* 1.3 67.9 + - - +
652C ALA* 3.1 17.3 - - - +
656C LEU 4.1 4.7 - - - +
657C GLY 4.4 2.3 + - - -
658C PRO* 4.7 7.0 - - + -
660C TYR* 5.2 4.7 - - + -
661C PHE* 4.5 12.8 - - + -
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Residues in contact with GLU 650 (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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382B ILE* 5.4 7.1 - - - +
630B GLN* 6.0 0.2 + - - -
631B GLU* 6.1 6.5 - - + -
634B PHE* 5.5 8.7 - - + -
646C PHE* 3.5 26.9 + - + +
647C ALA* 4.0 5.4 - - - +
648C GLU 3.4 0.2 - - - -
649C ILE* 1.3 80.9 - - - +
651C GLU* 1.3 79.2 + - - +
652C ALA 2.8 6.9 + - - -
653C ASN 3.2 22.0 + - - +
654C ARG* 3.7 27.9 + - - +
658C PRO* 3.4 25.1 - - + -
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Residues in contact with GLU 651 (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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271B LYS* 2.6 34.9 + - - +
454B SER* 3.9 14.6 - - - -
455B TRP* 2.8 67.0 + - + -
647C ALA* 3.1 22.5 + - - +
648C GLU* 3.1 4.1 + - - +
650C GLU* 1.3 87.8 + - - +
652C ALA* 1.3 65.4 + - - +
653C ASN* 4.5 0.4 - - - -
654C ARG* 4.1 23.9 + - - +
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Residues in contact with ALA 652 (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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455B TRP* 4.2 10.1 + - - +
456B GLN* 3.6 5.4 + - - +
619C PHE* 4.8 9.0 - - + -
621C THR* 4.6 17.5 - - - +
622C GLN 5.0 7.9 - - - +
623C VAL* 6.4 0.4 - - - +
648C GLU 2.9 10.4 + - - +
649C ILE* 3.1 16.4 - - - +
650C GLU 2.8 0.8 + - - -
651C GLU* 1.3 82.5 - - - +
653C ASN* 1.3 80.2 + - - +
654C ARG* 4.7 1.6 + - - -
656C LEU* 3.7 8.5 - - + +
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Residues in contact with ASN 653 (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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456B GLN* 2.4 41.8 + - - +
457B PHE 5.0 1.8 + - - +
458B GLN* 4.7 9.7 - - - +
556B ILE* 5.0 5.3 - - - +
560B ASN* 4.9 2.6 + - - -
1007B PX6 4.1 15.2 + - - +
621C THR* 5.1 7.6 - - - +
650C GLU 3.2 3.8 + - - +
651C GLU 4.5 0.4 - - - -
652C ALA* 1.3 88.6 + - - +
654C ARG* 1.3 63.2 + - - +
655C VAL 3.2 0.2 - - - -
656C LEU* 2.3 79.1 + - + +
658C PRO* 3.2 5.4 - - - +
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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