Contacts of the helix formed by residues 621 - 627 (chain C) in PDB entry 4MNE
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 ALA 621 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619C TRP 3.7 1.2 + - - -
620C MET* 1.3 73.3 - - - +
622C PRO* 1.3 71.1 - - + +
623C GLU* 3.3 26.2 - - - +
624C VAL* 2.7 34.0 + - + +
625C ILE* 3.0 10.7 + - - +
637C SER* 4.4 5.5 + - - +
640C TYR* 3.3 29.4 - - + -
704C ARG* 3.8 1.6 - - - +
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Residues in contact with PRO 622 (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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620C MET 3.9 1.1 - - - +
621C ALA* 1.3 87.4 - - + +
623C GLU* 1.3 61.5 + - - +
625C ILE* 3.7 3.0 + - + +
626C ARG* 3.1 50.5 + - - +
640C TYR* 4.1 17.0 - - + +
669C VAL* 3.3 41.7 - - + +
670C GLY* 4.1 2.9 - - - -
672C GLY* 5.7 0.7 - - - -
674C LEU 6.0 0.4 - - - +
699C LYS* 4.5 25.8 - - + +
704C ARG* 4.0 7.6 - - - +
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Residues in contact with GLU 623 (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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621C ALA* 3.3 11.1 - - + +
622C PRO* 1.3 75.5 - - - +
624C VAL* 1.3 68.5 + - + +
626C ARG* 3.8 22.6 + - - +
627C MET* 3.3 13.3 + - - -
628C GLN 4.6 1.2 + - - -
629C ASP* 5.2 7.4 + - + -
632C PRO* 3.6 30.3 - - + +
637C SER* 4.2 6.6 - - - -
699C LYS 3.9 8.5 - - - +
701C ARG* 3.7 32.5 - - + +
704C ARG* 2.8 45.7 + - - -
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Residues in contact with VAL 624 (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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613C LEU* 3.9 11.2 - - + +
620C MET* 4.2 14.8 - - + -
621C ALA* 2.7 32.0 + - + +
623C GLU* 1.3 69.8 - - + +
625C ILE* 1.3 66.6 + - - +
627C MET* 3.0 29.4 + - - +
632C PRO* 3.8 21.1 - - - +
633C TYR* 3.4 40.4 - - + +
637C SER* 3.8 24.0 - - - -
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Residues in contact with ILE 625 (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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613C LEU* 4.1 14.2 - - + +
617C ILE* 4.7 8.5 - - + +
620C MET* 3.7 29.6 - - + +
621C ALA 3.0 8.1 + - - +
622C PRO* 3.9 6.5 - - + +
624C VAL* 1.3 77.9 - - - +
626C ARG* 1.3 63.0 + - - +
627C MET* 3.2 7.1 + - - +
665C ILE* 4.7 1.6 - - + +
666C ILE* 3.4 46.9 - - + +
669C VAL* 3.6 37.5 - - + -
670C GLY* 4.3 3.1 - - - +
224D VAL* 6.1 0.9 - - + -
309D ALA* 5.6 0.3 - - - +
310D ILE* 5.5 0.6 - - + +
311D PHE* 3.3 22.0 + - + +
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Residues in contact with ARG 626 (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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622C PRO* 3.1 37.7 + - - +
623C GLU* 3.8 27.1 + - - +
624C VAL 3.2 0.2 - - - -
625C ILE* 1.3 76.0 - - - +
627C MET* 1.3 67.0 + - - +
628C GLN* 3.0 42.0 + - + +
670C GLY 3.0 29.7 + - - -
671C ARG* 5.2 3.5 - - - +
672C GLY* 5.1 3.0 - - - +
699C LYS* 5.1 6.1 + - - +
309D ALA* 4.9 1.0 - - - +
311D PHE* 3.6 33.5 - - + +
312D GLU* 4.3 4.5 - - - +
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Residues in contact with MET 627 (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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610C PHE* 6.0 3.1 - - + -
611C GLU* 3.8 24.0 - - + +
613C LEU* 4.0 33.4 - - + +
623C GLU 3.3 6.5 + - - -
624C VAL* 3.0 25.6 + - - +
625C ILE 3.8 7.0 - - - +
626C ARG* 1.3 79.4 - - - +
628C GLN* 1.3 57.4 + - - +
629C ASP 3.6 3.8 - - - -
632C PRO* 3.8 26.0 - - + -
633C TYR* 5.2 7.6 - - + -
309D ALA* 4.1 22.1 - - + +
312D GLU* 4.7 4.1 - - - +
630F LYS* 2.9 33.1 + - - +
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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