Contacts of the helix formed by residues 616 - 620 (chain F) 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 SER 616 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ASN* 5.0 3.1 + - - -
222E SER 3.6 10.6 + - - -
223E PHE* 3.5 13.0 - - - -
576F ASP* 4.4 5.4 + - - -
578F LYS* 3.0 29.2 + - - +
615F GLY* 1.3 69.8 - - - -
617F ILE* 1.3 65.6 + - - +
618F LEU 3.2 1.7 + - - -
619F TRP* 3.3 39.7 + - - +
620F MET* 3.3 14.6 + - - +
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Residues in contact with ILE 617 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ALA 4.1 16.6 - - - +
222E SER* 3.3 18.6 + - - +
223E PHE 4.4 1.6 - - - +
224E VAL* 3.9 29.2 - - + +
616F SER* 1.3 70.5 - - - +
618F LEU* 1.3 73.6 + - + +
620F MET* 3.1 28.7 + - + +
625F ILE* 4.8 7.6 - - + +
656F TYR* 5.5 1.2 - - - -
662F ARG* 3.8 29.4 - - + +
665F ILE* 3.9 27.0 - - + +
666F ILE* 4.0 25.4 - - + +
669F VAL* 5.8 1.6 - - - +
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Residues in contact with LEU 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ALA 5.1 2.5 - - - +
221E ASN* 3.8 37.5 - - + +
616F SER 3.2 1.2 - - - -
617F ILE* 1.3 93.0 - - + +
619F TRP* 1.3 77.1 + - + +
620F MET 3.8 0.5 + - - +
640F TYR* 4.7 2.8 + - - -
644F ILE* 3.6 21.5 - - - +
654F LEU* 4.1 29.8 - - + -
655F PRO* 4.1 19.8 - - + +
656F TYR* 3.7 33.0 - - + -
665F ILE* 4.4 13.9 - - + -
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Residues in contact with TRP 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ASN* 3.8 18.6 - - - -
538F TYR* 4.9 1.1 - + - -
577F LEU 3.6 25.6 - - - +
578F LYS* 3.4 27.7 - - + +
579F SER* 3.7 12.1 - - - +
580F ASN* 4.2 10.8 - - - -
616F SER* 3.3 31.8 + - - +
617F ILE 3.1 0.4 - - - -
618F LEU* 1.3 96.1 - - + +
620F MET* 1.3 63.1 + - - +
621F ALA 3.7 0.5 + - - -
637F SER 5.0 0.9 - - - +
640F TYR* 3.5 15.3 - - - -
641F ALA* 3.5 24.2 + - + +
644F ILE* 3.3 32.1 - - + +
645F VAL* 4.1 2.3 - - + +
648F GLU* 2.9 33.6 + - - -
654F LEU* 4.2 14.6 - - + -
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Residues in contact with MET 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E VAL* 3.6 28.7 - - + -
613F LEU* 3.6 18.2 - - + -
614F SER 4.8 3.6 - - - +
615F GLY* 4.5 1.3 - - - -
616F SER 3.3 16.2 - - - +
617F ILE* 3.1 24.4 + - + +
618F LEU 4.8 0.5 - - - +
619F TRP* 1.3 78.6 - - - +
621F ALA* 1.3 61.7 + - - +
622F PRO* 3.8 1.2 - - - +
624F VAL* 3.4 30.3 - - + -
625F ILE* 3.5 39.7 - - + +
633F TYR* 5.6 1.6 - - + +
640F TYR* 3.3 12.1 + - - -
669F VAL* 4.4 2.9 - - - +
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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