Contacts of the helix formed by residues 616 - 620 (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 SER 616 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C ASP* 4.7 2.4 + - - -
578C LYS* 2.4 37.9 + - - +
615C GLY* 1.3 71.0 - - - -
617C ILE* 1.3 66.6 + - - +
618C LEU 3.1 3.1 + - - -
619C TRP* 3.2 35.6 + - - +
620C MET* 3.4 12.9 + - - +
221D ASN* 5.1 3.6 - - - -
222D SER 3.5 11.2 - - - -
223D PHE* 3.5 12.8 - - - -
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Residues in contact with ILE 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615C GLY 4.0 0.2 + - - -
616C SER* 1.3 71.2 - - - +
618C LEU* 1.3 71.5 + - + +
619C TRP 3.0 1.6 + - - -
620C MET* 3.1 26.3 + - - +
625C ILE* 4.7 8.2 - - + +
656C TYR* 5.7 0.7 - - - -
662C ARG* 4.1 15.7 - - + +
665C ILE* 3.8 42.5 - - + +
666C ILE* 3.7 20.6 - - + -
220D ALA 3.7 19.3 - - - +
222D SER* 3.1 18.1 + - - +
223D PHE 4.3 1.8 - - - +
224D VAL* 3.4 34.3 - - + +
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Residues in contact with LEU 618 (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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616C SER* 3.1 1.8 + - - -
617C ILE* 1.3 95.9 - - + +
619C TRP* 1.3 74.6 + - + +
620C MET 3.5 0.8 + - - +
640C TYR* 4.8 1.9 + - - -
644C ILE* 3.5 24.8 - - - +
654C LEU* 4.0 42.6 - - + -
655C PRO* 4.1 17.4 - - + +
656C TYR* 3.9 32.2 - - + -
665C ILE* 4.3 8.5 - - + -
220D ALA* 5.0 2.9 - - + +
221D ASN* 4.1 22.9 - - + +
222D SER 5.3 0.4 - - - +
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Residues in contact with TRP 619 (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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538C TYR* 4.7 1.6 - + - -
577C LEU 3.8 19.3 - - - +
578C LYS* 3.4 30.7 - - + +
579C SER* 4.3 5.6 - - - -
580C ASN* 4.4 9.9 - - - -
616C SER* 3.2 29.3 + - - +
617C ILE 3.1 0.8 - - - -
618C LEU* 1.3 93.3 - - + +
620C MET* 1.3 64.4 + - - +
621C ALA 3.7 0.5 + - - -
637C SER 4.9 1.0 - - - +
640C TYR* 3.5 6.0 - - - -
641C ALA* 3.5 32.9 + - + +
644C ILE* 3.4 33.0 - - + +
645C VAL* 4.1 2.5 - - + +
648C GLU* 2.8 36.1 + - - -
654C LEU* 4.0 20.4 - - + -
221D ASN* 3.9 22.9 - - - -
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Residues in contact with MET 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C LEU* 3.8 24.7 - - + -
614C SER 3.7 6.7 - - - +
615C GLY* 3.4 42.0 - - - +
616C SER 3.4 12.3 - - - +
617C ILE* 3.1 14.0 + - - +
618C LEU 5.0 0.3 - - - +
619C TRP* 1.3 78.1 - - - +
621C ALA* 1.3 64.8 + - - +
622C PRO* 3.9 0.5 - - - +
624C VAL* 4.2 13.2 - - + -
625C ILE* 3.7 27.2 - - + +
633C TYR* 4.9 1.8 - - - +
640C TYR* 3.1 14.3 + - - -
669C VAL* 4.4 2.4 - - - +
224D VAL* 3.6 28.5 - - + -
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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
------------------------------------------------------------
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