Contacts of the helix formed by residues 616 - 620 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576G ASP* 4.4 3.8 + - - -
578G LYS* 2.5 35.2 + - - +
615G GLY* 1.3 70.5 - - - -
617G ILE* 1.3 66.3 + - - +
618G LEU 3.1 2.9 + - - -
619G TRP* 3.2 34.9 + - - +
620G MET* 3.7 11.3 + - - +
221H ASN* 4.7 4.0 - - - -
222H SER 3.4 10.8 - - - -
223H PHE* 3.2 15.9 - - - -
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Residues in contact with ILE 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615G GLY 3.9 0.2 + - - -
616G SER* 1.3 70.8 - - - +
618G LEU* 1.3 81.9 + - + +
620G MET* 3.0 28.1 + - + +
625G ILE* 4.8 7.6 - - + +
656G TYR* 5.5 1.0 - - - -
662G ARG* 4.0 26.2 - - + +
665G ILE* 4.3 16.6 - - + +
666G ILE* 3.9 20.4 - - + -
669G VAL* 6.0 0.3 - - - +
220H ALA 3.7 22.0 - - - +
222H SER* 3.1 21.3 + - - +
223H PHE 4.5 0.9 - - - -
224H VAL* 3.4 31.4 - - + +
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Residues in contact with LEU 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616G SER 3.1 2.0 + - - -
617G ILE* 1.3 97.3 - - + +
619G TRP* 1.3 72.9 + - + +
620G MET 3.9 0.2 + - - -
640G TYR* 4.6 1.9 - - - -
644G ILE* 3.1 27.5 - - - +
654G LEU* 4.1 20.2 - - + -
655G PRO* 3.8 34.4 - - + +
656G TYR* 4.2 26.1 + - + -
665G ILE* 4.2 10.1 - - + -
220H ALA* 5.2 0.4 - - + -
221H ASN* 4.0 35.0 - - + +
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Residues in contact with TRP 619 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538G TYR* 4.6 1.1 - + - -
577G LEU 3.4 27.1 - - - +
578G LYS* 3.5 30.0 - - + +
579G SER* 3.9 7.2 - - - -
580G ASN* 4.4 8.1 - - - -
616G SER* 3.2 25.3 + - - +
617G ILE 3.0 0.8 - - - -
618G LEU* 1.3 90.7 - - + +
620G MET* 1.3 61.0 + - - +
621G ALA 3.7 2.3 + - - -
637G SER 4.9 1.0 - - - +
640G TYR* 3.8 4.9 - - - -
641G ALA* 3.6 31.0 + - + +
644G ILE* 3.4 32.2 - - + +
645G VAL* 3.9 2.5 - - + +
648G GLU* 2.6 38.0 + - + -
654G LEU* 3.7 22.4 - - + -
221H ASN* 3.7 28.0 - - - -
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Residues in contact with MET 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613G LEU* 3.5 34.1 - - + -
614G SER 4.9 0.9 - - - +
615G GLY* 4.5 7.6 - - - -
616G SER 3.7 16.6 - - - +
617G ILE* 3.0 19.6 + - - +
618G LEU 3.5 0.4 - - - +
619G TRP* 1.3 76.9 - - - +
621G ALA* 1.3 64.1 + - - +
622G PRO 3.9 0.7 - - - -
624G VAL* 3.5 25.4 - - + -
625G ILE* 3.6 33.9 - - + +
633G TYR* 5.3 1.6 - - + +
640G TYR* 3.4 10.8 + - - -
669G VAL* 4.3 4.7 - - - +
224H VAL* 3.5 28.0 - - + -
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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