Contacts of the helix formed by residues 616 - 620 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASN* 4.7 3.6 + - - -
222A SER 3.7 11.1 + - - -
223A PHE* 3.7 11.9 - - - -
576B ASP* 4.3 6.2 + - - -
578B LYS* 2.9 31.0 + - - +
615B GLY* 1.3 71.2 - - - -
617B ILE* 1.3 63.5 + - - +
618B LEU 3.4 0.4 - - - -
619B TRP* 3.4 38.4 + - - +
620B MET* 3.2 15.0 + - - +
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Residues in contact with ILE 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ALA 3.9 12.6 - - - +
221A ASN* 5.6 0.2 + - - -
222A SER* 3.4 29.7 + - - +
223A PHE 4.7 0.7 - - - +
224A VAL* 3.4 29.6 - - + -
616B SER* 1.3 67.0 - - - +
618B LEU* 1.3 75.4 + - + +
619B TRP 3.0 7.3 + - - -
620B MET* 3.1 26.1 + - + +
625B ILE* 4.8 7.9 - - + +
656B TYR* 5.6 0.7 - - - -
662B ARG* 4.0 22.2 - - + +
665B ILE* 4.2 23.7 - - + +
666B ILE* 3.6 23.8 - - + -
669B VAL* 5.9 1.2 - - - +
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Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ALA 4.9 3.4 - - - +
221A ASN* 3.6 37.9 - - + +
616B SER 3.4 1.0 - - - -
617B ILE* 1.3 88.7 - - + +
619B TRP* 1.3 72.8 + - + +
620B MET 5.2 0.7 - - - -
640B TYR* 4.8 1.7 + - - -
644B ILE* 3.3 25.6 - - - +
654B LEU* 4.0 32.5 - - + -
655B PRO* 4.2 16.4 - - + +
656B TYR* 3.7 34.8 + - + -
665B ILE* 4.6 11.9 - - + -
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Residues in contact with TRP 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASN* 3.6 34.8 - - - -
538B TYR* 4.6 1.3 - + - -
577B LEU 3.7 12.8 - - - +
578B LYS* 3.4 38.6 - - + +
579B SER* 4.0 6.7 - - - +
580B ASN* 4.4 9.9 - - - -
616B SER* 3.4 31.6 + - - +
617B ILE 3.0 0.8 - - - -
618B LEU* 1.3 86.0 - - + +
620B MET* 1.3 62.4 + - - +
621B ALA 3.7 0.7 + - - -
637B SER 4.9 1.2 - - - +
640B TYR* 3.6 14.6 - - - -
641B ALA* 3.6 27.1 + - + +
644B ILE* 3.5 28.7 - - + +
645B VAL* 4.1 1.9 - - + +
648B GLU* 2.9 35.1 + - - -
654B LEU* 4.0 14.8 - - + -
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Residues in contact with MET 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 3.6 28.9 - - + -
613B LEU* 3.6 28.7 - - + -
614B SER 4.9 0.4 - - - +
615B GLY* 4.3 9.0 - - - +
616B SER 3.2 19.1 - - - +
617B ILE* 3.1 13.7 + - - +
619B TRP* 1.3 78.5 - - - +
621B ALA* 1.3 63.4 + - - +
622B PRO* 3.8 0.9 - - - +
624B VAL* 3.5 28.3 - - + -
625B ILE* 3.4 35.0 - - + +
633B TYR* 5.5 0.9 - - + +
640B TYR* 3.4 11.6 + - - -
669B VAL* 4.4 2.8 - - - +
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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