Contacts of the helix formed by residues 661 - 671 (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 ASN 661 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659G ILE* 3.6 2.5 - - - +
660G ASN* 1.3 78.4 + - - +
662G ARG* 1.3 70.1 + - - +
663G ASP* 3.2 17.3 + - - +
664G GLN* 3.3 27.9 + - + +
665G ILE* 3.1 25.3 + - - +
189H ARG* 5.6 0.4 - - - +
230H MET* 2.9 38.4 - - - +
234H ARG* 3.2 35.1 + - - +
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Residues in contact with ARG 662 (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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617G ILE* 4.0 13.0 - - + +
660G ASN 4.4 6.1 - - - -
661G ASN* 1.3 74.6 + - - +
663G ASP* 1.3 69.3 + - - +
665G ILE* 3.0 19.0 + - - +
666G ILE* 3.1 16.9 + - + +
78H ASN* 4.5 13.2 + - - +
190H ASP* 5.1 11.1 + - - -
216H ILE 5.9 0.2 - - - -
219H MET* 3.4 47.0 + - - +
220H ALA* 3.3 21.1 - - - +
222H SER* 3.2 28.0 + - - +
223H PHE 5.9 0.2 - - - +
230H MET* 6.2 2.0 - - - +
903H 573 3.7 15.4 - - - +
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Residues in contact with ASP 663 (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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661G ASN* 3.2 9.0 + - - +
662G ARG* 1.3 78.7 - - - +
664G GLN* 1.3 61.3 + - - +
666G ILE* 3.4 14.0 + - - +
667G PHE 3.1 19.1 + - - -
225H GLY* 5.6 1.6 + - - -
227H ARG 4.6 1.0 - - - +
228H SER* 2.8 34.1 + - - -
229H TYR 4.8 0.3 + - - -
230H MET* 4.1 13.3 - - + +
235H LEU* 3.7 19.9 - - + +
310H ILE* 4.3 7.0 - - - +
314H LEU* 3.2 18.4 - - + +
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Residues in contact with GLN 664 (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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659G ILE* 3.5 38.5 - - + +
661G ASN* 3.2 28.8 + - + +
662G ARG 3.1 1.0 - - - -
663G ASP* 1.3 78.7 - - - +
665G ILE* 1.3 62.9 + - - +
667G PHE* 3.9 0.7 - - - +
668G MET* 2.9 40.3 + - + +
234H ARG 3.2 22.5 - - - +
235H LEU* 3.8 21.5 - - - +
237H GLY* 3.6 22.2 - - - -
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Residues in contact with ILE 665 (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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617G ILE* 4.3 27.1 - - + +
618G LEU* 4.2 17.9 - - + -
625G ILE* 5.9 0.9 - - + -
656G TYR* 3.8 35.2 - - + -
659G ILE* 4.0 30.7 - - + +
661G ASN 3.4 13.9 - - - +
662G ARG* 3.0 8.9 + - - +
664G GLN* 1.3 76.5 - - - +
666G ILE* 1.3 56.7 + - - +
669G VAL* 2.9 40.8 + - + +
674G LEU* 3.9 13.7 - - + -
220H ALA* 5.0 8.1 - - + -
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Residues in contact with ILE 666 (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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617G ILE* 3.9 24.2 - - + -
625G ILE* 3.5 33.4 - - + +
662G ARG* 3.1 12.8 + - + +
663G ASP* 3.6 24.2 - - - +
665G ILE* 1.3 75.2 - - - +
667G PHE* 1.3 60.2 + - - +
670G GLY* 2.9 26.5 + - - -
224H VAL* 3.9 29.6 - - + -
225H GLY 4.8 0.4 - - - +
310H ILE* 4.1 21.1 - - + -
311H PHE* 4.5 5.6 - - + -
314H LEU* 3.8 11.4 - - + -
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Residues in contact with PHE 667 (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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663G ASP 3.1 14.3 + - - +
664G GLN 4.0 1.3 - - - +
666G ILE* 1.3 78.5 - - - +
668G MET* 1.3 63.8 + - + +
671G ARG* 2.9 45.3 + - + +
673G TYR* 4.1 23.6 - + - -
235H LEU* 3.4 26.0 - - + +
236H GLN* 4.6 7.6 - - + -
311H PHE* 3.5 15.4 - + - -
314H LEU* 3.7 31.9 - - + -
315H ASP* 3.3 27.6 - - - -
318H VAL* 3.5 37.9 - - + -
319H ASN* 4.4 3.1 - - - -
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Residues in contact with MET 668 (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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659G ILE* 5.3 2.0 - - + -
664G GLN* 2.9 36.7 + - - +
667G PHE* 1.3 91.4 - - + +
669G VAL* 1.3 64.1 + - - +
671G ARG* 4.4 1.1 - - - +
672G GLY 3.1 1.6 + - - -
673G TYR* 2.7 57.3 + - + +
674G LEU* 2.9 32.5 + - + +
235H LEU 4.0 2.2 - - - +
236H GLN* 3.8 31.0 - - + +
237H GLY* 5.8 0.2 - - - -
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Residues in contact with VAL 669 (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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617G ILE 6.0 0.4 - - - +
620G MET 4.3 8.5 - - - +
622G PRO* 3.7 28.0 - - + +
625G ILE* 3.6 22.2 - - + -
640G TYR* 4.5 5.2 - - - +
656G TYR* 3.5 33.4 - - + +
665G ILE* 2.9 27.9 + - + +
668G MET* 1.3 72.5 - - - +
670G GLY* 1.3 62.8 + - - +
672G GLY* 3.0 14.2 + - - -
674G LEU* 3.5 32.7 - - + +
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Residues in contact with GLY 670 (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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622G PRO 4.1 10.1 - - - -
625G ILE* 4.0 12.5 - - - +
626G ARG* 2.8 31.8 + - - -
666G ILE 2.9 13.4 + - - -
669G VAL* 1.3 79.2 - - - +
671G ARG* 1.3 57.4 + - - +
672G GLY 3.4 0.7 + - - -
311H PHE* 3.5 22.4 - - - -
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Residues in contact with ARG 671 (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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626G ARG* 5.7 0.2 - - - +
667G PHE* 2.9 23.6 + - + +
668G MET 4.2 0.2 - - - +
669G VAL 3.3 0.2 - - - -
670G GLY* 1.3 75.5 - - - +
672G GLY* 1.3 60.9 + - - +
673G TYR* 3.3 60.0 + - + +
311H PHE* 3.4 23.2 - - - -
315H ASP* 3.2 33.0 + - - -
319H ASN* 4.3 8.9 - - - +
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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