Contacts of the helix formed by residues 686 - 697 (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 PRO 686 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550G MET* 4.1 22.2 - - + -
554G ILE* 4.7 2.9 - - + -
650G MET* 4.7 0.7 - - - -
684G ASN 3.2 9.6 - - - +
685G CYS* 1.3 94.9 - - - +
687G LYS* 1.3 65.2 + - - +
688G ALA 3.2 0.7 - - - +
689G MET* 3.2 9.0 + - + +
690G LYS* 3.2 15.4 + - - +
717G LEU* 3.7 41.3 - - + -
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Residues in contact with LYS 687 (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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681G VAL* 5.3 4.2 - - - +
683G SER 6.2 0.2 - - - -
685G CYS 4.4 8.2 + - - +
686G PRO* 1.3 76.1 - - - +
688G ALA* 1.3 52.9 + - - +
690G LYS* 3.2 36.2 + - + +
691G ARG* 2.8 44.6 + - + +
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Residues in contact with ALA 688 (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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686G PRO* 3.2 1.0 - - - +
687G LYS* 1.3 77.7 - - - +
689G MET* 1.3 57.1 + - - +
691G ARG* 3.5 29.0 + - - +
692G LEU* 2.8 27.4 + - - +
713G SER* 5.8 1.6 - - - +
717G LEU* 3.6 33.4 - - + -
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Residues in contact with MET 689 (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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554G ILE* 4.9 10.8 - - + -
557G ALA* 4.9 7.2 - - + -
646G LEU* 3.7 32.8 - - + -
650G MET* 3.7 33.9 - - + +
685G CYS* 4.2 9.0 - - - -
686G PRO* 3.2 18.1 + - + +
687G LYS 3.2 0.4 - - - -
688G ALA* 1.3 75.4 - - - +
690G LYS* 1.3 57.2 + - - +
691G ARG 3.2 0.4 - - - -
692G LEU* 3.6 23.3 - - + +
693G MET* 2.8 36.8 + - + +
714G ILE* 4.7 11.2 - - + -
717G LEU* 4.0 22.4 - - + +
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Residues in contact with LYS 690 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678G LEU* 2.5 51.0 + - + +
679G SER* 4.2 3.4 - - - +
681G VAL* 3.8 21.8 - - + +
685G CYS* 4.1 6.6 - - - +
686G PRO 3.2 11.5 + - - +
687G LYS* 3.2 42.3 + - + +
689G MET* 1.3 76.4 - - - +
691G ARG* 1.3 63.1 + - + +
693G MET* 3.5 12.1 + - + +
694G ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 691 (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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687G LYS* 2.8 23.1 + - + +
688G ALA* 3.7 26.6 + - - +
690G LYS* 1.3 75.8 - - + +
692G LEU* 1.3 65.5 + - - +
694G ALA* 3.0 10.0 + - - +
695G GLU* 3.0 28.5 + - + +
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Residues in contact with LEU 692 (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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646G LEU* 4.1 12.6 - - + -
688G ALA 2.8 19.6 + - - +
689G MET* 3.6 21.3 - - + +
691G ARG* 1.3 76.5 - - - +
693G MET* 1.3 63.6 + - - +
695G GLU* 3.2 7.9 + - + +
696G CYS* 3.0 33.5 + - - -
705G PRO* 5.0 6.1 - - + -
710G ILE* 4.4 19.3 - - + +
713G SER* 4.3 24.5 - - - +
714G ILE* 3.5 35.2 - - + +
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Residues in contact with MET 693 (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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643G GLY 3.9 11.0 - - - +
646G LEU* 4.0 17.9 - - + +
647G TYR* 3.6 31.0 - - - -
650G MET* 4.0 23.1 - - + -
678G LEU* 4.0 19.5 - - + -
681G VAL* 3.8 26.5 - - + -
685G CYS* 4.7 0.2 - - - -
689G MET 2.8 22.1 + - - +
690G LYS* 3.6 12.6 - - + +
691G ARG 3.2 0.2 - - - -
692G LEU* 1.3 72.0 - - - +
694G ALA* 1.3 58.1 + - - +
696G CYS* 3.2 2.3 + - - +
697G LEU* 2.9 50.2 + - + +
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Residues in contact with ALA 694 (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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678G LEU* 3.9 21.1 - - + +
690G LYS 3.1 10.6 + - - +
691G ARG* 3.0 13.4 + - - +
693G MET* 1.3 78.9 - - - +
695G GLU* 1.3 64.8 + - + +
697G LEU* 3.4 4.8 + - - +
698G LYS* 3.1 28.4 + - + +
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Residues in contact with GLU 695 (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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691G ARG* 3.0 20.7 + - + +
692G LEU* 3.4 12.1 - - + +
694G ALA* 1.3 76.0 - - - +
696G CYS* 1.3 65.3 + - - +
697G LEU 3.1 1.6 - - - -
698G LYS* 3.0 32.9 + - - +
703G GLU* 3.7 18.4 - - - +
704G ARG* 3.4 7.1 - - - +
705G PRO* 3.7 22.7 - - + +
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Residues in contact with CYS 696 (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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639G VAL* 3.5 36.1 - - + +
640G TYR* 3.3 21.6 - - - -
642G PHE* 4.1 13.2 - - - -
643G GLY* 3.8 13.5 - - - -
646G LEU* 4.3 4.5 - - - -
692G LEU* 3.0 33.5 + - - +
693G MET 3.2 2.2 + - - +
695G GLU* 1.3 76.2 - - - +
697G LEU* 1.3 57.9 + - - +
704G ARG* 3.4 14.8 - - - -
705G PRO* 4.3 3.4 - - - -
710G ILE* 3.9 16.6 - - - -
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Residues in contact with LEU 697 (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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640G TYR* 3.3 46.0 - - + +
643G GLY 4.1 11.0 - - - +
644G ILE* 3.7 26.7 - - + +
647G TYR* 5.1 2.9 - - + -
676G PRO* 4.1 18.3 - - + +
678G LEU* 3.8 22.0 - - + -
693G MET* 2.9 39.2 + - + +
694G ALA* 3.7 5.8 - - - +
696G CYS* 1.3 77.2 - - - +
698G LYS* 1.3 67.2 + - - +
699G LYS* 3.4 4.7 + - - +
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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