Contacts of the helix formed by residues 686 - 697 (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 PRO 686 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550C MET* 4.1 15.9 - - + -
554C ILE* 4.5 7.9 - - + -
684C ASN 3.3 9.9 - - - +
685C CYS* 1.3 91.2 - - + +
687C LYS* 1.3 65.0 + - - +
688C ALA 4.1 6.1 - - - +
689C MET* 3.0 17.3 + - + +
690C LYS* 3.1 11.1 + - - +
717C LEU* 3.9 37.7 - - + -
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Residues in contact with LYS 687 (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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685C CYS 3.6 7.3 + - - +
686C PRO* 1.3 72.0 - - - +
688C ALA* 1.3 56.9 + - - +
690C LYS* 3.4 13.5 + - + +
691C ARG* 2.9 44.3 + - - +
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Residues in contact with ALA 688 (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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686C PRO* 3.0 1.4 - - + +
687C LYS* 1.3 76.8 - - - +
689C MET* 1.3 62.0 + - - +
691C ARG* 3.7 25.5 + - - +
692C LEU* 3.2 24.6 + - - +
713C SER* 5.9 1.4 - - - -
717C LEU* 3.8 32.8 - - + -
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Residues in contact with MET 689 (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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554C ILE* 3.9 32.8 - - + -
557C ALA* 4.5 8.3 - - + -
646C LEU* 4.2 23.3 - - - -
650C MET* 3.6 41.1 - - + -
685C CYS* 3.8 11.9 - - - -
686C PRO* 3.0 21.6 + - + +
688C ALA* 1.3 76.1 - - - +
690C LYS* 1.3 56.4 + - - +
692C LEU* 2.9 15.7 + - - +
693C MET* 2.9 34.5 + - + +
714C ILE* 4.6 9.0 - - + -
717C LEU* 4.5 10.0 - - + +
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Residues in contact with LYS 690 (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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678C LEU* 3.9 32.0 + - + +
679C SER* 5.7 2.0 - - - +
681C VAL* 3.8 37.5 - - + +
685C CYS* 4.0 9.1 - - - +
686C PRO 3.1 8.5 + - - +
687C LYS* 3.5 16.8 - - + +
689C MET* 1.3 79.0 - - - +
691C ARG* 1.3 60.9 + - - +
693C MET* 3.4 14.3 + - + +
694C ALA* 3.1 20.4 + - - +
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Residues in contact with ARG 691 (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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687C LYS* 2.9 41.5 + - - +
688C ALA* 3.7 22.6 + - - +
689C MET 3.2 0.2 - - - -
690C LYS* 1.3 76.3 - - - +
692C LEU* 1.3 62.5 + - - +
694C ALA* 3.1 10.6 + - + +
695C GLU* 3.0 41.1 + - + +
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Residues in contact with LEU 692 (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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646C LEU* 4.1 13.7 - - + -
688C ALA 3.2 11.9 + - - +
689C MET* 2.9 15.9 + - - +
691C ARG* 1.3 75.9 - - - +
693C MET* 1.3 67.1 + - - +
695C GLU* 3.4 6.5 + - + +
696C CYS* 3.1 44.3 + - - -
705C PRO* 4.4 9.2 - - + -
710C ILE* 4.0 25.1 - - + -
713C SER* 4.1 21.8 - - - +
714C ILE* 3.5 33.4 - - + -
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Residues in contact with MET 693 (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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643C GLY 4.1 12.6 - - - +
646C LEU* 4.0 19.0 - - + +
647C TYR* 3.9 29.4 - - - -
650C MET* 3.8 35.4 - - + -
678C LEU* 4.9 10.1 - - + -
681C VAL* 4.4 15.9 - - + -
685C CYS* 4.7 0.9 - - - -
689C MET* 2.9 9.4 + - + +
690C LYS* 3.5 22.9 - - - +
692C LEU* 1.3 77.4 - - - +
694C ALA* 1.3 63.3 + - - +
696C CYS* 3.2 4.2 + - - +
697C LEU* 3.0 46.5 + - + +
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Residues in contact with ALA 694 (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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678C LEU* 4.6 16.2 - - + +
690C LYS 3.1 9.2 + - - +
691C ARG* 3.1 14.5 + - + +
693C MET* 1.3 79.3 - - - +
695C GLU* 1.3 68.8 + - - +
697C LEU* 3.1 15.6 + - - +
698C LYS* 3.3 20.4 + - - +
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Residues in contact with GLU 695 (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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691C ARG* 3.0 31.0 + - + +
692C LEU* 3.4 10.1 + - + +
693C MET 3.4 0.2 - - - -
694C ALA* 1.3 78.0 - - - +
696C CYS* 1.3 60.4 + - - +
697C LEU 3.5 0.2 + - - -
698C LYS* 3.6 33.2 + - - +
703C GLU 4.2 4.3 - - - +
704C ARG* 3.4 14.4 - - - +
705C PRO* 3.2 31.1 - - + +
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Residues in contact with CYS 696 (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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639C VAL* 3.9 14.4 - - - +
640C TYR* 3.5 13.0 + - - -
642C PHE* 4.3 11.0 - - - -
643C GLY* 3.8 19.3 - - - -
646C LEU* 4.7 2.2 - - - -
692C LEU* 3.1 45.7 + - - +
693C MET 3.6 4.5 - - - +
695C GLU* 1.3 77.6 - - - +
697C LEU* 1.3 58.4 + - - +
698C LYS 3.3 0.9 - - - -
704C ARG* 3.1 22.0 - - - -
705C PRO* 4.2 2.9 - - - -
710C ILE* 3.9 24.9 - - - -
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Residues in contact with LEU 697 (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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640C TYR* 3.5 30.3 - - + +
643C GLY* 3.7 10.3 - - - +
644C ILE* 3.6 42.0 - - + +
647C TYR* 5.0 2.2 - - + -
675C SER* 6.1 0.4 - - - +
676C PRO* 4.1 26.6 - - + +
678C LEU* 5.0 9.4 - - + -
693C MET* 3.0 40.4 + - + +
694C ALA* 3.1 7.1 + - - +
696C CYS* 1.3 76.0 - - - +
698C LYS* 1.3 66.8 + - - +
699C LYS* 3.4 6.2 + - - +
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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