Contacts of the helix formed by residues 600 - 610 (chain A) in PDB entry 2MNG
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 ASP 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A ASN 4.5 5.6 - - - +
599A ALA* 1.3 76.7 - - - +
601A PRO* 1.3 70.3 - - + +
602A ASN* 3.0 11.0 - - + +
603A PHE* 2.8 48.5 + - + -
604A VAL* 3.1 10.0 + - - +
699A MET* 4.3 6.5 - - - +
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Residues in contact with PRO 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A ARG* 3.2 14.7 + - - +
599A ALA 3.8 2.4 - - - +
600A ASP* 1.3 89.1 - - + +
602A ASN* 1.3 60.6 + - - +
604A VAL* 4.3 5.8 - - + -
605A THR* 2.9 36.2 + - - +
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Residues in contact with ASN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ASP* 3.0 10.1 + - + +
601A PRO* 1.3 82.2 - - - +
603A PHE* 1.3 66.2 + - + +
605A THR* 3.9 5.9 - - - -
606A SER* 3.1 24.9 + - - -
695A GLU* 5.3 0.7 - - - +
696A TYR* 5.8 9.4 - - + -
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Residues in contact with PHE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A ALA* 4.3 5.6 - - + -
600A ASP* 2.8 33.2 + - + +
602A ASN* 1.3 82.6 - - + +
604A VAL* 1.3 59.3 + - - +
606A SER* 3.2 1.4 + - - -
607A MET* 2.9 28.3 + - + +
692A VAL* 3.1 52.5 - - + +
693A LEU* 3.9 15.3 - - + -
695A GLU* 4.3 6.3 - - + -
696A TYR* 3.8 34.3 - + + -
698A MET* 6.2 0.9 - - + -
699A MET* 3.5 49.1 - - + -
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Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A ARG* 3.6 41.7 - - + +
590A VAL* 4.2 20.4 - - + -
591A ALA* 5.1 6.1 - - + +
596A PHE* 3.3 28.3 - - + +
599A ALA* 4.2 7.2 - - + +
600A ASP 3.1 12.8 + - - +
601A PRO* 3.8 5.2 - - + +
603A PHE* 1.3 73.8 - - - +
605A THR* 1.3 64.4 + - - +
607A MET* 3.1 11.9 + - - +
608A LEU* 2.9 25.4 + - + +
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Residues in contact with THR 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A ARG* 2.5 38.5 + - - +
601A PRO* 2.9 14.8 + - - +
602A ASN* 3.9 7.9 - - - -
604A VAL* 1.3 75.2 - - - +
606A SER* 1.3 63.6 + - - +
608A LEU* 3.0 9.7 + - + +
609A THR* 3.0 32.1 + - + +
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Residues in contact with SER 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ASN 3.1 13.7 + - - -
603A PHE 3.2 9.9 + - - -
605A THR* 1.3 78.5 - - - +
607A MET* 1.3 61.9 + - - +
609A THR* 2.7 22.9 + - - -
610A LYS* 3.0 21.5 + - - +
692A VAL* 3.7 24.5 - - - -
695A GLU* 4.0 13.4 + - - -
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Residues in contact with MET 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A VAL* 3.9 24.0 - - + -
596A PHE* 3.9 26.9 - - + -
599A ALA* 4.9 3.6 - - + -
603A PHE* 2.9 18.9 + - + +
604A VAL* 3.3 12.3 - - - +
606A SER* 1.3 76.5 - - - +
608A LEU* 1.3 51.9 + - - +
610A LYS* 3.2 3.6 + - - -
611A LEU* 2.7 36.4 + - - +
684A LEU* 3.3 25.1 - - + +
689A PHE* 3.9 27.6 - - + -
692A VAL* 4.0 13.9 - - + -
693A LEU* 3.8 33.9 - - + -
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A ILE* 3.4 18.6 - - + +
586A CYS* 3.7 36.3 - - + +
587A ARG* 3.7 48.2 - - + +
590A VAL* 3.7 19.1 - - + -
604A VAL* 2.9 19.9 + - + +
605A THR* 3.0 8.0 + - + +
607A MET* 1.3 75.5 - - - +
609A THR* 1.3 60.7 + - + +
611A LEU* 3.1 27.7 + - + +
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Residues in contact with THR 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A THR* 3.0 22.4 + - + +
606A SER* 2.7 25.9 + - - -
608A LEU* 1.3 77.2 - - + +
610A LYS* 1.3 63.4 + - - +
611A LEU 3.3 2.2 + - - +
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Residues in contact with LYS 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A SER* 3.0 20.0 + - - +
607A MET* 3.3 5.2 - - - +
609A THR* 1.3 81.9 - - - +
611A LEU* 1.3 62.8 + - - +
612A ARG* 3.4 10.8 + - - +
684A LEU* 4.6 0.4 - - + -
688A ASN* 3.4 41.5 + - + +
691A GLU* 2.8 40.6 + - - +
692A VAL* 3.6 31.2 - - + -
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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