Contacts of the helix formed by residues 78 - 92 (chain 6) in PDB entry 1MVW
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 78 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686 LYS* 5.4 0.8 - - - +
706 PRO* 3.2 16.9 + - + +
766 ILE* 4.0 2.4 - - - +
776 THR* 1.3 81.3 - - + +
796 TRP* 1.3 63.5 + - - +
806 ASP* 3.3 16.5 + - - +
816 ASP* 3.0 46.0 + - + +
826 MET* 3.1 26.0 + - - +
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Residues in contact with TRP 79 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766 ILE* 3.8 49.1 + - + -
776 THR 4.6 7.3 + - - -
786 ASN* 1.3 73.7 + - - +
806 ASP* 1.3 63.7 + - - +
826 MET* 3.8 4.1 - - + +
836 GLU* 3.3 25.3 + - - +
866 TRP* 4.6 5.2 - + - -
1156 ASN* 3.6 53.4 - - + -
1186 LYS* 3.8 32.0 - - + +
1196 MET* 3.8 22.7 - - + -
1226 ILE* 3.6 23.9 - - + +
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Residues in contact with ASP 80 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376 ARG* 3.3 13.4 + - - -
786 ASN* 3.3 15.2 + - - +
796 TRP* 1.3 76.3 - - - +
816 ASP* 1.3 86.0 + - - +
836 GLU* 3.6 7.7 + - - +
846 LYS* 3.3 38.1 + - - +
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Residues in contact with ASP 81 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356 VAL* 3.4 19.8 - - + +
376 ARG* 2.9 25.7 + - - -
686 LYS* 3.1 32.0 - - - +
706 PRO* 3.4 19.6 - - + +
786 ASN* 3.0 26.7 + - + +
806 ASP* 1.3 90.6 + - - +
826 MET* 1.3 60.8 + - - +
846 LYS* 3.5 9.9 - - - +
856 ILE* 3.3 16.6 + - - +
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Residues in contact with MET 82 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 ASN* 3.5 27.1 - - + +
176 VAL* 5.8 0.7 - - + -
336 SER* 5.3 1.6 - - - +
706 PRO* 3.9 11.0 - - - -
716 ILE* 3.7 36.3 - - + -
766 ILE* 3.8 19.7 - - + -
786 ASN 3.1 17.4 + - - +
796 TRP* 4.0 6.7 - - + +
806 ASP 3.3 0.6 - - - -
816 ASP* 1.3 71.5 - - - +
836 GLU* 1.3 58.1 + - - +
846 LYS 3.0 1.3 - - - -
856 ILE* 2.7 45.1 + - + +
866 TRP* 2.9 44.2 + - + +
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Residues in contact with GLU 83 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 TRP 3.3 17.0 + - - +
806 ASP* 3.8 6.6 - - - +
826 MET* 1.3 76.8 - - - +
846 LYS* 1.3 56.8 + - - +
866 TRP* 3.5 14.2 + - + -
876 HIS* 2.9 32.1 + - + +
1226 ILE* 4.1 20.5 - - + +
1266 THR* 4.2 26.4 + - - +
1276 PHE* 3.7 17.5 - - + -
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Residues in contact with LYS 84 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356 VAL* 4.0 9.4 - - + -
376 ARG* 3.4 34.3 - - - +
516 ASP* 5.2 5.5 + - - +
526 SER* 3.5 26.9 - - - +
546 VAL* 4.4 10.7 - - + +
806 ASP* 3.3 26.1 + - - +
816 ASP* 3.5 24.7 - - - +
826 MET 3.0 0.2 - - - -
836 GLU* 1.3 78.0 - - - +
856 ILE* 1.4 61.7 + - - +
876 HIS* 3.2 7.9 + - + +
886 HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176 VAL* 3.7 28.9 - - + -
316 PHE* 4.2 11.2 - - + -
336 SER* 3.9 26.2 - - - +
346 ILE 4.1 1.1 - - - +
356 VAL* 3.8 12.3 - - + -
546 VAL* 4.0 13.2 - - + -
706 PRO* 3.6 36.1 - - + -
816 ASP 3.3 7.6 + - - +
826 MET* 2.7 28.0 + - + +
846 LYS* 1.4 70.4 - - - +
866 TRP* 1.3 55.3 + - + +
886 HIS* 3.3 3.6 + - - +
896 THR* 2.7 32.8 + - - +
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Residues in contact with TRP 86 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106 CYS* 4.0 17.3 - - - -
126 ASN* 2.9 37.6 + - - +
176 VAL* 6.1 0.2 - - + -
766 ILE* 4.2 10.5 - - + -
796 TRP* 4.6 2.0 - + - -
826 MET* 2.9 39.1 + - + +
836 GLU* 3.8 17.7 - - - +
856 ILE* 1.3 73.7 - - + +
876 HIS* 1.3 59.2 + - - +
896 THR* 2.8 23.9 + - - -
906 PHE* 3.0 27.4 + + + -
1056 LEU* 4.4 5.1 - - + +
1196 MET* 3.9 30.5 - - + -
1226 ILE* 4.1 24.7 - - + -
1236 MET* 3.3 30.2 - - + +
1276 PHE* 3.6 20.0 - + + -
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Residues in contact with HIS 87 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 GLU* 2.9 20.5 + - + +
846 LYS* 3.4 8.1 - - - +
866 TRP* 1.3 76.3 - - - +
886 HIS* 1.3 59.7 + - - +
906 PHE* 4.5 0.7 - - - -
916 TYR* 2.9 64.6 + + + +
926 ASN* 4.6 6.4 + - - -
1276 PHE* 3.9 17.4 - - + -
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Residues in contact with HIS 88 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316 PHE* 3.6 20.5 - + - -
546 VAL* 3.9 37.4 + - + +
556 GLY* 5.2 0.6 - - - -
846 LYS 3.1 9.2 + - - +
856 ILE 3.4 8.5 - - - +
876 HIS* 1.3 80.4 - - - +
896 THR* 1.3 61.9 + - - +
926 ASN* 2.8 55.0 + - + +
936 GLU* 2.9 41.4 + - + +
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Residues in contact with THR 89 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106 CYS* 4.7 9.0 - - + -
176 VAL* 4.5 7.3 - - + +
196 ALA* 3.6 31.0 - - + -
316 PHE* 3.7 20.1 - - + -
856 ILE* 2.7 26.7 + - - +
866 TRP* 2.8 14.7 + - - -
886 HIS* 1.3 76.1 - - - +
906 PHE* 1.3 64.7 + - + -
936 GLU* 3.9 8.3 - - + -
946 LEU* 2.9 37.5 + - + +
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Residues in contact with PHE 90 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 LEU* 4.0 28.7 - - + -
106 CYS* 5.8 5.8 - - + -
866 TRP* 3.0 29.2 + + + +
876 HIS* 4.1 2.2 - - - +
896 THR* 1.3 83.5 - - + +
916 TYR* 1.3 62.0 + + + +
946 LEU* 3.5 4.5 - - + -
956 ARG 2.8 25.6 + - - -
966 VAL* 3.1 23.8 + - + +
986 PRO* 3.9 25.8 - - + -
1036 THR* 4.4 16.8 - - + -
1056 LEU* 6.1 0.7 - - + -
1236 MET* 4.1 23.6 - - + -
1276 PHE* 3.6 45.3 - + - -
1296 VAL* 4.8 1.1 - - + -
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Residues in contact with TYR 91 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876 HIS* 2.9 60.9 + + - +
906 PHE* 1.3 84.0 - - + +
926 ASN* 1.3 71.5 + - - +
956 ARG* 3.4 16.7 - - - +
966 VAL 3.8 11.9 - - - -
976 ALA* 4.6 4.3 - - + -
986 PRO* 3.7 35.7 - - + +
996 GLU* 4.2 11.1 + - - -
1276 PHE* 4.9 9.7 - + - -
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Residues in contact with ASN 92 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876 HIS* 4.2 7.4 + - - +
886 HIS* 2.8 50.6 + - + +
916 TYR* 1.3 92.7 + - - +
936 GLU* 1.3 68.5 + - - +
946 LEU 3.6 0.2 - - - -
956 ARG* 3.3 17.2 - - - +
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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