Contacts of the helix formed by residues 78 - 92 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689 LYS* 5.7 0.8 - - - +
709 PRO* 3.2 16.7 + - + +
769 ILE* 4.1 2.5 - - - -
779 THR* 1.3 80.3 - - + +
799 TRP* 1.3 63.2 + - - +
809 ASP* 3.3 17.0 + - - +
819 ASP* 3.0 45.9 + - + +
829 MET* 3.1 26.0 + - - +
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Residues in contact with TRP 79 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769 ILE* 3.8 48.7 + - + -
779 THR 4.6 6.6 + - - -
789 ASN* 1.3 73.1 + - - +
809 ASP* 1.3 61.2 + - - +
829 MET* 3.8 3.5 - - + +
839 GLU* 3.3 25.5 + - - +
869 TRP* 4.6 5.2 - + - -
1159 ASN* 3.6 52.4 + - + -
1189 LYS* 3.8 32.4 - - + +
1199 MET* 3.8 23.1 - - + -
1229 ILE* 3.6 24.7 - - + +
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Residues in contact with ASP 80 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379 ARG* 3.3 14.0 + - - -
789 ASN* 3.3 16.6 + - - +
799 TRP* 1.3 75.5 - - - +
819 ASP* 1.3 86.4 + - - +
829 MET 3.5 0.2 + - - -
839 GLU* 3.6 7.3 + - - +
849 LYS* 3.3 37.2 + - - +
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Residues in contact with ASP 81 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 VAL* 3.4 19.1 - - + +
379 ARG* 2.9 26.8 + - - -
689 LYS* 3.1 33.0 - - - +
709 PRO* 3.4 19.6 - - + +
789 ASN* 3.0 27.0 + - + +
799 TRP 3.5 0.2 - - - -
809 ASP* 1.3 89.5 + - - +
829 MET* 1.3 61.8 + - - +
849 LYS* 3.5 9.6 - - - +
859 ILE* 3.3 16.8 + - - +
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Residues in contact with MET 82 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 ASN* 3.5 26.5 - - + +
179 VAL* 5.8 0.7 - - + -
339 SER* 5.3 1.6 - - - +
709 PRO* 3.9 10.5 - - - -
719 ILE* 3.7 36.6 - - + -
769 ILE* 3.8 19.5 - - + -
789 ASN 3.1 17.4 + - - +
799 TRP* 3.6 6.7 + - + +
809 ASP 3.3 0.6 - - - -
819 ASP* 1.3 71.2 - - - +
839 GLU* 1.3 59.4 + - - +
849 LYS 3.0 1.3 - - - -
859 ILE* 2.7 44.9 + - + +
869 TRP* 2.9 43.8 + - + +
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Residues in contact with GLU 83 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799 TRP 3.3 17.0 + - - +
809 ASP* 3.8 7.9 - - - +
829 MET* 1.3 75.5 - - - +
849 LYS* 1.3 57.1 + - - +
869 TRP* 3.9 14.0 - - + -
879 HIS* 2.9 31.8 + - + +
1229 ILE* 4.1 19.8 - - + +
1269 THR* 4.2 27.2 + - - +
1279 PHE* 3.7 15.9 - - + -
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Residues in contact with LYS 84 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359 VAL* 4.0 10.3 - - + -
379 ARG* 3.4 34.2 - - - +
519 ASP* 5.2 6.2 + - - +
529 SER* 3.5 26.2 - - - +
549 VAL* 4.4 10.5 - - + +
809 ASP* 3.3 25.9 + - - +
819 ASP* 3.5 26.2 - - - +
829 MET 3.0 0.2 - - - -
839 GLU* 1.3 78.2 - - - +
859 ILE* 1.4 61.8 + - - +
879 HIS* 3.2 7.3 + - + +
889 HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179 VAL* 3.7 28.5 - - + -
319 PHE* 4.2 11.3 - - + -
339 SER* 3.9 27.4 - - - +
349 ILE 4.1 0.9 - - - +
359 VAL* 3.8 12.8 - - + -
549 VAL* 4.0 12.8 - - + -
709 PRO* 3.6 36.1 - - + -
819 ASP 3.5 7.6 - - - +
829 MET* 2.7 29.5 + - + +
849 LYS* 1.4 70.1 - - - +
869 TRP* 1.3 55.5 + - + +
889 HIS* 3.3 4.2 + - - +
899 THR* 2.7 32.0 + - - +
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Residues in contact with TRP 86 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109 CYS* 4.0 16.7 - - - -
129 ASN* 2.9 37.8 + - - +
179 VAL* 6.1 0.2 - - + -
769 ILE* 4.2 10.5 - - + -
799 TRP* 4.6 1.8 - + - -
829 MET* 2.9 40.2 + - + +
839 GLU* 3.8 18.2 - - - +
859 ILE* 1.3 74.0 - - + +
879 HIS* 1.3 59.6 + - - +
899 THR* 2.8 23.1 + - - -
909 PHE* 3.0 27.9 + + + -
1059 LEU* 4.4 4.0 - - + +
1199 MET* 3.9 30.1 - - + -
1229 ILE* 4.1 25.1 - - + -
1239 MET* 3.3 28.2 - - + +
1279 PHE* 3.6 20.4 - + + -
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Residues in contact with HIS 87 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839 GLU* 2.9 19.3 + - + +
849 LYS* 3.4 8.7 - - + +
869 TRP* 1.3 77.9 - - - +
889 HIS* 1.3 59.5 + - - +
909 PHE* 3.4 1.1 + - - -
919 TYR* 2.9 64.8 + + + +
929 ASN* 4.6 6.3 + - - -
1279 PHE* 3.9 17.2 - - + -
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Residues in contact with HIS 88 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319 PHE* 3.6 20.9 - + - -
549 VAL* 3.9 38.9 + - + +
559 GLY* 5.2 0.4 - - - -
569 ASP 5.9 0.2 + - - -
849 LYS 3.1 9.0 + - - +
859 ILE 3.4 8.7 - - - +
879 HIS* 1.3 79.1 - - - +
899 THR* 1.3 61.7 + - - +
929 ASN* 2.8 54.2 + - + -
939 GLU* 2.9 40.5 + - + +
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Residues in contact with THR 89 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109 CYS* 4.7 9.2 - - + -
179 VAL* 4.5 7.5 - - + +
199 ALA* 3.6 31.2 - - + -
319 PHE* 3.7 19.8 - - + -
859 ILE* 2.7 26.4 + - - +
869 TRP* 2.8 16.1 + - - -
889 HIS* 1.3 76.7 - - - +
909 PHE* 1.3 63.1 + - + -
939 GLU* 3.9 8.3 - - + -
949 LEU* 2.9 37.0 + - + +
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Residues in contact with PHE 90 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89 LEU* 4.0 28.3 - - + -
109 CYS* 5.8 5.2 - - + -
869 TRP* 3.0 28.9 + + + +
879 HIS* 4.1 2.0 - - - +
899 THR* 1.3 83.4 - - + +
919 TYR* 1.3 62.8 + + + +
949 LEU* 3.5 3.8 - - + -
959 ARG 2.8 26.3 + - - -
969 VAL* 3.1 24.9 + - + +
989 PRO* 3.9 27.6 - - + -
1039 THR* 4.4 16.6 - - + -
1059 LEU* 6.1 0.7 - - + -
1239 MET* 4.1 24.0 - - + -
1279 PHE* 3.6 44.6 - + - -
1299 VAL* 4.8 1.3 - - + -
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Residues in contact with TYR 91 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879 HIS* 2.9 60.7 + + - +
909 PHE* 1.3 83.3 - - + +
929 ASN* 1.3 71.7 + - - +
959 ARG* 3.4 16.3 - - - +
969 VAL 3.8 12.6 - - - -
979 ALA* 4.6 4.3 - - + -
989 PRO* 3.7 35.8 - - + +
999 GLU* 4.2 10.1 + - - -
1279 PHE* 4.9 9.2 + + - -
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Residues in contact with ASN 92 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879 HIS* 4.2 7.3 + - - +
889 HIS* 2.8 50.5 + - + +
919 TYR* 1.3 92.7 + - - +
939 GLU* 1.3 69.2 + - - +
949 LEU 3.6 0.2 - - - -
959 ARG* 3.3 17.6 + - - +
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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