Contacts of the helix formed by residues 78 - 92 (chain 7) 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 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687 LYS* 5.7 0.8 - - - +
707 PRO* 3.2 16.0 + - + +
767 ILE* 4.0 2.6 - - - +
777 THR* 1.3 80.3 - - + +
797 TRP* 1.3 62.6 + - - +
807 ASP* 3.3 17.2 + - - +
817 ASP* 3.0 45.4 + - + +
827 MET* 3.1 26.5 + - - +
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Residues in contact with TRP 79 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 ILE* 3.8 50.5 + - + -
777 THR 4.6 6.9 + - - -
787 ASN* 1.3 73.7 + - - +
807 ASP* 1.3 61.7 + - - +
817 ASP 3.5 0.2 - - - -
827 MET* 3.8 3.9 - - + +
837 GLU* 3.3 26.3 + - - +
867 TRP* 4.6 5.4 - + - -
1157 ASN* 3.6 53.3 + - + -
1187 LYS* 3.8 31.3 - - + +
1197 MET* 3.8 23.1 - - + -
1227 ILE* 3.6 23.0 - - + +
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Residues in contact with ASP 80 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377 ARG* 3.3 14.6 + - - -
787 ASN* 3.3 14.0 + - - +
797 TRP* 1.3 76.1 - - - +
817 ASP* 1.3 87.5 + - - +
827 MET 3.5 0.2 + - - -
837 GLU* 3.6 8.1 + - - +
847 LYS* 3.3 37.8 + - - +
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Residues in contact with ASP 81 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357 VAL* 3.4 20.0 - - + +
377 ARG* 2.9 26.6 + - - -
687 LYS* 3.1 31.6 - - - +
707 PRO* 3.4 19.8 - - + +
787 ASN* 3.0 27.6 + - + +
807 ASP* 1.3 89.1 + - - +
827 MET* 1.3 61.3 + - - +
847 LYS* 3.5 9.4 - - - +
857 ILE* 3.3 16.6 + - - +
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Residues in contact with MET 82 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127 ASN* 3.5 26.7 - - + +
177 VAL* 5.8 0.4 - - + -
337 SER* 5.3 1.3 - - - +
707 PRO* 3.9 11.4 - - - +
717 ILE* 3.7 37.2 - - + -
767 ILE* 3.8 20.0 - - + -
787 ASN 3.1 16.8 + - - +
797 TRP* 4.0 7.0 - - + +
807 ASP 3.3 0.6 - - - -
817 ASP* 1.3 70.6 - - - +
837 GLU* 1.3 59.1 + - - +
847 LYS 3.0 1.1 - - - -
857 ILE* 2.7 45.8 + - + +
867 TRP* 2.9 45.0 + - + +
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Residues in contact with GLU 83 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797 TRP 3.3 15.7 + - - +
807 ASP* 3.8 7.4 - - - +
827 MET* 1.3 76.5 - - - +
847 LYS* 1.3 57.1 + - - +
867 TRP* 3.9 12.9 - - + -
877 HIS* 2.9 31.8 + - + +
1227 ILE* 4.1 20.6 - - + +
1267 THR* 4.2 26.7 + - - +
1277 PHE* 3.7 16.0 - - + -
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Residues in contact with LYS 84 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357 VAL* 4.0 9.4 - - + -
377 ARG* 3.4 34.5 - - - +
517 ASP* 5.2 5.5 + - - +
527 SER* 3.5 26.0 - - - +
547 VAL* 4.4 10.1 - - + +
807 ASP* 3.3 26.1 + - - +
817 ASP* 3.5 25.8 - - - +
827 MET 3.0 0.2 - - - -
837 GLU* 1.3 78.5 - - - +
857 ILE* 1.4 62.0 + - - +
877 HIS* 3.2 7.9 + - + +
887 HIS* 3.1 22.9 + - - +
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Residues in contact with ILE 85 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 VAL* 3.7 29.2 - - + -
317 PHE* 4.2 11.2 - - + -
337 SER* 3.9 26.9 - - - +
347 ILE 4.1 0.9 - - - +
357 VAL* 3.8 11.9 - - + -
547 VAL* 4.0 13.5 - - + -
707 PRO* 3.6 36.1 - - + -
817 ASP 3.3 7.6 + - - +
827 MET* 2.7 27.5 + - + +
847 LYS* 1.4 70.0 - - - +
867 TRP* 1.3 55.1 + - + +
887 HIS* 3.3 3.8 + - - +
897 THR* 2.7 32.0 + - - +
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Residues in contact with TRP 86 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107 CYS* 4.0 16.7 - - - -
127 ASN* 2.9 37.0 + - - +
177 VAL* 6.1 0.2 - - + -
767 ILE* 4.2 10.8 - - + -
797 TRP* 4.6 1.6 - + - -
827 MET* 2.9 39.5 + - + +
837 GLU* 3.8 17.7 - - - +
857 ILE* 1.3 73.8 - - + +
877 HIS* 1.3 58.9 + - - +
897 THR* 2.8 23.3 + - - -
907 PHE* 3.0 28.6 + + + -
1057 LEU* 4.4 4.2 - - + +
1197 MET* 3.9 30.1 - - + -
1227 ILE* 4.1 24.2 - - + -
1237 MET* 3.3 30.5 - - + +
1277 PHE* 3.6 20.0 - + + -
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Residues in contact with HIS 87 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 GLU* 2.9 19.7 + - + +
847 LYS* 3.4 8.1 - - - +
867 TRP* 1.3 76.9 - - - +
887 HIS* 1.3 61.0 + - - +
907 PHE* 4.5 0.2 - - - -
917 TYR* 2.9 66.3 + + + +
927 ASN* 4.6 6.8 + - - -
1277 PHE* 3.9 17.0 - - + -
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Residues in contact with HIS 88 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317 PHE* 3.6 20.9 - + - -
547 VAL* 3.9 37.6 + - + +
557 GLY* 5.2 0.6 - - - -
847 LYS 3.1 9.4 + - - +
857 ILE 3.4 8.3 - - - +
877 HIS* 1.3 79.1 - - - +
897 THR* 1.3 62.7 + - - +
927 ASN* 2.8 55.0 + - + -
937 GLU* 2.9 41.2 + - + -
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Residues in contact with THR 89 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 CYS* 4.7 9.2 - - + -
177 VAL* 4.5 7.5 - - + +
197 ALA* 3.6 31.2 - - + -
317 PHE* 3.7 20.0 - - + -
857 ILE* 2.7 26.6 + - - +
867 TRP* 2.8 14.3 + - - -
887 HIS* 1.3 76.8 - - - +
907 PHE* 1.3 63.1 + - + -
937 GLU* 3.4 8.6 - - + +
947 LEU* 2.9 36.7 + - + +
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Residues in contact with PHE 90 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87 LEU* 4.0 28.5 - - + -
107 CYS* 5.8 5.8 - - + -
867 TRP* 3.0 27.3 + + + +
877 HIS* 4.1 1.8 - - - +
897 THR* 1.3 83.1 - - + +
917 TYR* 1.3 62.9 + + + +
947 LEU* 3.5 4.3 - - + -
957 ARG 2.8 26.0 + - - -
967 VAL* 3.1 23.9 + - + +
987 PRO* 3.9 27.6 - - + -
1037 THR* 4.4 15.5 - - + -
1057 LEU* 6.1 0.4 - - + -
1237 MET* 4.1 23.8 - - + -
1277 PHE* 3.6 45.3 - + - -
1297 VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877 HIS* 2.9 63.0 + + - +
907 PHE* 1.3 84.2 - - + +
927 ASN* 1.3 71.1 + - - +
957 ARG* 3.4 17.5 - - - +
967 VAL 3.8 12.1 - - - -
977 ALA* 4.6 4.7 - - + -
987 PRO* 3.7 35.6 - - + +
997 GLU* 4.2 11.2 + - - -
1277 PHE* 4.9 9.5 - + - -
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Residues in contact with ASN 92 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877 HIS* 4.2 7.6 + - - +
887 HIS* 2.8 49.9 + - + +
917 TYR* 1.3 93.5 + - - +
937 GLU* 1.3 67.8 + - - +
957 ARG* 3.3 17.5 - - - +
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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