Contacts of the helix formed by residues 78 - 92 (chain 5) 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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685 LYS* 5.4 1.2 - - - +
705 PRO* 3.2 17.2 + - + +
765 ILE* 4.0 2.6 - - - +
775 THR* 1.3 80.1 - - + +
795 TRP* 1.3 62.7 + - - +
805 ASP* 3.3 17.4 + - - +
815 ASP* 3.0 45.2 + - + +
825 MET* 3.1 25.6 + - - +
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Residues in contact with TRP 79 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765 ILE* 3.8 50.0 + - + -
775 THR 4.6 7.7 + - - -
785 ASN* 1.3 73.1 + - - +
805 ASP* 1.3 62.2 + - - +
825 MET* 3.8 4.1 - - + +
835 GLU* 3.3 25.6 + - - +
865 TRP* 4.6 6.3 - + - -
1155 ASN* 3.6 53.5 + - + -
1185 LYS* 3.8 31.1 - - + +
1195 MET* 3.8 22.7 - - + -
1225 ILE* 3.6 23.7 - - + +
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Residues in contact with ASP 80 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 ARG* 3.3 13.9 + - - -
785 ASN* 3.3 15.7 + - - +
795 TRP* 1.3 76.7 - - - +
815 ASP* 1.3 85.3 + - - +
835 GLU* 3.6 7.6 + - - +
845 LYS* 3.3 37.5 + - - +
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Residues in contact with ASP 81 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 VAL* 3.4 19.3 - - + +
375 ARG* 2.9 27.0 + - - -
685 LYS* 3.1 32.0 - - - +
705 PRO* 3.4 19.1 - - + +
785 ASN* 3.0 27.8 + - - +
805 ASP* 1.3 89.9 + - - +
825 MET* 1.3 61.6 + - - +
845 LYS* 3.5 10.7 - - - +
855 ILE* 3.3 17.0 + - - +
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Residues in contact with MET 82 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125 ASN* 3.5 26.2 - - + +
175 VAL* 5.8 0.7 - - + -
335 SER* 5.3 1.6 - - - +
705 PRO* 3.9 10.5 - - - -
715 ILE* 3.7 36.3 - - + -
765 ILE* 3.8 20.4 - - + -
785 ASN 3.1 16.8 + - - +
795 TRP* 4.0 6.1 - - + +
805 ASP 3.3 0.6 - - - -
815 ASP* 1.3 70.5 - - - +
835 GLU* 1.3 59.0 + - - +
845 LYS 3.0 1.1 - - - -
855 ILE* 2.7 44.8 + - + +
865 TRP* 2.9 46.6 + - + +
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Residues in contact with GLU 83 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 TRP 3.3 16.2 + - - +
805 ASP* 3.8 7.3 - - - +
815 ASP 3.5 0.2 - - - -
825 MET* 1.3 75.6 - - - +
845 LYS* 1.3 57.5 + - - +
865 TRP* 3.9 12.9 - - + -
875 HIS* 2.9 31.2 + - + +
1225 ILE* 4.1 19.9 - - + +
1265 THR* 4.2 27.9 + - - +
1275 PHE* 3.7 17.1 - - + -
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Residues in contact with LYS 84 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355 VAL* 4.0 10.5 - - + -
375 ARG* 3.4 34.7 - - - +
515 ASP* 5.2 5.9 + - - +
525 SER* 3.5 26.2 - - - +
545 VAL* 4.4 9.9 - - + +
805 ASP* 3.3 26.5 + - - +
815 ASP* 3.5 25.4 - - - +
825 MET 3.0 0.2 - - - -
835 GLU* 1.3 78.7 - - - +
855 ILE* 1.4 61.6 + - - +
875 HIS* 3.2 8.0 + - - +
885 HIS* 3.1 22.3 + - - +
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Residues in contact with ILE 85 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 VAL* 3.7 30.1 - - + -
315 PHE* 4.2 10.7 - - + -
335 SER* 3.9 27.1 - - - +
345 ILE 4.1 0.9 - - - +
355 VAL* 3.8 12.3 - - + -
545 VAL* 4.0 12.8 - - + -
705 PRO* 3.6 36.3 - - + -
815 ASP 3.3 7.6 + - - +
825 MET* 2.7 26.7 + - + +
845 LYS* 1.4 71.0 - - - +
865 TRP* 1.3 55.3 + - + +
885 HIS* 3.3 3.8 + - - +
895 THR* 2.7 32.6 + - - +
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Residues in contact with TRP 86 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 CYS* 4.0 16.0 - - - -
125 ASN* 2.9 37.8 + - - +
175 VAL* 6.1 0.2 - - + -
765 ILE* 4.2 10.3 - - + -
795 TRP* 4.6 1.8 - + - -
825 MET* 2.9 37.5 + - + +
835 GLU* 3.8 17.9 - - - +
855 ILE* 1.3 75.5 - - + +
875 HIS* 1.3 60.4 + - - +
895 THR* 2.8 24.1 + - - -
905 PHE* 3.0 26.7 + + + -
1055 LEU* 4.4 4.7 - - + +
1195 MET* 3.9 30.1 - - + -
1225 ILE* 4.1 24.9 - - + -
1235 MET* 3.3 29.8 - - + +
1275 PHE* 3.6 20.2 - + + -
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Residues in contact with HIS 87 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835 GLU* 2.9 19.0 + - + +
845 LYS* 3.2 9.4 + - + +
865 TRP* 1.3 76.5 - - - +
885 HIS* 1.3 60.0 + - - +
905 PHE* 4.5 0.4 - - - -
915 TYR* 2.9 65.3 + + + +
925 ASN* 4.6 6.1 + - - -
1275 PHE* 3.9 17.2 - - + -
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Residues in contact with HIS 88 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 PHE* 3.6 20.9 - + - -
545 VAL* 3.9 38.9 + - + +
555 GLY* 5.2 0.6 - - - -
845 LYS 3.1 9.4 + - - +
855 ILE 3.4 8.5 - - - +
875 HIS* 1.3 80.6 - - - +
895 THR* 1.3 62.5 + - - +
925 ASN* 2.8 54.4 + - + +
935 GLU* 2.9 42.4 + - + +
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Residues in contact with THR 89 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 CYS* 4.7 9.6 - - + -
175 VAL* 4.5 7.1 - - + +
195 ALA* 3.6 31.2 - - + -
315 PHE* 3.7 19.9 - - + -
855 ILE* 2.7 27.1 + - - +
865 TRP* 2.8 14.1 + - - -
885 HIS* 1.3 76.6 - - - +
905 PHE* 1.3 62.8 + - + -
935 GLU* 3.4 7.8 - - + +
945 LEU* 2.9 36.9 + - + +
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Residues in contact with PHE 90 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85 LEU* 4.0 27.8 - - + -
105 CYS* 5.8 6.3 - - + -
865 TRP* 3.0 28.8 + + + +
875 HIS* 4.1 2.2 - - - +
895 THR* 1.3 82.7 - - + +
915 TYR* 1.3 63.7 + + + +
945 LEU* 3.5 4.5 - - + -
955 ARG 2.8 26.5 + - - -
965 VAL* 3.1 23.6 + - + +
985 PRO* 3.9 26.5 - - + -
1035 THR* 4.4 16.4 - - + -
1055 LEU* 6.1 0.4 - - + -
1235 MET* 4.1 24.2 - - + -
1275 PHE* 3.6 44.2 - + - -
1295 VAL* 4.8 1.1 - - + -
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Residues in contact with TYR 91 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875 HIS* 2.9 62.1 + + - +
905 PHE* 1.3 82.0 - - + +
925 ASN* 1.3 71.8 + - - +
955 ARG* 3.4 16.5 - - - +
965 VAL 3.8 12.3 - - - -
975 ALA* 4.6 5.2 - - + -
985 PRO* 3.7 35.4 - - + +
995 GLU* 4.1 10.5 + - - -
1275 PHE* 4.9 9.3 + + - -
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Residues in contact with ASN 92 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875 HIS* 4.2 7.1 + - - +
885 HIS* 2.8 49.8 + - + +
915 TYR* 1.3 93.5 + - - +
935 GLU* 1.3 69.3 + - - +
955 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