Contacts of the helix formed by residues 969 - 976 (chain A) in PDB entry 3MP1
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 ALA 969 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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948A TYR* 3.9 7.4 - - - +
952A GLU* 4.8 8.8 - - + +
965A ASN* 3.4 35.7 - - + +
966A GLY 3.2 11.8 + - - +
967A PRO 2.9 1.8 + - - -
968A TRP* 1.3 77.6 - - - +
970A TRP* 1.3 67.2 + - + +
971A SER 3.2 3.4 + - - -
972A ASN* 3.4 13.9 + - - +
973A ILE* 3.4 20.6 + - + +
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Residues in contact with TRP 970 (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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852A SER* 5.5 1.3 - - - -
854A ILE* 4.1 18.3 - - + +
965A ASN 5.4 0.4 + - - -
966A GLY 3.7 13.6 + - - -
967A PRO* 3.0 37.3 + - + +
969A ALA* 1.3 75.7 - - - +
971A SER* 1.3 64.3 + - - +
972A ASN 3.3 0.2 - - - -
973A ILE* 3.2 13.7 + - + +
974A ASP* 2.8 30.4 + - - +
980A TYR* 3.9 9.4 - + - +
982A VAL* 4.1 19.8 - - + +
1036A PRO* 3.9 18.6 - - + -
1052A ASP* 5.7 0.4 - - - -
1054A ARG* 3.2 68.6 - - + +
1055A ILE* 4.1 18.8 - - + -
1058A THR* 3.5 24.7 - - - -
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Residues in contact with SER 971 (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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968A TRP 4.6 0.7 - - - -
969A ALA 3.2 0.4 - - - -
970A TRP* 1.3 80.4 - - - +
972A ASN* 1.3 62.4 + - - +
974A ASP* 3.5 9.9 + - - +
975A THR* 3.3 22.6 + - - -
1033A LYS 4.2 2.6 + - - -
1034A ASP 2.4 30.8 + - - -
1035A LYS* 3.9 21.7 + - - -
1036A PRO* 3.8 17.6 - - - +
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Residues in contact with ASN 972 (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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952A GLU* 2.7 30.6 + - - +
956A ASN* 3.8 18.3 - - - +
968A TRP 5.7 0.2 + - - -
969A ALA* 3.4 8.4 + - - +
970A TRP 3.3 0.4 - - - -
971A SER* 1.3 74.4 - - - +
973A ILE* 1.3 66.8 + - + +
975A THR* 3.3 12.3 + - - +
976A SER* 3.2 20.3 + - - -
1035A LYS* 3.9 26.1 + - - +
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Residues in contact with ILE 973 (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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854A ILE* 3.9 31.6 - - + -
955A PHE* 4.1 18.6 - - + -
956A ASN* 3.8 18.2 - - - +
963A THR* 5.7 0.7 - - + -
969A ALA* 3.4 21.5 - - + +
970A TRP* 3.2 20.1 + - + +
972A ASN* 1.3 75.6 - - - +
974A ASP* 1.3 63.3 + - - +
976A SER* 2.6 31.8 + - - +
978A VAL* 4.3 10.3 - - + +
980A TYR* 3.1 34.8 - - + -
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Residues in contact with ASP 974 (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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970A TRP 2.8 19.6 + - - +
971A SER* 3.7 9.7 - - - +
972A ASN 3.3 0.2 - - - -
973A ILE* 1.3 75.1 - - - +
975A THR* 1.3 61.8 + - - +
976A SER 3.1 9.9 - - - +
978A VAL 5.8 0.2 - - - -
980A TYR* 2.4 32.8 + - - -
1036A PRO* 5.5 1.6 - - - +
1054A ARG* 4.0 9.6 + - - -
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Residues in contact with THR 975 (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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971A SER 3.3 11.9 + - - -
972A ASN* 3.3 17.1 + - - +
974A ASP* 1.3 78.9 - - - +
976A SER* 1.3 61.4 + - - +
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Residues in contact with SER 976 (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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956A ASN* 3.5 29.3 + - - -
972A ASN 3.2 10.2 + - - -
973A ILE* 2.6 25.9 + - - +
974A ASP 3.1 13.0 - - - +
975A THR* 1.3 80.6 - - - +
977A LYS* 1.3 67.0 + - - +
978A VAL* 3.3 14.6 + - - +
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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