Contacts of the helix formed by residues 947 - 957 (chain A) in PDB entry 3MP6
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 ASP 947 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888A ASN* 3.3 13.0 - - - +
890A GLN* 3.6 18.6 - - + -
945A ASP 3.3 3.5 + - - +
946A THR* 1.3 75.0 - - - +
948A TYR* 1.3 67.0 + - - +
949A SER* 3.3 8.9 + - - -
950A ILE* 2.9 38.2 + - - +
951A ALA* 3.1 24.3 + - - +
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Residues in contact with TYR 948 (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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752A ASP* 4.7 14.7 - - + +
888A ASN* 3.3 22.6 - - + +
894A PHE* 3.9 23.3 - + - -
947A ASP* 1.3 77.0 - - - +
949A SER* 1.3 62.5 + - - +
951A ALA* 4.0 2.7 - - - +
952A GLU* 3.0 56.5 + - + +
965A ASN* 3.3 36.7 + - - -
968A TRP* 3.0 33.0 + + - -
969A ALA* 3.7 6.9 - - - +
1B GLC 5.9 0.4 - - - -
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Residues in contact with SER 949 (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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947A ASP* 3.3 11.0 + - - -
948A TYR* 1.3 84.1 - - - +
950A ILE* 1.3 60.2 + - - +
952A GLU* 3.8 7.4 - - - +
953A ALA* 2.9 31.5 + - - +
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Residues in contact with ILE 950 (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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886A MET* 3.7 21.5 - - + -
945A ASP* 4.0 17.9 - - + +
946A THR* 4.0 9.2 - - + +
947A ASP* 2.9 32.5 + - - +
949A SER* 1.3 76.3 - - - +
951A ALA* 1.3 58.8 + - - +
953A ALA* 3.4 5.0 + - - +
954A ALA* 3.0 29.2 + - + +
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Residues in contact with ALA 951 (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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886A MET* 3.7 18.0 - - - +
887A PHE* 3.6 32.8 - - - +
888A ASN 4.1 1.3 - - - +
946A THR* 3.8 6.7 - - + +
947A ASP 3.1 18.6 + - - +
948A TYR* 4.0 2.5 - - - +
950A ILE* 1.3 77.5 - - - +
952A GLU* 1.3 62.4 + - - +
954A ALA* 3.4 1.7 + - - +
955A PHE* 3.0 25.6 + - - +
960A THR* 4.6 0.9 - - - +
963A THR* 4.3 7.2 + - - +
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Residues in contact with GLU 952 (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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948A TYR* 3.0 47.9 + - + +
949A SER* 3.8 7.0 + - - +
951A ALA* 1.3 77.7 - - - +
953A ALA* 1.3 57.7 + - - +
955A PHE* 4.9 2.5 - - - -
956A ASN* 2.9 52.0 + - + +
963A THR* 5.6 2.2 - - - -
965A ASN* 5.3 6.7 - - - +
969A ALA* 4.7 8.5 - - + +
972A ASN* 2.9 36.6 + - - +
973A ILE* 6.3 0.2 - - + -
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Residues in contact with ALA 953 (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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949A SER 2.9 18.8 + - - +
950A ILE* 3.8 5.2 - - - +
952A GLU* 1.3 77.1 - - - +
954A ALA* 1.3 57.9 + - - +
956A ASN* 3.4 3.9 + - - -
957A LYS* 2.9 57.7 + - - +
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Residues in contact with ALA 954 (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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886A MET* 3.4 33.9 - - + -
950A ILE* 3.0 16.3 + - + +
951A ALA 3.8 2.5 - - - +
953A ALA* 1.3 76.7 - - - +
955A PHE* 1.3 59.9 + - - +
957A LYS* 3.5 0.5 + - - +
958A GLY 3.2 2.9 + - - -
959A GLU* 2.9 53.3 + - + +
960A THR* 3.5 5.8 + - + -
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Residues in contact with PHE 955 (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* 3.8 31.0 - - + -
855A TYR 3.6 20.6 - - - -
856A ASN* 3.6 6.0 + - + -
951A ALA 3.0 17.7 + - - +
952A GLU* 4.0 1.1 - - - +
954A ALA* 1.3 76.9 - - - +
956A ASN* 1.3 75.7 + - - +
958A GLY* 3.0 16.8 + - - -
960A THR* 3.5 23.3 - - + +
961A ALA 3.5 23.6 - - - -
962A MET 3.8 15.7 - - - -
963A THR* 3.7 17.7 - - + -
973A ILE* 3.8 20.9 - - + -
978A VAL* 3.4 23.6 - - + +
980A TYR* 4.2 1.1 - - + -
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Residues in contact with ASN 956 (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* 2.9 37.6 + - - +
953A ALA* 4.2 4.3 - - - +
955A PHE* 1.3 96.8 - - - +
957A LYS* 1.3 61.0 + - + +
958A GLY 3.4 0.2 - - - -
963A THR* 5.9 0.2 - - - +
972A ASN* 3.7 24.3 - - - +
973A ILE* 3.5 25.1 + - - +
976A SER* 3.3 26.5 - - - -
977A LYS* 4.5 1.7 + - - +
978A VAL* 3.5 12.2 - - - +
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Residues in contact with LYS 957 (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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882A LYS* 5.1 1.7 + - - -
953A ALA* 2.9 44.0 + - - +
954A ALA 4.2 2.2 - - - +
956A ASN* 1.3 81.0 - - + +
958A GLY* 1.3 59.9 + - - +
959A GLU* 3.3 28.3 + - - +
978A VAL* 4.8 0.9 - - - -
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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