Contacts of the helix formed by residues 947 - 959 (chain A) in PDB entry 1Y5I
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 THR 947 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823A TRP* 3.6 10.2 + - - +
824A GLU* 4.6 5.6 - - - +
827A LYS* 5.8 0.7 - - - +
946A ASN* 1.3 85.0 + - + +
948A ALA* 1.3 65.8 + - - +
949A ILE* 3.4 11.2 + - - +
950A ASP* 3.0 40.0 + - - +
951A ALA* 3.2 10.0 + - - +
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Residues in contact with ALA 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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197A VAL* 4.0 24.1 - - + +
795A ASP* 3.6 33.0 - - + +
796A ASP* 6.0 0.2 - - - -
821A SER* 5.6 4.3 - - - +
823A TRP* 3.7 18.9 - - + -
824A GLU* 5.1 0.8 + - - -
947A THR* 1.3 73.7 - - - +
949A ILE* 1.3 58.5 + - - +
951A ALA* 3.1 4.4 + - - +
952A ALA* 2.8 29.0 + - - +
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Residues in contact with ILE 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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795A ASP* 3.8 25.6 - - + +
947A THR* 3.1 10.1 + - - +
948A ALA* 1.3 79.3 - - - +
950A ASP* 1.3 65.7 + - - +
952A ALA* 3.1 6.4 + - - +
953A GLU* 2.9 35.3 + - + +
996A PHE* 3.7 39.5 - - + -
997A ARG* 4.2 32.3 - - + +
1000A GLN* 5.5 2.2 - - - +
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Residues in contact with ASP 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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930A LEU 4.6 2.3 - - - +
931A ASN* 3.1 52.6 + - - +
944A MET* 3.7 9.8 - - - +
945A LEU* 4.0 7.4 - - - -
946A ASN* 3.2 13.5 + - - +
947A THR* 3.0 40.5 + - - +
949A ILE* 1.3 78.8 - - - +
951A ALA* 1.3 57.1 + - - +
953A GLU* 3.3 1.8 + - - +
954A MET* 3.0 23.9 + - - +
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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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197A VAL* 3.8 26.5 - - + -
592A LEU* 4.0 14.1 - - + +
823A TRP* 4.2 17.0 - - + -
945A LEU* 3.9 9.8 - - + +
947A THR 3.2 8.5 + - - +
948A ALA 3.1 8.7 + - - +
949A ILE 3.1 0.4 - - - -
950A ASP* 1.3 78.4 - - - +
952A ALA* 1.3 65.2 + - - +
954A MET* 3.1 5.8 + - - +
955A ILE* 3.1 24.4 + - - +
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Residues in contact with ALA 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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197A VAL* 3.9 9.6 - - + +
796A ASP* 5.5 2.2 - - - -
797A MET* 3.5 25.3 - - + +
948A ALA 2.8 17.1 + - - +
949A ILE* 3.1 5.1 + - - +
951A ALA* 1.3 78.5 - - - +
953A GLU* 1.3 57.0 + - - +
955A ILE* 3.2 4.5 + - - +
956A LEU* 2.9 32.7 + - - +
996A PHE* 3.8 27.8 - - + -
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Residues in contact with GLU 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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927A LEU* 4.0 5.4 - - + -
930A LEU* 4.9 12.9 - - + +
931A ASN* 4.0 14.4 - - - +
949A ILE* 2.9 31.0 + - + +
950A ASP* 3.7 5.2 - - - +
952A ALA* 1.3 72.8 - - - +
954A MET* 1.3 65.7 + - - +
956A LEU* 3.5 3.8 - - - +
957A THR* 2.8 31.5 + - - +
995A ARG* 2.9 41.7 + - - +
996A PHE* 3.0 31.9 + - + +
997A ARG* 4.0 17.5 + - - +
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Residues in contact with MET 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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588A GLY 4.6 0.9 - - - +
591A PRO* 4.0 9.9 - - + -
592A LEU* 3.5 52.0 - - + +
597A ASP* 4.4 9.6 - - + +
902A ILE* 3.8 45.8 - - + -
906A MET* 5.3 0.2 - - + -
927A LEU* 3.8 11.8 - - - +
945A LEU* 3.9 6.1 - - + -
950A ASP 3.0 13.5 + - - +
951A ALA 3.1 10.3 + - - +
953A GLU* 1.3 76.1 - - - +
955A ILE* 1.3 64.7 + - - +
957A THR* 3.9 0.5 - - - -
958A LEU* 3.0 50.9 + - + +
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Residues in contact with ILE 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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196A MET* 3.9 27.8 - - + -
197A VAL* 4.1 8.3 - - + +
585A PRO* 3.7 29.8 - - + +
588A GLY* 3.7 11.0 - - - +
589A TRP* 3.9 29.4 - - + +
592A LEU* 3.9 23.6 - - + -
797A MET* 3.9 17.0 - - + -
951A ALA 3.1 11.4 + - - +
952A ALA 3.2 5.8 + - - +
954A MET* 1.3 77.4 - - - +
956A LEU* 1.3 64.1 + - - +
959A ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 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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797A MET* 3.7 31.0 - - + -
806A ILE* 3.8 11.0 - - + -
952A ALA 2.9 17.2 + - - +
953A GLU* 3.5 8.7 - - - +
955A ILE* 1.3 77.1 - - + +
957A THR* 1.3 62.9 + - - +
959A ALA 3.9 0.3 + - - -
962A THR* 2.6 57.3 + - + +
963A ASN* 3.9 1.4 - - - +
994A ILE* 3.4 27.8 - - + +
995A ARG* 3.7 9.4 + - - +
996A PHE* 3.3 33.9 - - + +
999A ILE* 4.8 1.1 - - + -
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Residues in contact with THR 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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923A GLU* 3.3 34.1 - - + +
926A LEU* 3.8 25.8 - - + -
927A LEU* 3.8 17.9 - - + +
930A LEU* 4.2 1.4 - - - +
953A GLU 2.8 22.4 + - - -
954A MET 4.1 0.2 - - - -
956A LEU* 1.3 78.8 - - - +
958A LEU* 1.3 59.9 + - - +
963A ASN* 2.9 31.8 + - - +
995A ARG* 2.7 26.2 + - - +
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Residues in contact with LEU 958 (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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588A GLY* 3.8 17.9 - - - +
591A PRO* 4.2 10.8 - - + -
902A ILE* 5.5 1.3 - - + -
906A MET* 4.5 11.0 - - + -
911A ASN* 4.0 15.0 + - - +
918A TRP* 4.6 0.5 + - - -
920A THR* 3.4 35.6 + - + +
923A GLU* 3.9 13.5 - - + -
924A MET* 4.8 6.1 - - - -
927A LEU* 4.3 12.6 - - + -
954A MET* 3.0 52.0 + - + +
957A THR* 1.3 77.9 - - - +
959A ALA* 1.3 62.8 + - - +
960A PRO* 3.8 1.6 - - - +
966A VAL* 3.3 18.2 - - - +
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Residues in contact with ALA 959 (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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585A PRO* 3.3 40.4 - - + +
588A GLY* 3.8 6.9 - - - +
955A ILE 3.1 13.0 + - - +
956A LEU 3.9 0.4 + - - -
957A THR 3.5 0.8 - - - -
958A LEU* 1.3 77.9 - - - +
960A PRO* 1.3 64.9 - - + +
961A GLU* 3.2 10.5 - - - +
962A THR* 3.3 6.3 + - - +
963A ASN* 3.0 31.2 + - - +
966A VAL* 4.1 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