Contacts of the helix formed by residues 944 - 954 (chain A) in PDB entry 4AY6
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 ARG 944 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A GLU* 2.7 32.1 + - - +
673A THR* 3.2 26.4 + - + +
675A PRO* 3.9 20.5 - - - +
678A VAL* 5.9 0.9 - - - -
918A ASN* 3.5 1.8 - - - -
937A PRO* 4.1 21.9 + - + +
938A GLY 2.9 34.6 + - - +
939A GLU 3.4 16.6 - - - -
940A THR 3.3 10.3 - - - +
941A LEU 2.7 9.6 + - - +
943A SER* 1.3 81.3 - - - +
945A VAL* 1.3 63.7 + - - +
946A ALA 3.4 2.9 - - - -
947A ALA* 3.1 17.9 + - - +
948A SER* 3.2 11.1 + - - -
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Residues in contact with VAL 945 (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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673A THR* 3.9 11.6 - - + +
693A PHE* 3.9 14.6 - - + -
694A PHE* 4.2 15.9 - - + -
918A ASN* 3.6 1.0 + - - -
919A GLY 4.4 1.1 - - - +
920A HIS* 3.9 37.2 - - + +
941A LEU* 3.2 31.7 + - + +
942A ALA 4.2 0.6 + - - -
944A ARG* 1.3 74.6 - - - +
946A ALA* 1.3 64.4 + - - +
948A SER* 3.0 7.5 + - - +
949A GLN* 2.9 43.6 + - + +
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Residues in contact with ALA 946 (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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913A ASP* 3.6 22.7 - - - +
918A ASN* 3.1 23.5 + - + +
919A GLY 4.4 4.0 - - - +
933A MET* 4.1 14.7 - - - +
935A THR* 3.8 10.1 - - - +
945A VAL* 1.3 77.5 - - - +
947A ALA* 1.3 62.1 + - - +
949A GLN* 3.1 14.9 + - - +
950A LEU* 3.0 28.6 + - - +
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Residues in contact with ALA 947 (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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672A GLU* 5.2 4.9 - - + +
918A ASN* 4.1 1.0 + - - -
935A THR* 3.8 16.4 - - + +
937A PRO* 3.8 31.2 - - + -
944A ARG* 3.1 12.6 + - + +
946A ALA* 1.3 76.8 - - - +
948A SER* 1.3 59.6 + - - +
950A LEU 3.1 1.4 + - - -
951A THR* 2.9 32.1 + - - -
959A ILE* 3.5 16.6 - - + +
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Residues in contact with SER 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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670A ASP* 3.4 3.6 + - - -
672A GLU* 3.8 22.0 - - - +
673A THR* 3.2 25.1 + - - -
691A HIS 4.5 1.9 + - - +
692A THR* 2.6 33.6 + - - -
693A PHE* 5.1 0.2 - - - -
944A ARG 3.2 7.5 + - - -
945A VAL* 3.2 11.7 - - - -
947A ALA* 1.3 82.1 - - - +
949A GLN* 1.3 60.1 + - - +
951A THR* 3.7 2.8 - - - +
952A CYS* 3.3 21.3 + - - +
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Residues in contact with GLN 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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692A THR* 4.7 2.2 - - - +
694A PHE* 3.4 18.5 - - + -
919A GLY 4.3 0.8 + - - -
920A HIS 3.1 25.1 + - - -
923A GLY* 3.5 22.7 - - - -
924A MET* 3.3 28.0 - - - -
927A LEU* 4.2 10.1 - - + +
933A MET* 4.0 5.2 - - - +
945A VAL* 2.9 30.3 + - + +
946A ALA* 3.1 12.9 + - - +
948A SER* 1.3 74.6 - - - +
950A LEU* 1.3 64.4 + - - +
952A CYS* 3.5 4.1 + - - +
953A LEU* 3.2 22.3 + - - +
996A LEU* 4.0 20.9 - - + +
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Residues in contact with LEU 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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927A LEU* 4.4 15.5 - - + -
933A MET* 3.3 42.2 - - + +
935A THR* 3.3 34.8 - - + -
946A ALA 3.0 14.7 + - - +
947A ALA 3.6 4.9 - - - +
949A GLN* 1.3 74.0 - - - +
951A THR* 1.3 60.7 + - - +
953A LEU* 3.3 12.8 + - + +
954A GLY 2.9 22.3 + - - -
955A CYS* 3.0 19.0 + - + +
958A LEU* 4.3 21.1 - - + +
959A ILE* 3.8 15.7 - - + -
987A VAL* 6.2 0.2 - - + -
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Residues in contact with THR 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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672A GLU* 3.9 36.1 + - + +
691A HIS 5.4 3.1 - - - +
947A ALA 2.9 17.4 + - - -
948A SER 3.7 5.4 - - - +
949A GLN 3.2 0.2 - - - -
950A LEU* 1.3 74.2 - - - +
952A CYS* 1.3 67.5 - - - +
954A GLY* 2.8 16.3 + - - -
955A CYS 4.9 0.4 - - - +
956A LEU* 3.5 30.1 - - + +
959A ILE* 3.8 4.7 - - - +
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Residues in contact with CYS 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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691A HIS* 4.0 32.2 - - + +
692A THR* 4.1 15.9 - - + -
948A SER 3.3 11.0 + - - +
949A GLN 3.7 8.3 - - - +
951A THR* 1.3 81.8 - - - +
953A LEU* 1.3 61.2 + - - +
954A GLY* 4.4 0.5 - - - -
994A SER* 3.7 1.2 - - - -
995A PRO* 3.7 24.1 - - - +
996A LEU* 3.7 39.3 - - - -
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Residues in contact with LEU 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* 4.3 31.6 - - + -
949A GLN 3.2 12.5 + - - +
950A LEU* 3.5 16.4 - - + +
951A THR 3.1 0.4 - - - -
952A CYS* 1.3 76.1 - - - +
954A GLY* 1.3 58.4 + - - +
955A CYS* 4.5 14.6 - - - +
987A VAL* 4.6 16.8 - - + -
990A GLN* 3.3 59.3 + - + +
991A ARG* 3.7 11.9 - - + +
994A SER* 3.4 21.9 - - - +
996A LEU* 4.1 13.2 - - + -
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Residues in contact with GLY 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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950A LEU 2.9 0.6 + - - -
951A THR 2.8 15.3 + - - -
952A CYS 4.4 0.4 - - - -
953A LEU* 1.3 80.2 - - - +
955A CYS* 1.3 67.4 + - - +
956A LEU* 3.9 6.3 - - - -
986A LYS* 3.4 17.7 + - - -
990A GLN* 5.1 2.5 - - - +
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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