Contacts of the helix formed by residues 957 - 973 (chain A) in PDB entry 2AA2
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 PRO 957 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A ASN* 3.0 35.7 - - + +
771A ARG* 3.5 21.1 - - + +
774A GLY* 4.4 12.3 - - - -
956A PHE* 1.3 88.8 - - + +
958A ALA* 1.3 67.4 + - - +
959A MET* 4.3 5.2 - - + +
960A LEU* 2.9 20.8 + - + +
961A VAL* 3.0 11.0 + - - +
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Residues in contact with ALA 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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956A PHE 4.0 0.4 + - - -
957A PRO* 1.3 71.9 - - - +
959A MET* 1.3 63.2 + - - +
961A VAL* 3.2 10.2 + - - +
962A GLU* 2.9 27.4 + - - +
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Residues in contact with MET 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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774A GLY* 3.9 27.8 - - - +
777A MET* 3.8 18.6 - - + +
778A ILE* 3.6 44.6 - - + +
781A VAL* 4.4 13.0 - - + -
957A PRO* 3.1 3.4 + - + +
958A ALA* 1.3 77.9 - - - +
960A LEU* 1.3 59.3 + - + +
962A GLU* 3.3 19.8 - - - +
963A ILE* 3.1 42.7 + - + +
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Residues in contact with LEU 960 (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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201A AS4 4.5 0.7 - - - +
770A ASN* 3.6 38.8 - - + +
773A ALA* 3.7 18.8 - - + +
774A GLY* 3.8 26.0 - - - +
777A MET* 4.6 1.1 - - + -
806A TRP* 4.2 28.9 - - + -
956A PHE* 4.1 10.5 - - + -
957A PRO* 2.9 15.1 + - + +
959A MET* 1.3 81.9 - - + +
961A VAL* 1.3 61.2 + - - +
962A GLU 3.1 1.3 - - - -
963A ILE* 4.4 9.9 - - + +
964A ILE* 2.8 46.1 + - + +
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Residues in contact with VAL 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A PHE* 4.0 19.3 - - + -
956A PHE* 3.9 24.7 - - + +
957A PRO 3.0 15.8 + - - +
958A ALA* 3.6 10.3 - - - +
960A LEU* 1.3 74.3 - - - +
962A GLU* 1.3 56.9 - - - +
965A SER* 2.7 48.6 + - - +
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Residues in contact with GLU 962 (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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803A GLN* 5.1 1.6 - - - +
958A ALA* 2.9 18.8 + - - +
959A MET* 3.3 22.1 - - - +
961A VAL* 1.3 80.0 - - - +
963A ILE* 1.3 66.4 + - - +
965A SER* 3.9 3.6 - - - -
966A ASP* 3.7 16.5 + - - +
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Residues in contact with ILE 963 (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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777A MET* 4.1 29.2 - - + -
802A ILE* 5.6 4.0 - - + -
803A GLN* 4.2 28.3 - - + +
806A TRP* 3.6 37.9 - - + +
959A MET* 3.1 40.2 + - + +
960A LEU* 3.2 10.1 + - + +
962A GLU* 1.3 82.9 - - + +
964A ILE* 1.3 59.0 + - + +
966A ASP* 3.8 2.4 - - - +
967A GLN* 2.9 31.2 + - + +
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Residues in contact with ILE 964 (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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806A TRP* 4.2 16.8 - - + -
942A CYS* 3.6 24.7 - - - -
943A PHE* 4.1 21.8 - - + -
946A PHE* 3.5 35.7 - - + -
956A PHE* 3.7 29.6 - - + -
960A LEU* 2.8 33.0 + - + +
963A ILE* 1.3 69.9 - - + +
965A SER* 1.3 66.2 + - - +
967A GLN* 4.2 8.7 - - - +
968A LEU* 2.9 27.5 + - + +
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Residues in contact with SER 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A PHE* 4.0 14.5 - - - -
961A VAL* 2.7 40.7 + - - +
962A GLU* 3.9 5.6 - - - -
964A ILE* 1.3 72.4 - - - +
966A ASP* 1.3 58.8 + - - +
968A LEU* 4.7 0.6 - - - +
969A PRO* 3.0 24.8 - - - +
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Residues in contact with ASP 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLN* 2.6 37.2 + - - +
962A GLU 3.7 8.7 + - - +
963A ILE 3.4 6.0 + - - +
964A ILE 3.1 0.4 - - - -
965A SER* 1.3 81.3 - - - +
967A GLN* 1.3 63.8 + - - +
969A PRO* 3.4 10.2 - - - +
970A LYS* 2.8 40.6 + - - +
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Residues in contact with GLN 967 (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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803A GLN* 3.5 28.1 - - + +
804A TYR* 4.2 13.2 - - + +
806A TRP* 2.8 31.4 + - - +
939A LEU* 3.6 24.2 - - - +
943A PHE* 3.6 25.1 - - + -
963A ILE* 2.9 20.6 + - + +
964A ILE* 4.0 5.4 - - - +
966A ASP* 1.3 76.3 + - - +
968A LEU* 1.3 65.7 + - - +
970A LYS* 3.1 10.7 + - - +
971A VAL* 2.9 35.5 + - + +
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Residues in contact with LEU 968 (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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943A PHE* 3.8 48.8 - - + +
946A PHE* 4.2 23.8 - - + -
947A ARG* 4.1 16.4 - - + +
964A ILE* 2.9 17.8 + - + +
965A SER* 4.7 0.7 - - - +
967A GLN* 1.3 74.0 - - - +
969A PRO* 1.3 77.1 - - + +
971A VAL* 3.9 0.3 - - - -
972A GLU* 2.9 57.1 + - - +
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Residues in contact with PRO 969 (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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965A SER 3.0 28.3 - - - +
966A ASP* 3.4 9.2 - - - +
968A LEU* 1.3 99.0 - - + +
970A LYS* 1.3 59.1 + - + +
972A GLU* 3.9 2.5 - - + +
973A SER* 2.9 30.9 + - - -
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Residues in contact with LYS 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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800A THR* 5.7 5.2 - - - -
803A GLN* 3.9 9.2 - - - +
804A TYR* 3.3 37.0 - - + +
966A ASP* 2.8 48.1 + - - +
967A GLN* 3.1 7.7 + - - +
969A PRO* 1.3 78.3 - - + +
971A VAL* 1.3 60.3 + - - +
973A SER* 2.9 19.1 + - - -
975A ASN* 2.9 27.7 + - + -
976A ALA 4.7 0.9 - - - -
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Residues in contact with VAL 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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804A TYR* 4.3 6.3 - - + -
939A LEU* 5.3 9.4 - - + -
943A PHE* 4.1 21.8 - - + -
967A GLN* 2.9 41.0 + - + +
968A LEU 3.9 2.5 - - - +
970A LYS* 1.3 76.0 - - - +
972A GLU* 1.3 61.4 + - + +
974A GLY* 3.0 19.2 + - - -
976A ALA* 4.1 25.1 + - + +
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Residues in contact with GLU 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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943A PHE* 3.9 17.4 - - + +
947A ARG* 2.3 36.2 + - - -
968A LEU* 2.9 37.2 + - + +
969A PRO* 4.4 2.7 - - + +
971A VAL* 1.3 78.4 - - + +
973A SER* 1.3 56.7 + - - +
974A GLY 3.2 1.3 + - - -
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Residues in contact with SER 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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969A PRO 2.9 16.3 + - - -
970A LYS* 2.9 18.0 + - - -
971A VAL 3.2 0.2 - - - -
972A GLU* 1.3 76.7 - - - +
974A GLY* 1.3 59.3 + - - +
975A ASN* 2.8 27.1 + - - +
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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