Contacts of the helix formed by residues 977 - 988 (chain A) in PDB entry 5AMN
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 SER 977 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A MET* 4.9 21.5 - - - +
972A ARG* 5.0 0.7 - - - +
976A CYS* 1.3 81.7 - - - +
978A GLU* 1.3 64.1 + - - +
979A GLU* 3.7 7.8 + - - +
980A MET* 3.2 24.7 + - - +
981A TYR* 3.1 18.7 + - - +
1008A MET* 5.3 1.4 - - - -
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Residues in contact with GLU 978 (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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972A ARG* 3.9 22.0 - - - +
977A SER* 1.3 72.2 - - - +
979A GLU* 1.3 65.3 + - - +
981A TYR* 3.2 6.6 + - - +
982A ARG* 3.0 25.5 + - - +
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Residues in contact with GLU 979 (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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977A SER* 3.3 7.5 - - - +
978A GLU* 1.3 80.9 - - - +
980A MET* 1.3 60.8 + - - +
982A ARG* 3.6 7.1 + - - +
983A LEU* 3.4 13.7 + - - +
1008A MET* 3.1 31.6 - - + +
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Residues in contact with MET 980 (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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848A MET* 6.4 0.2 - - + -
851A LEU 6.1 0.2 - - - -
852A ILE* 3.8 26.7 - - + -
855A ALA* 5.8 0.2 - - + -
941A LEU* 3.7 32.1 - - + -
945A VAL* 3.9 17.0 - - + -
976A CYS* 3.8 3.4 - - - -
977A SER* 3.2 20.2 + - - +
978A GLU 3.2 0.6 - - - -
979A GLU* 1.3 78.2 - - - +
981A TYR* 1.3 64.3 + - - +
983A LEU* 3.3 5.9 + - - +
984A MET* 3.2 38.7 + - + +
1005A LEU* 4.2 9.4 - - + -
1008A MET* 3.4 31.6 - - - +
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Residues in contact with TYR 981 (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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942A TRP* 6.0 0.2 - + - -
969A ARG* 5.3 0.3 - - - +
970A MET 2.6 27.3 + - - -
971A GLU* 3.4 8.4 - - - -
972A ARG* 3.5 57.4 - - + -
973A PRO* 4.5 0.7 - - + -
976A CYS* 3.9 4.9 - - - -
977A SER 3.1 11.4 + - - +
978A GLU* 3.2 5.8 + - - +
980A MET* 1.3 74.6 - - - +
982A ARG* 1.3 66.3 + - - +
984A MET* 3.1 20.5 + - - +
985A LEU* 3.0 58.2 + - + +
988A TRP* 4.4 8.1 - + - -
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Residues in contact with ARG 982 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978A GLU 3.0 16.8 + - - +
979A GLU* 3.7 8.7 - - - +
980A MET 3.3 0.2 - - - -
981A TYR* 1.3 78.6 - - - +
983A LEU* 1.3 56.0 + - - +
985A LEU* 3.4 10.7 + - - +
986A GLN* 3.0 38.4 + - - +
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Residues in contact with LEU 983 (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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941A LEU* 3.5 25.4 - - + -
979A GLU 3.4 8.9 + - - +
980A MET* 3.3 13.3 + - - +
981A TYR 3.2 0.4 - - - -
982A ARG* 1.3 77.3 - - - +
984A MET* 1.3 65.5 + - - +
986A GLN* 3.2 11.3 + - - +
987A CYS* 3.0 31.6 + - - -
996A PRO* 4.6 8.7 - - + -
1001A ILE* 4.3 27.4 - - + -
1004A ASP* 3.6 27.4 - - + +
1005A LEU* 3.8 30.5 - - + -
1008A MET* 4.5 8.1 - - + -
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Residues in contact with MET 984 (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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938A GLY* 3.8 14.8 - - - +
941A LEU* 3.9 20.4 - - + +
942A TRP* 4.1 20.9 - - - -
945A VAL* 4.2 11.4 - - + -
973A PRO* 4.8 3.4 - - + -
976A CYS* 3.4 33.2 - - + -
980A MET* 3.2 22.8 + - + +
981A TYR* 3.1 20.7 + - + +
983A LEU* 1.3 79.1 - - - +
985A LEU* 1.3 62.0 + - - +
987A CYS* 3.2 9.0 + - - +
988A TRP* 3.1 55.8 + - + -
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Residues in contact with LEU 985 (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 ARG* 4.4 15.5 - - + -
981A TYR* 3.0 57.2 + - + +
982A ARG* 3.7 11.4 - - - +
984A MET* 1.3 76.4 - - - +
986A GLN* 1.3 62.9 + - + +
988A TRP* 3.1 30.1 + - + +
989A LYS* 3.4 18.0 + - + +
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Residues in contact with GLN 986 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982A ARG* 3.0 29.0 + - + +
983A LEU* 3.2 16.6 + - - +
985A LEU* 1.3 78.1 - - + +
987A CYS* 1.3 61.4 + - - +
988A TRP 3.0 1.3 + - - -
989A LYS* 3.1 27.3 + - + +
994A LYS 5.7 1.1 - - - +
995A ARG* 3.6 3.8 - - - +
996A PRO* 3.5 29.4 - - + +
1004A ASP* 4.7 12.8 - - - -
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Residues in contact with CYS 987 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934A VAL* 3.5 38.6 - - - +
935A TRP* 3.4 15.2 - - - +
937A PHE* 4.5 5.2 - - - -
938A GLY* 3.9 20.6 - - - -
941A LEU* 4.8 0.4 - - - -
983A LEU* 3.0 27.3 + - - -
984A MET 3.2 8.0 + - - +
986A GLN* 1.3 75.4 - - - +
988A TRP* 1.3 58.4 + - + +
989A LYS 3.4 0.2 - - - -
995A ARG* 3.3 19.4 + - - -
996A PRO* 4.2 5.8 - - - -
1001A ILE* 4.2 16.8 - - - -
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Residues in contact with TRP 988 (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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935A TRP* 3.3 45.1 + + + +
938A GLY* 3.3 27.1 - - - -
939A VAL* 3.6 8.3 - - + +
942A TRP* 4.5 1.8 - + - -
952A TYR* 5.3 4.5 - - - -
969A ARG* 2.8 53.8 + - + +
970A MET* 3.7 56.5 - - + -
981A TYR* 4.4 3.4 - + - -
984A MET* 3.1 45.5 + - + +
985A LEU* 3.1 22.8 + - + +
986A GLN 3.0 1.4 - - - -
987A CYS* 1.3 85.8 - - + +
989A LYS* 1.3 60.2 + - - +
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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