Contacts of the helix formed by residues 938 - 949 (chain A) in PDB entry 3CMM
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 LYS 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937A ILE* 1.3 80.7 - - - +
939A LEU* 1.3 66.0 + - - +
940A SER* 3.2 6.7 - - - +
941A ASP* 3.1 23.8 + - - +
942A LEU* 3.0 18.5 + - - +
978A LEU 4.4 0.4 - - - +
979A ASN* 3.1 44.8 + - - +
980A LEU 3.3 7.2 - - - +
981A PRO* 4.2 16.8 - - + -
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Residues in contact with LEU 939 (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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937A ILE 3.9 0.4 + - - -
938A LYS* 1.3 72.1 - - - +
940A SER* 1.3 61.9 + - - +
942A LEU* 3.4 12.6 + - + +
943A ILE* 3.2 44.0 + - + +
954A ILE* 6.1 0.4 - - + -
957A LEU* 3.9 21.1 - - + -
965A TYR* 3.8 40.4 - - + -
977A ARG* 3.4 41.3 - - + +
978A LEU* 3.6 6.0 + - - +
980A LEU 2.9 12.7 + - - +
982A ILE* 4.6 4.0 - - + +
985A LEU* 3.7 21.1 - - + -
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Residues in contact with SER 940 (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 LYS* 4.6 5.2 - - - +
939A LEU* 1.3 70.8 - - - +
941A ASP* 1.3 76.4 + - - +
943A ILE* 3.5 4.4 + - - +
944A GLU* 3.2 24.8 + - - +
978A LEU* 2.8 42.8 + - - -
979A ASN* 5.2 2.8 + - - -
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Residues in contact with ASP 941 (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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937A ILE* 3.6 21.9 - - + +
938A LYS* 3.1 25.3 + - - +
940A SER* 1.3 86.7 + - - +
942A LEU* 1.3 56.3 + - - +
944A GLU* 3.3 6.5 + - - +
945A HIS* 2.7 38.9 + - - +
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Residues in contact with LEU 942 (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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933A ILE* 3.4 32.3 - - + -
937A ILE* 3.7 19.2 - - + +
938A LYS 3.0 12.3 + - - +
939A LEU* 3.4 17.0 - - + +
941A ASP* 1.3 78.3 - - - +
943A ILE* 1.3 61.8 + - - +
945A HIS* 3.2 4.9 + - - +
946A PHE* 3.0 38.9 + - + -
954A ILE* 4.1 12.3 - - + -
957A LEU* 4.0 37.5 - - + -
982A ILE* 4.7 6.7 - - + -
1003A LEU* 4.7 1.6 - - + -
1020A ILE* 4.4 7.6 - - + -
1022A ILE* 4.8 8.1 - - + -
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Residues in contact with ILE 943 (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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939A LEU* 3.2 30.6 + - + +
940A SER* 3.9 5.6 - - - +
941A ASP 3.3 0.2 - - - -
942A LEU* 1.3 73.5 - - - +
944A GLU* 1.3 60.1 + - - +
946A PHE* 3.3 5.0 + - - +
947A GLU* 3.2 40.0 + - - +
952A LEU 4.1 0.3 - - - +
953A GLU* 5.3 1.8 - - + -
954A ILE* 4.1 37.9 - - + +
965A TYR* 4.0 23.6 - - + +
978A LEU* 3.6 27.8 - - + -
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Residues in contact with GLU 944 (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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940A SER 3.2 17.7 + - - +
941A ASP* 3.8 5.6 - - - +
943A ILE* 1.3 72.5 - - - +
945A HIS* 1.3 65.1 + - - +
946A PHE 3.1 1.6 - - - -
947A GLU* 2.9 9.8 + - + +
948A LYS* 2.8 34.5 + - + +
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Residues in contact with HIS 945 (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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931A PHE* 6.2 1.8 - - - +
932A ASP 5.3 3.0 + - - -
933A ILE* 4.2 30.7 - - + +
937A ILE* 5.4 9.6 - - + -
941A ASP 2.7 23.0 + - - +
942A LEU* 3.5 5.2 - - - +
944A GLU* 1.3 72.0 - - - +
946A PHE* 1.3 70.9 + + - +
948A LYS* 5.3 1.6 - - - -
949A ASP* 2.7 73.4 + - + +
950A GLU* 5.0 5.5 + - - +
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Residues in contact with PHE 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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931A PHE* 3.7 40.4 - + + -
933A ILE* 4.0 9.6 - - + -
942A LEU* 3.0 38.2 + - + -
943A ILE 3.6 7.0 - - - +
944A GLU 3.1 0.4 - - - -
945A HIS* 1.3 87.8 - + - +
947A GLU* 1.3 51.2 + - - +
950A GLU* 3.6 20.6 + - + -
951A GLY 3.2 7.1 + - - -
952A LEU* 2.7 56.0 + - + +
954A ILE* 3.7 20.6 - - + -
1005A ILE* 4.0 6.5 - - + -
1017A VAL* 6.0 0.2 - - + -
1020A ILE* 3.4 39.0 - - + -
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Residues in contact with GLU 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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943A ILE* 3.2 27.9 + - - +
944A GLU* 2.9 11.1 + - + +
946A PHE* 1.3 77.0 - - - +
948A LYS* 1.3 60.8 + - + +
949A ASP 3.2 5.6 + - - -
951A GLY* 3.8 14.4 + - - -
952A LEU 3.4 18.8 - - - +
953A GLU* 3.2 31.5 - - + +
1010A LYS* 5.8 0.3 + - - -
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Residues in contact with LYS 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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944A GLU* 2.8 23.8 + - + +
945A HIS* 5.3 0.9 - - - -
947A GLU* 1.3 75.5 - - + +
949A ASP* 1.3 93.8 + - - +
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Residues in contact with ASP 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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922A LYS* 5.8 0.7 - - - -
945A HIS* 2.7 52.5 + - + +
947A GLU 3.2 0.2 - - - -
948A LYS* 1.3 115.7 - - - +
950A GLU* 1.3 77.5 + - + +
951A GLY 3.9 0.4 - - - -
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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