Contacts of the helix formed by residues 938 - 949 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936C ASP 4.0 0.8 + - - +
937C ILE* 1.3 82.7 - - - +
939C LEU* 1.3 68.1 + - - +
940C SER* 4.2 11.4 - - - +
941C ASP* 3.2 23.6 + - + +
942C LEU 3.0 15.6 + - - -
979C ASN* 3.3 47.6 + - - +
980C LEU 3.4 5.8 - - - -
981C PRO* 3.8 11.0 - - + -
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Residues in contact with LEU 939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C ILE 3.7 1.0 + - - -
938C LYS* 1.3 70.1 - - - +
940C SER* 1.3 63.9 + - - +
942C LEU* 2.9 19.0 + - + +
943C ILE* 3.2 19.6 + - + +
957C LEU* 4.5 16.2 - - + -
965C TYR* 3.9 44.4 - - + -
974C LEU* 6.0 0.4 - - + -
977C ARG* 3.4 46.7 - - + +
978C LEU* 3.8 15.4 + - + +
980C LEU 2.8 12.8 + - - +
982C ILE* 5.2 4.0 - - + +
985C LEU* 4.1 19.7 - - + -
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Residues in contact with SER 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C LYS* 4.2 9.5 - - - +
939C LEU* 1.3 72.7 - - - +
941C ASP* 1.3 67.7 + - - +
943C ILE* 3.2 14.7 + - - +
944C GLU* 3.2 27.7 + - - +
978C LEU* 2.9 44.4 + - - -
979C ASN* 4.7 2.4 + - - -
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Residues in contact with ASP 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C ILE* 3.6 22.9 - - + +
938C LYS* 3.2 34.6 + - - +
940C SER* 1.3 83.2 + - - +
942C LEU* 1.3 56.1 + - - +
944C GLU* 3.4 7.3 + - - +
945C HIS* 3.0 30.9 + - - +
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Residues in contact with LEU 942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933C ILE* 4.2 15.3 - - + -
937C ILE* 3.7 11.4 - - + +
938C LYS 3.0 9.4 + - - +
939C LEU* 2.9 14.3 + - + +
941C ASP* 1.3 76.6 - - - +
943C ILE* 1.3 67.0 + - + +
945C HIS* 3.5 5.9 + - - +
946C PHE* 3.2 45.7 + - + -
954C ILE* 3.6 20.9 - - + -
957C LEU* 3.5 33.9 - - + -
982C ILE* 3.8 27.8 - - + -
1003C LEU* 4.3 7.4 - - + -
1005C ILE* 4.0 2.0 - - + -
1020C ILE* 4.7 2.0 - - + -
1022C ILE* 4.4 0.4 - - + -
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Residues in contact with ILE 943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939C LEU* 3.2 18.9 + - + +
940C SER* 3.2 7.4 + - - +
942C LEU* 1.3 79.3 - - + +
944C GLU* 1.3 64.9 + - + +
946C PHE* 3.7 4.3 + - - +
947C GLU* 3.5 18.9 + - + +
952C LEU 4.5 2.6 - - - +
953C GLU* 5.8 2.9 - - + -
954C ILE* 4.1 25.8 + - + +
965C TYR* 3.6 46.9 - - + +
978C LEU* 4.1 21.1 - - + -
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Residues in contact with GLU 944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940C SER* 3.2 24.2 + - - +
941C ASP* 4.0 6.7 - - - +
942C LEU 3.3 0.2 - - - -
943C ILE* 1.3 79.5 - - + +
945C HIS* 1.3 65.4 + - - +
947C GLU* 3.0 17.2 + - - +
948C LYS* 3.0 45.4 + - - +
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Residues in contact with HIS 945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C PHE* 5.7 4.4 - - - +
932C ASP 5.3 3.1 + - - -
933C ILE* 4.6 19.7 - - + +
937C ILE* 6.4 1.1 - - + -
941C ASP 3.0 18.0 + - - +
942C LEU* 3.7 5.6 - - - +
944C GLU* 1.3 77.0 - - - +
946C PHE* 1.3 84.1 + + - +
948C LYS* 5.1 0.9 - - - -
949C ASP* 3.0 74.4 + - + +
950C GLU* 5.0 4.6 + - - -
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Residues in contact with PHE 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C PHE* 3.4 44.0 - + + -
933C ILE* 4.1 6.5 - - + -
942C LEU* 3.2 41.8 + - + +
943C ILE 4.0 1.3 - - - +
944C GLU 3.3 0.2 - - - -
945C HIS* 1.3 94.8 - + - +
947C GLU* 1.3 51.3 - - - +
950C GLU* 2.5 36.4 + - + +
952C LEU* 3.0 46.3 + - + +
954C ILE* 3.6 25.4 - - + -
1005C ILE* 5.3 4.7 - - + -
1020C ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943C ILE 3.5 11.7 + - - +
944C GLU* 3.0 12.3 + - - +
945C HIS 3.0 1.0 - - - -
946C PHE* 1.3 76.7 - - - +
948C LYS* 1.3 69.5 + - + +
950C GLU 2.8 14.8 - - - +
951C GLY* 4.3 6.6 - - - -
952C LEU 3.9 18.6 + - - +
953C GLU* 4.2 9.5 + - - +
1010C LYS* 5.7 4.5 - - - +
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Residues in contact with LYS 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944C GLU* 3.0 52.3 + - - +
945C HIS* 5.1 0.4 - - - -
947C GLU* 1.3 84.4 - - + +
949C ASP* 1.3 77.3 + - - +
950C GLU 3.9 0.7 - - - +
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Residues in contact with ASP 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C LYS* 4.9 4.9 + - - -
945C HIS* 3.0 49.3 + - + +
948C LYS* 1.3 89.9 - - - +
950C GLU* 1.3 77.3 + - - +
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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