Contacts of the strand formed by residues 1019 - 1023 (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 PHE1019 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557C VAL* 5.5 6.1 - - + -
558C PHE* 5.1 6.1 - + - -
926C LYS 5.8 3.1 - - - -
927C ILE 4.1 16.6 - - - -
929C ASP 3.8 15.0 - - - -
930C ARG* 3.3 44.3 - - + -
931C PHE* 2.9 24.6 + - - -
1002C ILE* 4.1 24.9 - - + -
1003C LEU 3.6 11.4 - - - +
1004C GLU* 4.9 14.1 - - + +
1005C ILE 5.4 0.9 - - - +
1017C VAL 3.9 0.4 + - - -
1018C PRO* 1.3 77.8 - - - +
1020C ILE* 1.3 72.9 + - - +
1021C THR* 3.7 13.2 - - - -
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Residues in contact with ILE1020 (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* 3.5 11.7 - - + +
933C ILE* 3.7 17.7 - - + -
942C LEU* 4.7 4.9 - - + -
946C PHE* 3.7 26.5 - - + -
1002C ILE* 3.3 5.9 - - - -
1003C LEU* 2.8 49.9 + - + +
1005C ILE* 3.4 43.5 - - + -
1019C PHE* 1.3 84.5 - - - +
1021C THR* 1.3 64.5 + - - +
1022C ILE* 3.4 29.2 - - + -
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Residues in contact with THR1021 (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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558C PHE* 4.1 20.2 - - + -
930C ARG* 3.6 19.1 + - - +
931C PHE 3.0 9.0 + - - +
932C ASP* 4.1 6.5 - - - -
933C ILE 3.2 24.6 + - - -
1000C THR* 3.3 26.0 - - - +
1001C MET 3.5 5.8 - - - +
1002C ILE* 4.7 0.7 - - - +
1019C PHE* 3.7 10.6 - - - -
1020C ILE* 1.3 76.8 + - - +
1022C ILE* 1.3 59.7 + - - +
1023C HIS* 3.5 26.7 - - + +
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Residues in contact with ILE1022 (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* 4.1 20.2 - - + -
935C GLY 3.8 13.7 - - - +
936C ASP* 4.2 6.3 - - + -
942C LEU* 4.4 0.9 - - + -
982C ILE* 3.6 22.2 - - + -
1000C THR* 3.3 9.5 + - - -
1001C MET* 2.7 50.3 + - + +
1003C LEU* 3.6 26.9 - - + -
1020C ILE* 3.4 29.6 - - + -
1021C THR* 1.3 71.5 - - - +
1023C HIS* 1.3 60.6 + - - +
1024C LEU* 3.7 28.4 + - + -
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Residues in contact with HIS1023 (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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534C GLU* 5.9 2.8 + - - -
558C PHE* 6.2 0.2 - + - -
560C ARG* 6.2 0.2 - - - -
932C ASP* 2.8 30.9 + - + +
933C ILE 3.0 25.7 + - - +
934C LYS* 5.1 1.6 - - - -
935C GLY* 3.0 28.0 + - - +
999C SER 3.9 5.8 + - - +
1000C THR* 4.5 5.3 + - - -
1021C THR* 3.5 27.6 - - + +
1022C ILE* 1.3 74.2 - - - +
1024C LEU* 1.3 64.4 + - - +
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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