Contacts of the strand formed by residues 572 - 578 (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 572 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C GLU* 2.5 35.2 + - - -
568C THR* 3.5 0.3 - - - -
569C LEU* 2.9 41.9 + - + +
571C THR* 1.3 82.0 - - - +
573C GLY* 1.3 58.2 + - - +
869C THR* 3.3 10.8 - - - +
899C VAL 3.2 7.0 - - - +
900C ASN* 3.8 24.2 - - + +
8D LEU* 4.2 13.3 - - + +
9D THR* 3.6 23.2 - - - +
71D LEU* 5.7 5.3 - - + +
73D LEU* 3.7 28.3 - - + -
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Residues in contact with GLY 573 (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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567C GLY 3.3 12.8 - - - -
571C THR 3.8 0.4 + - - -
572C LYS* 1.3 74.9 - - - +
574C ASN* 1.3 63.2 + - - +
869C THR* 4.2 1.1 - - - -
873C VAL* 3.9 17.0 - - - -
898C PHE* 3.5 1.0 - - - -
899C VAL* 2.8 38.1 + - - +
8D LEU* 5.0 1.4 - - - +
73D LEU* 3.4 10.0 - - - +
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Residues in contact with ASN 574 (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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565C GLU* 5.0 7.3 + - - +
566C SER* 3.2 5.9 - - - +
567C GLY 3.0 45.5 + - - +
573C GLY* 1.3 76.4 - - - +
575C THR* 1.3 73.8 + - - +
576C GLN* 4.6 3.8 - - - +
873C VAL* 3.8 6.5 - - - +
897C GLY 3.0 15.5 - - - +
898C PHE* 3.8 15.9 - - + -
71D LEU 3.9 3.8 - - - +
72D ARG* 3.5 36.0 - - - +
73D LEU* 3.1 20.0 + - + +
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Residues in contact with THR 575 (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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565C GLU 3.4 5.4 - - - -
566C SER* 4.0 1.6 - - - -
574C ASN* 1.3 82.4 + - - +
576C GLN* 1.3 63.8 + - - +
873C VAL* 3.6 16.2 - - + +
876C LEU* 4.0 14.2 - - + +
877C VAL* 3.4 38.8 - - + +
880C GLU* 5.4 5.0 - - - +
895C LYS 4.2 5.7 + - - -
896C ASN* 3.3 8.4 - - - +
897C GLY* 2.8 58.7 + - - +
898C PHE* 5.1 1.6 - - - -
908C PHE* 5.4 0.2 - - - -
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Residues in contact with GLN 576 (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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563C LEU 3.8 0.3 - - - +
564C LEU* 3.8 2.1 - - - +
565C GLU* 2.8 53.9 + - + +
574C ASN* 4.8 3.8 - - - +
575C THR* 1.3 77.8 - - - +
577C VAL* 1.3 68.7 + - - +
578C ILE* 3.8 21.4 - - + +
584C GLU* 4.5 7.5 + - - +
585C SER 3.8 20.2 + - - -
586C TYR* 4.2 4.4 - - - -
589C SER* 5.7 1.2 - - - -
880C GLU* 6.1 0.2 - - - -
895C LYS 5.9 0.2 - - - -
896C ASN* 3.4 20.2 - - - +
42D ARG* 5.1 2.0 + - - +
72D ARG* 3.1 38.0 + - - +
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Residues in contact with VAL 577 (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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563C LEU 3.8 2.2 - - - +
564C LEU* 3.5 30.3 - - + -
576C GLN* 1.3 78.8 + - - +
578C ILE* 1.3 63.8 + - - +
579C ILE* 4.0 12.1 - - + -
583C THR* 3.7 9.0 + - - +
584C GLU 4.7 0.2 - - - +
880C GLU* 3.5 35.2 - - + +
884C LEU* 5.0 3.6 - - + -
894C TYR* 3.9 15.3 - - + -
895C LYS 4.4 4.5 - - - +
896C ASN* 3.1 15.4 + - - +
911C PRO* 3.6 25.2 - - + +
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Residues in contact with ILE 578 (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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553C ASP* 4.3 6.5 - - - +
556C CYS* 5.6 2.0 - - + -
557C VAL* 5.9 0.2 - - + -
561C LYS 5.0 0.7 - - - +
562C PRO* 3.4 3.6 - - - +
563C LEU* 2.9 62.1 + - + +
565C GLU* 4.2 11.4 - - + -
576C GLN* 3.8 28.5 - - + +
577C VAL* 1.3 78.2 - - - +
579C ILE* 1.3 62.9 + - - +
583C THR* 3.4 3.6 - - - -
584C GLU 3.6 17.3 - - - +
585C SER* 3.9 6.1 - - - -
586C TYR* 3.7 21.3 - - + +
884C LEU* 5.3 0.2 - - - +
928C TRP* 3.6 30.3 - - + -
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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