Contacts of the strand formed by residues 653 - 658 (chain C) in PDB entry 6CIM
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 653 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566C ALA* 3.9 21.0 + - + +
569C ASP* 3.6 19.4 + - - -
570C MET* 5.6 5.1 - - - +
623C SER* 3.3 1.1 - - - -
624C PHE* 2.7 58.1 + - + +
625C THR* 5.7 0.4 - - - -
626C VAL* 5.9 2.2 - - + +
651C CYS* 3.1 11.8 + - - +
652C CYS* 1.3 70.0 - - - +
654C PRO* 1.3 68.8 - - - +
655C LEU 3.6 0.3 + - - -
992C TRP* 3.3 43.1 - - + +
995C THR* 3.2 40.9 + - - +
996C SER* 4.2 4.9 - - - +
997C LYS* 4.4 4.4 - - - +
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Residues in contact with PRO 654 (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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557C PHE* 3.5 9.9 - - - -
621C ARG* 5.1 1.3 - - + -
622C PHE 4.2 0.7 - - - +
623C SER* 4.0 10.1 - - - -
624C PHE* 5.6 0.2 - - - -
652C CYS 3.3 7.4 - - - +
653C LYS* 1.3 82.6 - - - +
655C LEU* 1.3 60.0 + - - +
657C LEU* 4.9 9.9 - - + -
988C LEU* 4.1 15.0 - - + -
991C HIS* 3.8 25.1 - - + +
992C TRP* 3.3 48.2 - - + +
995C THR* 3.8 19.7 - - + +
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Residues in contact with LEU 655 (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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556C ARG* 3.4 1.6 - - - +
557C PHE* 2.9 44.9 + - + +
559C TYR* 3.5 51.6 - - + +
562C ALA* 3.8 28.7 - - + -
622C PHE* 2.8 34.6 + - + +
623C SER* 4.2 3.6 - - - -
624C PHE* 3.7 15.0 - - + -
653C LYS 3.6 0.6 + - - -
654C PRO* 1.3 73.9 - - - +
656C CYS* 1.3 58.5 + - - +
675C LEU* 4.0 11.4 - - + -
988C LEU* 4.6 3.4 - - - -
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Residues in contact with CYS 656 (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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537C GLY* 5.3 0.4 - - - -
554C ALA* 4.8 2.0 - - - -
555C LYS 3.5 12.8 - - - -
556C ARG* 3.6 11.4 - - + -
620C VAL 4.0 0.7 - - - +
621C ARG* 3.6 0.9 - - - -
622C PHE* 2.9 33.3 + - + +
654C PRO 3.9 0.4 - - - -
655C LEU* 1.3 80.1 - - - +
657C LEU* 1.3 73.3 + - - +
658C MET* 3.8 28.0 - - - -
671C ILE* 4.0 14.8 - - - -
672C LEU* 4.7 0.2 - - - -
675C LEU* 3.6 25.6 - - + -
988C LEU* 4.9 0.4 - - - -
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Residues in contact with LEU 657 (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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554C ALA* 3.2 2.6 - - - +
555C LYS* 2.9 35.0 + - + +
602C MET* 4.4 9.6 - - + -
620C VAL 3.7 2.0 - - - +
621C ARG* 3.3 40.4 - - + -
654C PRO* 4.9 5.2 - - + -
656C CYS* 1.3 77.7 - - - +
658C MET* 1.3 60.4 + - - +
968C PHE* 3.9 9.6 - - + -
984C MET* 3.4 17.6 - - + +
987C VAL* 3.7 29.2 - - + -
988C LEU* 4.1 29.8 - - + +
991C HIS* 4.5 14.4 - - - +
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Residues in contact with MET 658 (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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552C THR* 4.6 0.4 - - - +
553C ILE 3.8 1.3 - - - -
554C ALA* 3.4 20.4 - - + -
619C ALA* 3.0 9.0 - - - +
620C VAL* 2.9 68.2 + - + +
622C PHE* 5.5 1.3 - - + -
656C CYS* 3.8 15.3 - - - +
657C LEU* 1.3 74.9 - - - +
659C LEU* 1.3 62.8 + - - +
660C ALA* 4.1 11.2 - - + -
668C LEU* 4.4 11.2 - - + -
671C ILE* 3.5 43.1 - - + -
672C LEU* 4.0 20.9 - - + -
968C PHE* 5.5 0.2 - - - -
984C MET* 4.2 2.2 - - - +
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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