Contacts of the strand formed by residues 436 - 440 (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 436 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C ASN 4.4 2.5 - - - +
435C SER* 1.3 73.9 - - - +
437C VAL* 1.3 61.1 + - - +
463C ASP* 2.8 35.0 + - - +
465C TYR* 3.4 47.2 - - + +
535C SER* 3.6 25.1 - - - +
536C LEU* 3.8 3.9 - - - -
537C ASP* 2.7 55.7 + - - +
538C PHE 3.5 2.3 + - - +
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C SER* 4.3 4.5 - - - -
436C LYS* 1.3 79.5 - - - +
438C PHE* 1.3 60.4 + - - +
453C TRP* 3.4 33.9 - - + -
458C LEU* 3.6 26.2 - - + -
465C TYR* 3.1 5.0 + - - +
466C ILE* 3.6 16.5 - - + -
467C VAL* 3.0 27.2 + - - +
536C LEU* 4.1 5.9 - - - +
538C PHE* 3.3 43.3 - - + +
540C THR* 5.6 0.2 - - - +
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Residues in contact with PHE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C VAL* 1.3 74.1 - - - +
439C LEU* 1.3 72.7 + - - +
440C VAL* 3.7 12.8 - - + -
453C TRP* 4.8 2.9 - - - -
467C VAL* 3.6 18.8 - - + -
469C THR* 4.0 9.2 - - + -
520C VAL* 3.7 25.1 - - + -
528C PHE* 4.0 9.6 - + - -
532C PHE* 3.6 38.4 - + - -
533C TRP* 3.9 22.9 - + - -
536C LEU* 3.5 24.2 - - + -
538C PHE 3.2 5.7 + - - -
539C VAL* 3.4 22.9 - - + +
540C THR* 2.7 33.3 + - - +
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Residues in contact with LEU 439 (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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437C VAL 4.1 1.0 - - - -
438C PHE* 1.3 78.7 - - - +
440C VAL* 1.3 65.8 + - - +
441C GLY 3.5 17.0 - - - +
446C GLY* 4.0 22.4 - - - +
449C MET* 4.4 9.0 - - + -
450C LEU* 4.0 13.7 - - + -
453C TRP* 3.8 21.7 - - + -
467C VAL 2.9 13.8 + - - +
468C VAL* 3.5 19.0 - - + -
469C THR 3.2 22.5 + - - -
540C THR* 3.3 32.5 - - + +
542C ALA* 3.9 17.7 - - + -
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Residues in contact with VAL 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 3.7 30.7 - - + -
439C LEU* 1.3 75.8 - - - +
441C GLY* 1.3 61.2 + - - +
469C THR* 4.0 5.4 - - + -
520C VAL* 3.7 26.2 - - + +
539C VAL* 4.1 9.9 - - + -
540C THR 3.0 14.6 + - - +
541C ASN* 4.2 11.2 - - - +
542C ALA* 2.8 30.0 + - - -
543C LEU* 3.6 22.1 - - + +
552C VAL* 4.3 14.1 - - + -
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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