Contacts of the strand formed by residues 355 - 358 (chain A) in PDB entry 4CCZ
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 MET 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A HIS* 1.3 70.5 - - - +
356A LEU* 1.3 61.5 + - - +
357A LEU* 3.5 20.5 + - + +
363A PHE 3.7 1.0 - - - +
364A ARG* 3.5 4.9 - - - -
365A ILE* 2.9 69.9 + - + +
468A ILE* 3.4 28.0 - - + -
494A ALA* 4.4 10.5 - - + -
532A ASN* 3.3 25.4 - - - +
533A ASP* 4.7 3.6 - - - +
534A ILE 5.8 0.4 - - - +
535A ILE* 3.9 16.8 - - - -
572A ARG* 3.7 14.4 - - - +
609A MET* 3.5 19.7 - - + -
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.9 27.8 - - + -
351A PHE* 6.4 2.0 - - + -
354A HIS* 3.6 8.1 + - + +
355A MET* 1.3 71.9 - - - +
357A LEU* 1.3 65.0 + - - +
363A PHE 4.3 1.3 - - - -
364A ARG* 4.9 8.3 - - + -
466A LYS* 3.1 36.9 - - - +
533A ASP* 4.6 1.1 + - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.5 12.2 - - - +
355A MET* 3.5 19.3 - - + +
356A LEU* 1.3 83.6 - - - +
358A SER* 1.3 65.6 + - - +
363A PHE* 3.0 46.9 + - + +
365A ILE* 4.8 0.7 - - + -
412A VAL* 4.2 8.1 - - + -
445A PRO* 3.6 25.6 - - + -
466A LYS* 3.8 15.9 - - + +
467A CYS 4.2 2.9 - - - +
468A ILE* 3.3 40.8 - - + -
494A ALA* 3.8 15.7 - - + -
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLY* 3.8 27.1 - - - -
246A ILE* 3.8 12.6 - - - -
247A SER* 3.8 10.1 - - - -
357A LEU* 1.3 79.5 - - - +
359A GLY* 1.3 62.4 + - - +
361A GLU 3.6 10.3 - - - -
362A PRO* 4.4 0.7 - - - -
445A PRO* 3.8 12.4 - - - +
465A GLY* 3.1 4.9 - - - -
466A LYS 3.0 31.1 + - - +
467A CYS* 5.5 0.5 - - - -
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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