Contacts of the strand formed by residues 412 - 416 (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 VAL 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A LEU* 4.2 8.5 - - + -
363A PHE* 4.0 22.0 - - + -
372A VAL* 4.1 9.6 - - + -
373A ASN 3.3 3.9 + - - +
374A ILE* 3.3 25.5 - - + -
375A GLY* 2.7 30.8 + - - -
410A ALA* 4.0 5.2 - - - +
411A GLN* 1.3 81.8 - - - +
413A LEU* 1.3 62.7 + - - +
444A VAL* 4.5 0.7 - - - -
445A PRO* 3.4 33.4 - - + +
446A LEU 4.0 1.8 - - - +
447A CYS* 4.0 15.5 - - + +
468A ILE* 4.6 8.7 - - + -
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Residues in contact with LEU 413 (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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374A ILE* 4.3 0.2 - - - -
375A GLY* 4.3 1.6 - - - +
378A CYS* 5.2 3.1 - - - -
402A ALA* 3.7 16.4 - - + +
405A GLN* 3.9 42.4 - - + +
406A VAL* 4.1 11.4 - - + -
410A ALA* 4.2 3.6 - - + -
412A VAL* 1.3 80.7 - - - +
414A ASP* 1.3 59.7 + - - +
415A VAL* 3.7 3.6 + - + -
435A ILE* 5.0 2.0 - - + -
441A ILE* 3.4 33.2 - - + -
444A VAL* 3.9 16.8 - - + -
445A PRO 3.2 4.6 + - - -
446A LEU* 3.5 20.5 - - + +
447A CYS* 2.7 33.5 + - - +
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Residues in contact with ASP 414 (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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374A ILE* 3.9 10.3 - - + +
375A GLY 3.0 24.8 + - - +
376A GLU* 4.7 3.1 - - - +
378A CYS* 3.3 26.2 - - - +
379A ASN* 4.7 7.3 + - - +
405A GLN* 5.6 0.3 + - - -
413A LEU* 1.3 70.8 - - - +
415A VAL* 1.3 60.2 + - - +
416A ASN* 4.3 6.2 - - - +
447A CYS* 3.1 31.7 - - - +
449A ASP* 2.9 36.3 - - - +
470A ASN* 3.6 2.3 + - - -
611A ILE* 3.9 17.7 - - + +
1652A THG 4.7 2.1 + - - -
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Residues in contact with VAL 415 (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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378A CYS* 3.5 5.4 - - + -
413A LEU* 4.3 10.1 - - + +
414A ASP* 1.3 77.0 - - - +
416A ASN* 1.3 62.3 + - - +
417A MET* 3.7 25.1 - - + -
428A MET* 3.6 29.6 - - + +
431A PHE* 3.8 13.0 - - + -
432A CYS* 5.0 3.8 - - - -
435A ILE* 4.1 24.2 - - + -
446A LEU* 4.4 13.2 - - + -
447A CYS 2.9 13.4 + - - +
448A ILE* 5.2 2.7 - - + -
449A ASP* 2.8 30.1 + - - +
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Residues in contact with ASN 416 (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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378A CYS 2.9 10.5 + - - +
379A ASN* 3.5 37.4 + - + +
380A VAL* 3.1 26.5 + - - +
381A ALA* 5.8 1.1 - - - +
386A PHE* 4.5 0.2 - - - -
414A ASP* 4.3 1.3 - - - +
415A VAL* 1.3 76.2 - - - +
417A MET* 1.3 62.3 + - - +
418A ASP* 3.0 33.4 + - - +
449A ASP* 2.8 40.1 + - + +
1652A THG 4.8 3.4 - - - -
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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