Contacts of the strand formed by residues 470 - 477 (chain A) in PDB entry 3CB4
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 TYR 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A HIS* 5.0 11.0 - - - -
82A VAL* 3.3 27.7 - - + +
83A ASP* 3.7 13.5 + - - -
294A GLN* 3.4 31.0 + - - -
345A LEU* 3.6 36.4 + - + +
346A LEU* 6.0 0.6 - - + +
404A ALA* 4.2 7.0 - - + -
405A GLU 3.2 9.6 - - - +
406A CYS* 3.9 19.3 - - - -
447A MET* 3.9 17.0 - - + -
450A VAL* 4.1 21.1 - - + -
451A VAL* 5.0 3.1 - - + +
468A LEU* 4.1 18.4 - - + -
469A ASP* 1.3 76.2 - - - +
471A ASN* 1.3 69.4 + - - +
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Residues in contact with ASN 471 (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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82A VAL* 5.4 8.6 - - + +
85A SER* 5.4 8.7 - - - +
294A GLN* 5.6 1.3 - - - -
404A ALA* 3.5 5.9 - - - -
405A GLU* 2.9 44.8 + - - +
407A HIS* 4.0 18.2 + - - -
447A MET* 4.6 1.3 - - - -
469A ASP* 5.2 2.8 - - - +
470A TYR* 1.3 80.3 - - - +
472A PHE* 1.3 75.9 + - - +
473A LYS* 4.9 2.8 - - - +
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Residues in contact with PHE 472 (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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294A GLN* 5.0 6.2 + - + +
402A PRO* 4.2 15.9 - - + -
403A ILE 3.9 4.5 - - - -
447A MET* 3.9 23.0 - - + +
471A ASN* 1.3 84.3 + - - +
473A LYS* 1.3 65.8 + - - +
474A ARG* 3.6 32.8 - - - -
475A PHE* 3.5 42.6 - + - -
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Residues in contact with LYS 473 (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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403A ILE* 2.9 20.7 + - + +
404A ALA 4.7 0.2 - - - -
405A GLU* 3.5 44.7 + - + +
444A GLU* 3.5 27.6 - - - +
471A ASN* 5.3 2.0 - - - +
472A PHE* 1.3 86.0 - - - +
474A ARG* 1.3 73.3 + - + +
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Residues in contact with ARG 474 (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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402A PRO* 3.6 2.4 - - - +
403A ILE* 2.8 41.0 + - + +
444A GLU* 2.8 38.0 + - - -
472A PHE* 3.6 13.8 - - - -
473A LYS* 1.3 89.7 - - + +
475A PHE* 1.3 72.2 - - - +
476A GLN* 2.7 40.1 + - - +
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Residues in contact with PHE 475 (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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371A VAL* 3.5 29.8 - - + -
373A GLU* 3.6 57.2 - - + +
383A TYR* 4.1 17.0 - + - -
400A ARG* 3.8 15.7 - - + -
401A GLU 3.4 1.1 - - - -
402A PRO* 3.7 23.6 - - + -
472A PHE* 3.5 25.1 - + - -
474A ARG* 1.3 92.5 - - - +
476A GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 476 (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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400A ARG* 3.6 6.3 - - - -
401A GLU* 2.7 38.0 + - - +
403A ILE* 4.1 19.3 - - + +
444A GLU* 5.4 0.5 - - - +
474A ARG* 2.7 31.3 + - - +
475A PHE* 1.3 77.3 - - - +
477A ALA* 1.3 78.1 + - + +
478A SER* 3.4 0.9 + - - -
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Residues in contact with ALA 477 (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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398A GLU* 3.4 36.6 - - + +
399A LEU 3.7 7.0 - - - -
400A ARG* 3.5 8.3 - - - +
476A GLN* 1.3 85.8 - - + +
478A SER* 1.3 61.3 + - - +
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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