Contacts of the strand formed by residues 45 - 48 (chain G) in PDB entry 6CNB
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 CYS 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34G PHE* 4.5 21.8 - - + -
35G ALA 3.5 17.8 - - - +
36G ASN* 4.8 1.0 - - - +
37G LYS 3.9 9.2 + - - +
39G ILE* 4.5 8.0 - - + +
43G GLY 3.7 1.4 + - - -
44G LEU* 1.3 93.6 - - - +
46G ILE* 1.3 80.7 + - - +
47G THR* 3.3 27.4 - - - -
48G ILE* 5.3 0.2 - - - -
74G ALA* 3.8 15.9 - - + -
75G VAL 3.1 14.8 - - - -
76G VAL* 3.7 9.4 - - + +
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Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.8 12.3 - - + -
55D LEU* 4.8 0.7 - - - +
58D ILE* 4.1 20.9 - - + +
62D VAL* 4.1 28.0 - - + -
2G PHE 4.8 3.4 - - - +
35G ALA* 3.8 20.5 - - - +
44G LEU* 3.9 15.7 - - + -
45G CYS* 1.3 88.5 - - - +
47G THR* 1.3 66.9 + - + +
75G VAL* 2.4 45.9 + - + +
76G VAL 4.1 10.1 - - - +
77G PHE* 4.6 5.8 - - + -
104G ILE* 5.8 4.9 - - + -
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Residues in contact with THR 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.1 26.2 - - + -
23D LEU* 4.7 10.8 - - + +
55D LEU* 4.0 14.5 - - - +
58D ILE* 5.2 2.7 - - + -
31G ASN* 2.7 34.3 + - - -
34G PHE* 6.3 0.2 - - - -
35G ALA* 5.3 2.5 - - - +
45G CYS* 3.4 10.3 - - - -
46G ILE* 1.3 86.6 - - + +
48G ILE* 1.3 75.3 + - - +
49G TYR* 5.3 0.9 - - - -
74G ALA* 3.3 2.6 - - - +
75G VAL* 2.9 28.6 + - + +
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Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.7 8.1 - - - +
27G THR* 4.4 21.1 - - + +
30G LEU* 3.5 40.2 - - + -
31G ASN* 3.4 17.5 - - - +
34G PHE* 4.3 11.4 - - + -
45G CYS* 5.3 0.7 - - - -
47G THR* 1.3 93.2 + - - +
49G TYR* 1.3 62.5 + - - +
50G ASP 3.3 24.9 - - - +
51G LEU* 5.4 3.6 - - + -
72G PHE* 3.5 31.0 - - + -
74G ALA* 3.7 7.6 - - + -
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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