Contacts of the strand formed by residues 41 - 47 (chain C) 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 GLU 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LYS 4.7 1.4 - - - +
38C LYS* 4.7 5.7 - - - +
39C ASP 3.5 11.0 + - - +
40C PHE* 1.3 101.7 - - - +
42C VAL* 1.3 64.9 + - - +
43C ASN* 5.8 1.1 - - - +
57C ILE* 3.1 38.9 + - + +
58C ASN* 4.9 3.0 - - - +
134K LYS* 4.3 19.4 + - - +
138K LYS* 3.5 22.7 + - - -
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Residues in contact with VAL 42 (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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40C PHE* 4.4 3.8 - - + -
41C GLU* 1.3 81.6 + - - +
43C ASN* 1.3 82.8 + - - +
44C ILE* 5.5 1.3 - - + -
54C PHE* 4.8 1.6 - - + -
55C ASP 3.1 15.7 - - - +
56C LEU* 3.9 18.4 - - + -
57C ILE* 4.2 4.3 - - - -
134K LYS* 3.9 29.8 - - + +
135K PHE* 4.0 31.0 - - + -
138K LYS* 3.6 30.5 + - + +
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Residues in contact with ASN 43 (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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41C GLU* 5.8 1.0 - - - +
42C VAL* 1.3 91.2 - - - +
44C ILE* 1.3 75.8 + - - +
54C PHE* 3.4 2.3 - - - +
55C ASP* 2.7 49.4 + - + +
57C ILE* 5.2 6.3 - - + +
297C HIS* 5.7 1.2 + - - -
138K LYS* 4.7 5.7 + - - -
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Residues in contact with ILE 44 (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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42C VAL* 5.5 1.3 - - + -
43C ASN* 1.3 85.3 - - - +
45C SER* 1.3 71.1 + - - +
47C LEU* 4.5 8.7 - - + -
54C PHE* 3.5 21.1 - - + +
55C ASP* 4.8 1.3 - - - -
135K PHE* 5.3 7.4 - - + -
138K LYS* 5.7 9.9 - - + +
139K ILE* 4.5 22.9 - - + -
142K MET* 3.7 44.0 - - + -
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Residues in contact with SER 45 (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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44C ILE* 1.3 85.7 + - - +
46C SER* 1.3 67.4 + - - +
53C ASN* 3.0 29.2 + - - -
54C PHE* 3.8 4.8 - - - +
55C ASP* 5.2 2.6 + - - +
271C ARG* 4.4 15.6 + - - -
142K MET* 5.5 0.3 - - - +
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Residues in contact with SER 46 (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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45C SER* 1.3 83.2 - - - +
47C LEU* 1.3 73.6 + - - +
48C ASP* 4.2 4.8 + - - -
51C GLU* 4.5 7.1 + - - -
52C ALA* 3.6 0.3 - - - -
53C ASN* 3.0 39.6 + - - +
142K MET* 5.3 3.4 - - - -
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Residues in contact with LEU 47 (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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44C ILE* 4.5 15.0 - - + -
46C SER* 1.3 85.7 - - - +
48C ASP* 1.3 72.1 + - - +
51C GLU 3.9 3.1 - - - -
52C ALA* 3.8 16.2 - - + -
53C ASN 5.1 1.3 - - - +
54C PHE* 5.3 3.8 - - + -
309C THR* 5.4 0.9 - - - +
310C PRO* 5.9 0.4 - - + -
311C GLU* 3.3 40.6 - - + +
139K ILE* 3.6 24.5 - - + -
142K MET* 4.2 25.8 - - + +
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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