Contacts of the strand formed by residues 40 - 46 (chain C) in PDB entry 4BEI
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 ILE 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C VAL* 1.3 84.4 + - + +
41C GLU* 1.3 72.8 + - - +
42C ALA 4.1 1.9 + - - +
64C ILE* 3.9 22.9 - - + -
65C ARG 3.5 6.1 - - - +
66C ASN* 4.9 2.5 - - + -
67C GLU* 5.4 0.9 - - - -
72C VAL* 3.8 30.1 - - + -
74C PHE* 4.0 23.8 - - + -
106C LEU* 5.4 0.2 - - + -
135C VAL* 4.2 17.0 - - + -
137C ALA* 4.5 8.3 - - + -
143C PHE* 3.2 51.6 - - + +
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Residues in contact with GLU 41 (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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39C VAL 4.2 0.2 + - - -
40C ILE* 1.3 75.0 - - - +
42C ALA* 1.3 60.6 + - - +
43C ASN* 4.3 7.6 + - - +
63C GLY 3.7 1.0 - - - +
64C ILE* 3.5 2.8 - - - -
65C ARG* 2.8 53.0 + - + +
67C GLU* 5.0 8.5 - - + +
111C MET* 5.1 0.2 - - - +
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Residues in contact with ALA 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 ILE* 4.1 2.3 + - + -
41C GLU* 1.3 72.7 - - - +
43C ASN* 1.3 70.1 + - - +
63C GLY 3.4 7.6 - - - +
64C ILE* 4.7 0.2 - - - +
133C LEU* 4.2 14.8 - - + -
135C VAL* 4.3 20.2 - - + -
143C PHE* 4.7 9.6 - - + +
144C LYS 4.4 15.1 - - - +
145C ALA* 3.5 16.1 - - + +
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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* 5.1 5.9 - - - +
42C ALA* 1.3 83.6 + - - +
44C LEU* 1.3 63.6 + - - +
61C GLN 4.4 0.7 - - - -
62C LEU* 3.7 0.3 - - - -
63C GLY* 2.9 32.7 + - - +
111C MET* 4.2 19.6 - - - +
133C LEU* 3.2 10.6 - - - +
145C ALA* 3.7 6.7 - - - -
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Residues in contact with LEU 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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43C ASN* 1.3 80.6 - - - +
45C SER* 1.3 68.7 + - - +
46C LEU* 4.4 2.7 - - + -
60C SER* 3.9 16.4 - - - -
61C GLN 3.5 4.7 - - - +
62C LEU* 3.4 31.4 - - + -
78C LEU* 4.2 4.7 - - + -
131C VAL* 3.7 32.1 - - + +
133C LEU* 3.8 13.0 - - + +
145C ALA* 3.3 34.1 - - + +
147C GLN* 3.0 37.6 - - + +
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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 LEU* 1.3 77.1 - - - +
46C LEU* 1.3 67.5 + - - +
60C SER* 3.4 6.1 - - - -
61C GLN* 3.0 46.3 + - - +
147C GLN* 4.1 5.2 - - - -
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Residues in contact with LEU 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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47B ASN 3.2 12.5 - - - +
48B GLN* 4.9 4.2 - - - +
44C LEU* 4.4 7.6 - - + -
45C SER* 1.3 82.8 - - - +
47C ASN* 1.3 61.6 + - - +
48C GLN* 3.4 25.3 + - - +
49C ASN* 4.5 8.6 + - - +
58C ILE* 4.3 12.3 - - + -
59C SER 3.9 2.0 - - - -
60C SER* 3.9 17.3 - - - -
118C PHE* 4.9 0.7 - - + -
131C VAL* 4.3 14.8 - - + -
147C GLN* 3.6 25.3 - - + +
148C GLU 3.6 27.8 - - - +
149C PHE* 4.2 15.9 - - + -
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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