Contacts of the strand formed by residues 63 - 69 (chain C) in PDB entry 4BEJ
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 LEU 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C LEU* 5.2 0.4 - - + -
50C LEU* 6.0 0.4 - - + -
51C LEU* 5.0 12.3 - - + -
59C THR* 5.5 3.4 - - + -
61C ARG 3.5 5.2 + - - +
62C PRO* 1.3 71.4 - - - +
64C ILE* 1.3 58.6 + - - +
65C LEU* 3.4 32.7 + - + -
93C PHE* 5.7 0.4 - - + -
111C ILE* 3.7 29.4 - - + -
130C ILE* 3.6 33.7 - - + +
132C LEU* 4.0 22.2 - - + -
146C ASP* 2.7 54.4 + - + +
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Residues in contact with ILE 64 (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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12C GLN* 4.0 27.6 - - + +
27C GLN* 5.1 1.6 - - - +
63C LEU* 1.3 72.1 - - - +
65C LEU* 1.3 58.7 + - - +
66C GLN* 3.6 19.5 + - + +
129C PRO* 3.6 25.8 - - + -
130C ILE 2.6 13.1 + - - +
131C HIS* 3.2 30.7 - - + +
132C LEU 3.1 25.6 + - - +
143C THR* 4.3 4.3 - - + -
144C LEU 3.5 8.5 - - - +
145C VAL* 4.0 26.5 - - + +
173C PHE* 5.9 2.2 - - + -
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Residues in contact with LEU 65 (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 LEU* 4.3 37.5 - - + +
45C LEU* 6.1 1.1 - - + -
46C VAL* 5.2 3.1 - - + -
50C LEU* 4.5 5.4 - - + -
51C LEU* 4.7 11.0 - - + -
63C LEU* 3.4 18.3 + - + -
64C ILE* 1.3 70.7 - - - +
66C GLN* 1.3 62.3 + - - +
67C LEU* 3.9 22.8 + - + +
132C LEU* 3.7 21.5 - - + +
134C ILE* 3.8 29.2 - - + -
142C LEU 4.2 0.5 - - - +
143C THR* 3.6 2.4 - - - -
144C LEU* 2.8 39.9 + - + +
146C ASP* 6.0 0.4 - - + +
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Residues in contact with GLN 66 (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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9C ASN* 3.4 43.6 + - - +
12C GLN* 3.2 24.5 + - - +
13C ASP* 4.0 15.1 + - - +
64C ILE* 4.0 13.8 - - + +
65C LEU* 1.3 71.3 - - - +
67C LEU* 1.3 63.2 + - - +
68C VAL* 4.6 0.4 - - - -
131C HIS* 4.5 4.3 - - - +
132C LEU 2.9 14.1 + - - +
133C LYS* 3.3 34.6 + - + +
134C ILE* 2.9 26.0 + - - +
143C THR* 3.6 18.6 - - + -
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Residues in contact with LEU 67 (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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5C ILE* 5.8 0.9 - - - +
9C ASN* 5.2 1.4 + - - -
45C LEU* 4.0 31.0 - - + -
46C VAL* 4.0 28.7 - - + +
65C LEU* 4.1 26.9 - - + +
66C GLN* 1.3 73.5 - - - +
68C VAL* 1.3 63.9 + - - +
69C HIS 4.2 0.2 - - - -
134C ILE* 3.6 20.6 - - + -
139C VAL* 4.0 15.3 - - + -
140C VAL* 3.8 14.8 - - + +
141C ASN* 3.8 4.0 + - - -
142C LEU* 2.9 45.3 + - + +
143C THR* 5.0 1.4 + - - -
144C LEU* 6.3 0.7 - - + -
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Residues in contact with VAL 68 (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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6C PRO* 6.6 0.4 - - + -
9C ASN* 4.7 11.9 - - - +
66C GLN 4.3 2.7 - - - +
67C LEU* 1.3 80.3 - - - +
69C HIS* 1.3 74.1 + - - +
70C VAL* 3.7 1.4 - - + +
133C LYS* 4.1 28.5 - - + -
134C ILE 2.9 12.5 + - - +
135C PHE* 3.5 25.8 - - + -
136C SER 3.3 20.4 + - - -
139C VAL* 4.1 3.5 - - - +
141C ASN* 3.5 12.3 - - - +
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Residues in contact with HIS 69 (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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68C VAL* 1.3 79.6 - - - +
70C VAL* 1.3 70.9 + - - +
71C SER 3.2 27.4 + - - -
136C SER 3.4 5.4 - - - -
137C PRO* 3.7 18.0 + - - +
139C VAL* 3.2 27.8 - - - +
140C VAL* 4.7 1.3 - - - -
141C ASN* 3.3 32.8 + - - +
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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