Contacts of the strand formed by residues 8 - 13 (chain C) in PDB entry 4BL5
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 MET 8 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3C PHE* 5.7 5.4 - - + -
-2C GLN 3.5 20.2 - - - +
-1C SER* 1.3 74.0 - - - +
9C ARG* 1.3 57.3 + - - +
10C ILE* 3.7 24.2 + - + -
35C GLY 2.7 13.1 + - - +
36C GLU* 3.4 16.1 - - + +
37C ASP* 2.6 35.6 + - - +
64C THR* 3.3 5.8 - - - +
65C HIS* 3.6 36.8 - - + +
107C ARG* 4.4 4.3 - - - +
231C LEU* 6.0 1.6 - - - +
232C ARG* 5.0 22.0 - - + +
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Residues in contact with ARG 9 (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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8C MET* 1.3 70.5 - - - +
10C ILE* 1.3 59.5 + - - +
11C LEU 3.9 0.2 - - - -
37C ASP* 3.6 23.8 - - + +
39C VAL* 5.4 1.6 - - + -
61C VAL* 4.2 17.7 - - + -
62C GLN* 3.5 36.1 - - - +
63C PRO* 3.2 5.5 - - - +
64C THR* 2.7 44.7 + - + +
65C HIS 3.0 4.0 + - - +
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 3.9 30.5 - - + -
9C ARG* 1.3 71.6 - - - +
11C LEU* 1.3 62.2 + - - +
12C VAL* 3.6 10.4 + - + +
36C GLU* 4.2 9.6 - - + -
37C ASP 2.6 13.2 + - - +
38C TRP* 3.3 65.6 - - + +
39C VAL* 2.8 28.1 + - - +
61C VAL* 5.8 0.4 - - - -
65C HIS* 3.5 22.2 - - + +
67C ILE* 4.9 7.9 - - + -
231C LEU* 6.2 2.9 - - + -
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Residues in contact with LEU 11 (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 ARG 3.7 2.0 + - - -
10C ILE* 1.3 69.8 - - - +
12C VAL* 1.3 67.3 + - - +
13C THR* 4.5 6.5 - - + -
39C VAL* 3.3 24.9 - - + +
41C VAL* 3.6 26.9 - - + -
57C LEU* 4.2 15.7 - - + +
58C PHE* 3.8 39.9 - - + -
61C VAL* 4.7 13.4 - - + +
63C PRO* 3.7 23.8 - - + -
65C HIS 2.9 9.4 + - - +
66C VAL* 3.2 9.2 - - + +
67C ILE 3.0 23.7 + - - +
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.0 7.9 - - + +
11C LEU* 1.3 76.2 - - - +
13C THR* 1.3 74.1 + - - +
15C GLY* 4.3 4.9 + - - -
20C GLY* 5.2 0.2 - - - -
23C ILE* 4.9 4.3 - - + -
38C TRP* 4.0 22.9 - - + -
39C VAL 2.9 7.7 + - - +
40C PHE* 3.9 38.4 - - + -
41C VAL* 3.1 28.4 + - - +
67C ILE* 3.4 19.1 - - + +
69C LEU* 3.6 19.5 - - + -
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Residues in contact with THR 13 (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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11C LEU* 4.5 15.5 - - + -
12C VAL* 1.3 75.3 - - - +
14C GLY* 1.3 66.2 + - - +
15C GLY 3.2 0.8 + - - -
41C VAL* 3.8 15.0 - - + -
48C LEU* 3.8 28.3 - - + -
57C LEU* 5.6 0.7 - - + -
58C PHE* 4.9 2.9 - - + -
66C VAL* 4.8 4.7 - - + -
67C ILE 3.0 7.6 + - - +
68C HIS* 3.0 29.4 + - - +
69C LEU* 3.1 32.2 + - - +
70C ALA* 3.2 3.1 + - - -
97C VAL* 4.5 11.2 - - + -
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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
------------------------------------------------------------
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