Contacts of the strand formed by residues 23 - 30 (chain C) in PDB entry 4LCC
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 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.5 30.3 - - + -
10C TYR 3.7 6.7 - - - +
11C SER* 5.0 0.7 - - - +
22C TYR* 1.3 70.9 - - - +
24C ASN* 1.3 65.3 + - - +
39C LEU* 3.8 25.8 - - + +
46C ILE* 5.4 4.5 - - + -
65C SER 3.5 1.9 - - - +
66C HIS* 3.1 23.6 - - - -
67C ALA* 3.1 15.7 + - + +
70C THR* 3.1 23.9 - - + +
77C TYR* 3.6 44.6 - - + -
78C SER 5.3 3.8 - - - +
94C TRP* 4.7 11.2 - - + -
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Residues in contact with ASN 24 (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 GLN 3.8 0.9 - - - +
9C VAL* 3.3 9.7 - - - +
10C TYR* 2.8 70.8 + - + +
12C ARG* 3.9 16.2 + - - +
22C TYR* 4.2 9.3 - - - +
23C LEU* 1.3 75.1 - - - +
25C CYS* 1.3 59.5 + - - +
26C TYR 4.0 0.4 - - - -
64C LEU* 3.8 15.6 - - + +
65C SER 3.7 2.0 - - - -
66C HIS* 3.5 21.8 - - - +
345C PRO 4.0 0.4 + - - -
346C SER 3.0 29.8 + - - +
347C GLY* 5.6 0.3 - - - -
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.5 19.1 - - - -
8C GLN 4.0 1.6 - - - -
9C VAL* 4.3 2.7 - - + +
24C ASN* 1.3 73.6 - - - +
26C TYR* 1.3 60.4 + - - +
27C VAL* 3.9 4.0 + - - +
37C ILE* 3.9 14.3 - - + +
39C LEU* 3.7 11.9 - - + -
63C LEU 3.4 2.3 - - - +
64C LEU* 3.4 4.5 - - - +
65C SER* 2.8 42.5 + - - +
79C CYS* 2.0 52.5 - - + -
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Residues in contact with TYR 26 (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 LYS 3.5 1.7 - - - +
7C ILE* 3.4 1.9 - - - -
8C GLN 3.1 31.2 + - - +
10C TYR* 3.5 25.8 - - + +
25C CYS* 1.3 72.4 - - - +
27C VAL* 1.3 60.3 + - - +
28C TYR* 3.2 45.9 - + + +
62C TYR* 3.8 39.9 - + + +
63C LEU 3.4 9.0 - - - -
64C LEU* 3.9 7.4 - - + -
343C ILE 4.4 7.5 + - - -
344C LEU* 3.8 24.7 - - + -
345C PRO* 3.4 35.1 - - + +
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Residues in contact with VAL 27 (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 PRO* 3.7 28.3 - - + -
6C LYS 3.4 6.1 - - - +
7C ILE* 4.1 20.2 - - + -
25C CYS* 4.4 3.1 - - - -
26C TYR* 1.3 74.8 - - - +
28C TYR* 1.3 62.9 + - - +
30C PHE* 3.4 7.6 - - + -
35C ILE* 3.9 15.0 - - + -
37C ILE* 3.6 35.0 - - + -
62C TYR* 3.1 2.8 - - - +
63C LEU 2.6 39.0 + - - +
81C VAL* 4.1 16.4 - - + -
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Residues in contact with TYR 28 (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 PRO* 3.8 0.7 - - - +
6C LYS* 2.8 90.6 + - + +
8C GLN* 3.3 33.2 + - + +
26C TYR* 3.2 41.1 - + + +
27C VAL* 1.3 73.8 - - - +
29C GLY* 1.3 67.2 + - - +
30C PHE* 3.4 3.7 + - - -
61C PHE 3.3 7.2 - - - -
62C TYR* 3.6 16.2 - - + -
341C GLY 4.7 4.0 + - - -
344C LEU* 4.8 3.8 - - + -
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Residues in contact with GLY 29 (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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3C ARG* 3.6 14.1 + - - +
4C PRO 3.4 15.9 - - - +
6C LYS* 5.4 5.4 + - - +
28C TYR* 1.3 81.3 - - - +
30C PHE* 1.3 55.9 + - - -
56C SER* 6.0 0.2 + - - -
58C ASP* 5.2 1.8 - - - -
60C SER* 3.6 25.0 + - - -
61C PHE 2.7 10.9 + - - -
62C TYR* 4.6 0.2 - - - +
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Residues in contact with PHE 30 (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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3C ARG* 3.3 8.7 - - - +
5C PRO* 3.6 22.9 - - + -
27C VAL* 3.4 36.1 - - + -
28C TYR* 3.8 11.9 - - - -
29C GLY* 1.3 78.8 - - - +
31C HIS* 1.3 66.6 + - - +
32C PRO 3.7 12.1 - - - -
33C PRO* 3.7 22.9 - - + -
35C ILE* 4.1 10.1 - - + -
53C LEU* 4.4 1.1 - - + -
60C SER* 3.7 1.8 - - - -
61C PHE* 3.1 60.2 + - + -
62C TYR* 3.8 2.0 - - - -
63C LEU* 3.9 24.0 - - + -
83C HIS* 4.1 11.4 - + - +
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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