Contacts of the strand formed by residues 61 - 67 (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 PHE 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C TYR* 3.3 1.9 - - - -
29C GLY 2.7 28.4 + - - -
30C PHE* 3.1 40.6 + - + -
31C HIS* 3.1 26.7 - + - -
33C PRO* 3.7 29.6 - - + -
53C LEU* 3.7 21.3 - - + -
54C SER 3.4 17.5 - - - +
55C PHE* 3.4 29.8 - + - +
56C SER* 5.0 0.2 - - - -
59C TRP 3.6 6.3 - - - -
60C SER* 1.3 76.3 + - - +
62C TYR* 1.3 61.9 + - - +
123C LEU* 3.7 16.4 - - + -
206C GLN* 3.3 17.7 - - - -
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Residues in contact with TYR 62 (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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26C TYR* 3.8 29.2 - + + +
27C VAL 3.1 11.2 - - - +
28C TYR* 3.6 16.8 - - + -
30C PHE* 3.8 1.1 - - - -
52C ASP 4.4 0.2 - - - +
53C LEU* 4.4 0.2 - - - +
54C SER* 3.2 52.4 + - - -
55C PHE 3.4 21.3 + - - -
56C SER* 3.2 21.3 - - - +
57C LYS* 6.1 0.7 - - - -
61C PHE* 1.3 77.9 - - - +
63C LEU* 1.3 66.6 + - - +
64C LEU* 5.6 0.9 - - + -
140C TYR* 4.2 13.2 - - - -
143C SER* 4.4 14.0 + - - -
145C PRO* 5.7 1.2 - - - +
345C PRO* 6.0 1.6 - - + -
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Residues in contact with LEU 63 (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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25C CYS 3.4 2.1 - - - +
26C TYR* 3.4 6.7 - - - -
27C VAL* 2.6 40.5 + - - +
30C PHE* 3.9 9.4 - - + -
33C PRO 5.3 0.7 - - - +
35C ILE* 3.9 26.2 - - + -
37C ILE* 3.7 15.4 - - + +
50C GLN* 3.2 22.4 - - + +
51C SER* 3.7 18.4 - - - +
52C ASP 3.4 23.8 - - - +
53C LEU* 3.6 26.0 - - + +
62C TYR* 1.3 78.4 - - - +
64C LEU* 1.3 61.1 + - - +
65C SER 4.1 0.4 - - - -
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Residues in contact with LEU 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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10C TYR* 3.9 3.4 - - - +
24C ASN* 3.8 32.3 - - + +
25C CYS 3.5 17.7 - - - +
26C TYR* 3.9 20.0 - - + -
49C GLU 4.2 0.7 - - - +
50C GLN* 3.9 1.3 - - - -
51C SER* 3.1 38.8 + - - +
62C TYR* 5.6 0.6 - - + -
63C LEU* 1.3 74.6 - - - +
65C SER* 1.3 62.9 + - - +
66C HIS* 4.1 10.5 + - + +
345C PRO* 3.7 30.3 - - + +
347C GLY* 4.5 15.9 - - - -
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Residues in contact with SER 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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23C LEU 3.5 1.7 - - - +
24C ASN* 3.7 0.7 - - - -
25C CYS* 2.8 41.1 + - - +
37C ILE* 4.0 28.4 + - - +
39C LEU* 4.2 3.7 - - - +
48C SER* 3.3 30.9 + - - -
49C GLU 3.5 9.0 + - - -
50C GLN* 3.8 15.8 - - - +
63C LEU 4.1 0.6 - - - -
64C LEU* 1.3 74.3 - - - +
66C HIS* 1.3 59.6 + - - +
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Residues in contact with HIS 66 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C ARG* 4.3 21.5 + - - +
22C TYR* 4.4 12.2 - + + -
23C LEU 3.1 6.5 - - - +
24C ASN* 3.5 21.5 - - - +
39C LEU* 4.0 2.7 - - - -
48C SER* 3.4 1.0 - - - -
49C GLU* 2.9 69.3 + - + +
50C GLN 5.9 0.2 - - - -
51C SER* 5.6 2.9 - - - -
64C LEU* 4.6 13.9 - - + -
65C SER* 1.3 76.9 - - - +
67C ALA* 1.3 66.1 + - - +
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Residues in contact with ALA 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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21C ASN 4.2 2.0 - - - +
22C TYR* 3.7 16.1 - - - -
23C LEU* 3.1 30.5 + - + +
39C LEU* 3.6 18.4 - - + -
46C ILE* 4.0 18.2 - - + -
47C LYS 3.5 22.4 - - - +
66C HIS* 1.3 82.0 - - - +
70C THR* 3.7 16.5 + - - +
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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