Contacts of the strand formed by residues 73 - 78 (chain B) 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 GLU 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 5.8 0.8 - - - +
23B CYS 3.5 11.7 - - - +
24B ALA* 4.5 12.2 - - + +
32B MET* 4.3 1.8 - - - -
68B ARG* 3.8 5.9 - - - -
69B LEU* 3.3 49.2 + - + +
70B ASN* 3.4 37.7 + - + +
72B ARG* 1.3 82.1 - - + +
74B PHE* 1.3 60.9 + - - +
75B SER 4.2 0.7 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B CYS* 3.1 36.5 + - + +
32B MET* 3.4 51.7 - - + -
33B TYR* 4.1 6.1 - - - -
34B TRP* 3.2 35.8 + + - +
47B TYR 4.4 1.8 - - - -
48B TYR* 3.8 8.7 - - - -
49B SER* 3.4 34.5 - - - -
55B THR* 4.1 6.1 - - + -
66B VAL* 3.3 25.6 - - + -
67B SER 3.4 12.6 - - - -
68B ARG* 3.5 20.2 - - + -
73B GLU* 1.3 71.8 - - - +
75B SER* 1.3 60.1 + - - +
91B CYS* 4.8 0.2 - - - -
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 5.4 6.5 - - - -
21B LEU 3.3 11.2 - - - -
22B GLN* 4.4 14.1 - - - +
34B TRP* 3.9 2.2 - - - -
66B VAL* 3.3 4.3 - - - +
67B SER* 3.2 37.8 + - - -
69B LEU* 4.0 26.9 - - - +
73B GLU 4.2 0.6 - - - -
74B PHE* 1.3 74.8 - - - +
76B LEU* 1.3 62.4 - - - +
77B ARG* 3.9 2.5 + - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 3.2 3.1 - - - -
21B LEU* 2.5 56.3 + - + +
34B TRP* 3.4 57.8 - - + +
46B ILE* 3.6 21.3 - - + -
47B TYR* 6.3 1.8 - - + -
64B TYR* 3.9 24.7 - - + -
65B ASN 4.2 4.7 - - - +
66B VAL* 4.4 4.7 - - + -
75B SER* 1.3 73.0 - - - +
77B ARG* 1.3 83.7 + - - +
78B LEU* 4.8 3.8 - - + +
89B TYR* 4.1 9.2 - - + -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B MET 4.1 4.5 - - - -
20B THR* 3.8 19.3 - - + +
64B TYR* 3.8 0.9 - - - -
65B ASN* 2.9 45.1 + - + +
66B VAL* 5.5 0.2 - - - -
75B SER* 3.9 2.4 + - - +
76B LEU* 1.3 82.2 - - - +
78B LEU* 1.3 65.5 + - - +
79B GLU* 4.3 6.3 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.7 10.8 - - + -
18B SER* 3.4 0.9 - - - -
19B MET* 3.1 45.7 + - + +
20B THR* 6.2 0.2 - - - -
21B LEU* 5.1 15.0 - - + -
63B GLY 3.6 20.9 - - - +
64B TYR* 4.5 15.9 - - + +
65B ASN* 5.1 0.7 - - - +
76B LEU* 4.8 4.7 - - + -
77B ARG* 1.3 78.3 - - - +
79B GLU* 1.3 64.0 + - - +
80B SER 3.6 3.3 + - - +
81B ALA* 4.1 18.6 - - + +
85B GLN* 3.0 28.9 - - + +
89B TYR* 5.8 4.5 - - + +
112B LEU* 5.7 6.7 - - + -
114B VAL* 5.6 2.7 - - + -
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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