Contacts of the strand formed by residues 44 - 51 (chain C) in PDB entry 5LPN
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 ILE 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004B GLN* 4.4 1.0 - - - +
1037B LEU* 4.7 3.1 - - + +
1038B VAL* 4.8 12.3 - - + -
1041B VAL* 3.7 37.3 - - + +
13C LEU* 4.8 4.7 - - + -
41C THR* 4.8 3.1 - - - -
42C ILE 3.0 11.8 + - - +
43C GLY* 1.3 75.1 - - - +
45C ASP* 1.3 66.0 + - - +
63C TRP* 3.5 32.1 - - + -
64C ASP 3.1 27.1 - - - +
65C THR* 4.1 10.5 - - - +
74C ILE* 6.3 0.9 - - + -
75C THR* 5.5 6.1 - - + -
78C TYR* 4.0 36.3 - - + +
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Residues in contact with ASP 45 (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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1004B GLN* 3.5 21.7 + - - +
1041B VAL* 4.7 4.7 - - - -
1044B ARG* 3.5 10.7 + - - -
41C THR* 4.8 9.4 - - + -
44C ILE* 1.3 77.6 - - - +
46C PHE* 1.3 90.4 + - - +
47C LYS* 3.4 24.5 + - - -
63C TRP* 3.3 11.7 - - - -
64C ASP* 2.9 39.9 + - + +
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Residues in contact with PHE 46 (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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1041B VAL* 3.8 24.9 - - + -
1044B ARG* 2.8 61.9 + - + -
1045B ASP* 3.9 8.3 - - - -
1048B ILE* 4.2 6.7 - - + -
26C LEU* 5.3 0.2 - - - -
45C ASP* 1.3 88.6 + - - +
47C LYS* 1.3 72.5 + - - +
48C ILE* 3.5 36.6 - - + -
61C GLN* 3.7 19.1 - - + -
62C ILE 3.0 19.1 - - - +
63C TRP* 3.6 37.7 - + + +
64C ASP* 4.4 2.7 - - - +
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Residues in contact with LYS 47 (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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1001B GLU* 4.7 13.1 + - - +
1004B GLN* 4.8 6.3 - - - +
1044B ARG* 4.6 4.2 - - - +
26C LEU* 4.5 28.4 - - + +
27C PHE* 6.2 5.8 - - + -
30C SER* 4.6 16.8 - - - +
31C ASP* 5.8 0.2 - - - +
45C ASP* 3.4 30.2 + - - -
46C PHE* 1.3 80.8 + - - +
48C ILE* 1.3 67.0 + - - +
60C LEU 3.8 0.2 - - - +
61C GLN* 3.6 2.9 - - - -
62C ILE* 2.9 36.3 + - + +
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Residues in contact with ILE 48 (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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997B GLU* 5.6 1.6 - - - +
1048B ILE* 4.0 21.3 - - + -
30C SER* 5.9 1.6 - - - -
46C PHE* 3.5 30.1 - - + -
47C LYS* 1.3 77.5 - - - +
49C LYS* 1.3 67.5 + - - +
50C THR* 4.7 3.8 - - - +
59C LYS* 3.7 33.7 - - + -
60C LEU 3.2 6.5 - - - +
61C GLN* 3.7 28.0 - - + -
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Residues in contact with LYS 49 (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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29C PHE* 3.7 57.1 + - + -
30C SER* 4.5 20.9 - - - +
47C LYS 4.2 0.8 + - - -
48C ILE* 1.3 75.5 - - - +
50C THR* 1.3 69.1 + - - +
51C VAL* 3.8 18.1 - - + +
60C LEU* 2.8 43.8 + - + +
62C ILE* 4.3 9.2 - - + +
160C GLU* 4.1 19.4 + - - -
164C LEU* 6.1 0.2 - - - +
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Residues in contact with THR 50 (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 TYR* 4.8 6.5 - - + -
48C ILE* 4.7 4.7 - - - +
49C LYS* 1.3 79.1 + - - +
51C VAL* 1.3 63.8 + - - +
52C GLU* 3.5 8.1 - - - +
57C LYS* 3.9 28.3 - - + +
58C ILE 3.4 13.9 - - - +
59C LYS* 4.3 19.3 - - + +
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Residues in contact with VAL 51 (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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29C PHE* 4.4 11.9 - - + -
49C LYS* 3.8 30.7 - - + +
50C THR* 1.3 78.9 - - - +
52C GLU* 1.3 69.4 + - - +
53C LEU* 4.2 14.8 - - + +
57C LYS* 3.6 6.6 - - - +
58C ILE* 2.8 42.8 + - + +
60C LEU* 3.7 23.3 - - + -
164C LEU* 5.1 14.4 - - + -
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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