Contacts of the strand formed by residues 47 - 55 (chain L) in PDB entry 1CBV
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 GLN 47 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97H TYR* 3.6 7.2 + - - -
113H GLN 5.2 3.4 - - - -
43L GLN* 2.6 34.6 + - - +
44L LYS* 2.9 49.5 + - - +
45L PRO 3.3 3.3 - - - +
46L GLY* 1.3 79.2 - - - +
48L SER* 1.3 65.9 + - - +
50L LYS* 3.2 30.4 - - - +
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Residues in contact with SER 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H TYR* 4.0 5.3 - - - -
111H TRP 3.7 14.8 + - - -
112H GLY 3.2 28.6 + - - -
113H GLN* 3.4 17.4 + - - +
43L GLN* 3.9 9.3 - - - -
47L GLN* 1.3 81.2 + - - +
49L PRO* 1.3 77.0 - - - +
50L LYS* 3.3 25.2 + - - +
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Residues in contact with PRO 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 4.7 17.3 - - + -
97H TYR* 4.0 14.1 - - + -
111H TRP* 3.7 57.9 + - + +
41L TYR* 4.6 11.2 - - + -
42L LEU 3.5 6.5 - - - +
43L GLN* 3.8 31.4 - - + +
48L SER* 1.3 90.1 - - - +
50L LYS* 1.3 67.6 + - - +
92L PHE* 5.4 1.8 - - + -
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Residues in contact with LYS 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLU* 6.1 6.1 - - - -
109H ALA 5.3 0.4 - - - -
111H TRP* 4.8 7.2 - - - +
41L TYR* 3.1 9.8 - - - -
42L LEU* 2.5 60.2 + - + +
44L LYS* 6.5 0.7 - - - -
47L GLN* 3.2 31.6 - - - +
48L SER* 3.3 24.2 + - - +
49L PRO* 1.3 86.6 - - - +
51L LEU* 1.3 65.1 + - - +
52L LEU* 5.6 2.5 - - + -
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Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ALA* 5.3 4.0 - - + -
107H TRP 5.1 4.5 - - - +
108H PHE 4.8 1.1 - - - +
109H ALA* 3.7 37.3 + - + +
39L HIS* 4.5 7.0 - - + +
40L TRP 3.7 11.0 - - - +
41L TYR* 3.7 27.3 - - + +
50L LYS* 1.3 74.7 - - - +
52L LEU* 1.3 69.5 - - - +
53L ILE 3.9 13.2 - - - +
54L TYR* 4.8 10.8 - - + -
60L PHE* 3.5 57.4 - - + +
63L VAL* 3.7 6.9 - - - +
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Residues in contact with LEU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L TRP* 3.0 17.5 + - + +
41L TYR 4.6 0.9 - - - -
42L LEU* 4.0 25.6 - - + +
50L LYS* 3.6 3.3 + - + +
51L LEU* 1.3 76.3 - - - +
53L ILE* 1.3 64.8 - - + +
59L ARG* 3.5 2.4 - - - -
60L PHE* 2.7 31.3 + - - -
63L VAL* 3.0 33.4 - - + +
64L PRO* 5.7 1.1 - - + -
67L PHE* 3.6 26.5 - - + -
78L LEU* 4.3 11.2 - - + -
91L TYR* 3.4 35.2 - - + -
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Residues in contact with ILE 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LEU 5.3 0.2 - - - +
39L HIS* 3.6 3.5 - - - +
40L TRP* 3.2 35.6 + - + +
51L LEU* 3.9 3.1 - - - +
52L LEU* 1.3 85.8 - - + +
54L TYR* 1.3 64.9 + - - +
56L VAL* 3.0 37.7 - - - +
57L SER 3.8 7.4 - - - +
58L ASN 3.3 7.0 - - - +
59L ARG* 4.1 14.4 - - + +
67L PHE* 3.9 22.0 - - + +
68L SER 4.0 1.6 - - - +
69L GLY* 3.7 21.3 - - - +
78L LEU* 3.7 28.9 - - + -
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Residues in contact with TYR 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H THR* 3.8 37.4 - - - +
106H ALA* 4.1 19.1 - - + -
38L LEU 4.2 2.5 - - - -
39L HIS* 4.3 14.1 - - + +
51L LEU* 4.8 7.4 - - + -
53L ILE* 1.3 75.5 - - - +
55L LYS* 1.3 94.4 + - + +
56L VAL 3.3 2.5 - - - -
58L ASN* 2.5 69.4 + - + +
59L ARG 3.5 21.4 + - - -
60L PHE* 3.9 26.5 - + + -
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Residues in contact with LYS 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D T 6.3 0.4 - - + -
105H THR 4.4 8.7 + - - -
106H ALA* 5.6 2.5 - - + -
34L GLY 4.5 9.4 + - - +
35L ASN 3.9 12.9 - - - +
36L THR* 3.1 26.4 - - - +
37L TYR* 3.9 32.8 - - + -
38L LEU 3.1 8.6 + - - +
39L HIS* 3.8 5.9 - - - +
54L TYR* 1.3 100.2 - - + +
56L VAL* 1.3 62.5 + - - +
57L SER* 2.8 14.2 + - - -
58L ASN* 3.4 17.6 + - - +
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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