Contacts of the strand formed by residues 48 - 56 (chain B) in PDB entry 5F0P
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 VAL 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.8 21.8 - - + -
42B PHE* 3.8 27.1 - - + -
47B SER* 1.3 74.5 - - - +
49B SER* 1.3 60.8 + - - +
72B PHE* 3.8 24.7 - - + -
109B PHE* 4.4 2.2 - - + -
110B GLU* 3.6 0.3 - - - -
111B PHE* 2.7 49.1 + - + +
114B VAL* 3.9 13.0 - - + -
116B LYS* 4.2 4.5 - - - -
132B LEU* 4.1 25.1 - - + -
149B LEU* 4.6 4.3 - - + -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.4 12.0 - - - +
19B ASN* 3.1 36.0 + - - +
20B ASP* 5.0 1.7 + - - +
47B SER* 4.1 4.1 + - - -
48B VAL* 1.3 77.9 - - - +
50B GLY* 1.3 59.2 + - - +
109B PHE* 3.2 23.6 - - - -
110B GLU* 3.7 24.0 + - - -
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Residues in contact with GLY 50 (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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17B VAL 3.3 12.3 - - - -
18B LEU* 4.0 0.4 - - - -
19B ASN* 3.5 18.8 + - - +
49B SER* 1.3 75.1 + - - +
51B LYS* 1.3 70.1 + - - +
108B ASP* 3.7 4.9 - - - +
109B PHE* 3.1 38.0 + - - +
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Residues in contact with LYS 51 (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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15B ASP 3.8 0.9 - - - +
16B ILE* 3.4 3.8 - - - -
17B VAL* 2.8 37.6 + - + +
19B ASN* 4.6 9.9 - - - +
50B GLY* 1.3 79.3 - - - +
52B VAL* 1.3 59.1 + - - +
53B ASN* 3.8 23.5 - - - +
106B SER* 4.9 10.1 - - - +
107B TYR 3.3 8.7 - - - +
108B ASP* 3.4 22.0 - - - +
109B PHE* 3.5 8.8 - - - -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.8 27.4 - - + -
15B ASP 3.6 3.6 - - - +
16B ILE* 4.7 2.2 - - + +
51B LYS* 1.3 71.2 - - - +
53B ASN* 1.3 61.3 + - - +
54B LEU* 3.9 11.2 + - + -
68B ILE* 5.7 0.7 - - + -
70B ILE* 3.6 31.4 - - + -
95B LEU* 3.6 25.4 - - + -
105B ARG 4.1 0.2 - - - +
106B SER* 3.2 4.3 - - - -
107B TYR* 2.9 39.7 + - + +
109B PHE* 3.8 8.1 - - + -
134B VAL* 3.8 16.6 - - + -
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Residues in contact with ASN 53 (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 GLU 3.5 4.2 - - - +
14B ILE* 3.8 0.2 - - - -
15B ASP* 2.6 45.4 + - + +
17B VAL* 3.8 29.9 - - - +
51B LYS* 3.8 15.4 - - - +
52B VAL* 1.3 72.2 - - - +
54B LEU* 1.3 64.2 + - - +
55B ALA* 3.6 1.6 + - + +
105B ARG 3.9 3.8 - - - +
106B SER* 3.1 24.0 - - - -
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Residues in contact with LEU 54 (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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12B CYS* 3.8 12.1 - - - -
13B GLU 3.6 2.7 - - - -
14B ILE* 3.8 35.7 - - + -
52B VAL* 4.1 10.5 - - + -
53B ASN* 1.3 74.5 - - - +
55B ALA* 1.3 59.9 + - - +
56B PHE* 6.3 0.9 - - + -
68B ILE* 4.0 12.6 - - + -
101B LEU* 3.4 33.9 - - + -
103B GLN 5.6 1.6 - - - +
104B SER* 3.3 9.2 - - - -
105B ARG* 2.8 39.6 + - + +
107B TYR* 4.1 14.6 - - + -
134B VAL* 5.2 0.9 - - + -
136B ILE* 3.9 19.5 - - + -
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Residues in contact with ALA 55 (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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12B CYS* 3.5 6.9 - - - -
13B GLU* 3.0 37.6 + - + +
15B ASP* 6.5 0.2 - - + -
53B ASN* 3.6 3.3 + - - +
54B LEU* 1.3 70.8 - - - +
56B PHE* 1.3 61.4 + - - +
57B LYS* 3.8 28.8 + - - +
104B SER* 3.8 6.3 - - - +
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Residues in contact with PHE 56 (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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11B ILE* 4.1 23.6 - - + -
12B CYS* 4.8 9.2 - - + -
54B LEU* 3.9 1.7 + - + -
55B ALA* 1.3 71.6 - - - +
57B LYS* 1.3 66.1 + - - +
58B GLN 3.4 22.4 - - - -
59B PRO* 4.6 6.9 - - + +
61B LYS 3.3 22.4 - - - -
62B ARG* 4.2 2.0 - - - -
63B LEU* 4.1 16.4 - - + -
101B LEU* 3.2 35.7 - - + -
102B THR 3.2 19.3 - - - -
103B GLN* 3.6 32.3 - - - -
104B SER* 3.1 13.6 + - - +
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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