Contacts of the strand formed by residues 52 - 59 (chain F) in PDB entry 2P5V
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 52 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ALA* 4.2 8.5 - - + -
58E LEU 3.7 10.5 - - - +
59E LEU* 3.7 4.9 - - + -
14F LEU* 3.6 30.5 - - + -
17F LEU* 5.6 0.9 - - + -
43F LEU* 4.5 11.2 - - + -
46F LEU* 3.3 16.0 + - + +
47F GLU* 3.9 28.2 - - + +
50F GLY* 4.1 2.8 - - - -
51F ILE* 1.3 74.8 - - - +
53F ARG* 1.3 60.7 + - - +
54F GLN 4.1 10.1 - - - +
55F TYR* 3.7 35.0 - - + +
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 2.9 39.8 + - - +
59E LEU 3.3 24.3 + - - -
60E SER* 4.1 10.5 - - - +
61E PRO* 5.1 3.4 - - - +
148E HIS* 3.7 39.6 + - - -
149E THR* 6.0 0.4 - - - +
150E THR* 5.5 1.4 - - - +
50F GLY* 4.4 11.7 - - - +
51F ILE 3.4 1.4 + - - -
52F VAL* 1.3 74.5 - - - +
54F GLN* 1.3 86.4 + - + +
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLN 3.5 16.1 - - - +
19E GLU* 3.1 26.7 + - - +
57E ALA* 3.5 2.8 - - - -
58E LEU* 2.6 50.9 + - + +
149E THR* 5.4 8.6 + - - +
150E THR* 5.1 0.9 + - - -
151E SER* 5.3 0.5 + - - -
52F VAL* 3.5 4.3 - - - +
53F ARG* 1.3 104.6 - - + +
55F TYR* 1.3 73.8 + - - +
56F ALA* 3.7 4.7 - - - +
1018F CL 3.6 14.1 - - + -
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Residues in contact with TYR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLU 3.3 16.5 - - - +
21E GLY 2.9 17.4 + - - -
22E ARG* 3.5 45.1 - - + +
56E ALA 3.4 2.2 - - - +
57E ALA* 3.7 31.0 - - + -
1017E CL 3.8 6.3 - - + -
17F LEU* 3.8 10.5 - - + +
21F GLY* 3.4 20.0 - - - +
43F LEU* 3.2 24.8 - - - +
47F GLU* 2.7 32.2 + - + -
52F VAL* 3.7 15.2 - - + +
54F GLN* 1.3 74.9 - - - +
56F ALA* 1.3 63.2 + - - +
1018F CL 3.0 16.0 - - + +
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Residues in contact with ALA 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU 3.9 2.5 - - - -
18E GLN 3.3 20.0 - - - +
21E GLY* 3.8 5.7 - - - +
55E TYR* 3.5 1.7 - - - -
56E ALA* 2.9 33.5 + - - +
58E LEU* 3.9 15.0 - - + -
150E THR* 3.7 18.4 - - - +
54F GLN* 3.7 9.4 - - - +
55F TYR* 1.3 75.5 - - - +
57F ALA* 1.3 61.5 + - - +
58F LEU* 3.6 8.1 + - + +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 6.2 0.2 - - + -
17E LEU* 2.8 43.3 + - + +
18E GLN* 3.4 25.6 - - - +
21E GLY* 3.8 1.2 - - - -
52E VAL* 4.4 9.4 - - + -
54E GLN 3.7 4.9 - - - -
55E TYR* 3.7 20.6 - - + -
150E THR* 4.9 2.4 + - - +
56F ALA* 1.3 71.2 - - - +
58F LEU* 1.3 64.7 + - - +
59F LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 3.6 4.3 - - - -
53E ARG* 2.9 59.0 + - - +
54E GLN* 2.8 30.9 + - - +
56E ALA* 3.9 12.3 - - + -
58E LEU* 4.9 0.7 - - + -
150E THR* 3.6 41.1 - - + +
56F ALA* 4.1 13.0 - - + +
57F ALA* 1.3 77.4 - - - +
59F LEU* 1.3 61.6 + - - +
150F THR* 3.9 30.5 - - + +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 4.0 26.5 - - + +
18E GLN* 3.2 39.6 + - + +
51E ILE* 3.1 13.7 - - + +
52E VAL* 4.0 20.6 - - + -
53E ARG* 3.1 19.4 + - - +
150E THR 5.6 1.2 + - - -
152E LEU* 3.7 18.2 - - + +
154E LEU* 4.0 23.6 - - + -
57F ALA* 4.1 6.0 + - + +
58F LEU* 1.3 81.3 - - - +
60F SER* 1.3 64.0 + - - +
61F PRO* 3.3 8.9 - - - +
64F VAL* 4.3 7.0 - - + -
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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