Contacts of the strand formed by residues 52 - 59 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.8 17.3 - - + -
17G LEU* 5.0 2.5 - - + -
43G LEU* 4.8 5.4 - - + -
46G LEU* 3.5 12.5 + - + -
47G GLU* 4.1 30.3 - - + +
50G GLY* 4.2 3.5 - - - -
51G ILE* 1.3 73.1 - - - +
53G ARG* 1.3 61.2 + - - +
54G GLN 4.0 15.3 - - - +
55G TYR* 3.7 39.9 - - + +
57H ALA* 4.3 10.5 - - + -
58H LEU 4.2 1.1 - - - +
59H LEU* 3.6 20.0 - - + -
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Residues in contact with ARG 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLY* 4.5 8.3 - - - +
51G ILE 3.5 2.0 + - - -
52G VAL* 1.3 73.5 - - - +
54G GLN* 1.3 88.1 + - - +
58H LEU* 2.9 43.1 + - - +
59H LEU 3.5 23.2 + - - -
60H SER* 4.2 12.8 - - - +
61H PRO* 5.0 4.0 - - - +
145H GLU* 6.1 0.4 - - - -
148H HIS* 3.4 41.8 + - - -
149H THR* 6.0 0.8 - - - +
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Residues in contact with GLN 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G VAL* 3.5 4.4 - - - +
53G ARG* 1.3 102.5 + - - +
55G TYR* 1.3 70.5 + - - +
56G ALA* 3.6 12.1 - - - +
18H GLN 3.6 16.6 + - - -
19H GLU* 3.3 33.1 + - - +
57H ALA* 3.5 2.8 - - - -
58H LEU* 2.7 47.2 + - + +
149H THR* 5.4 4.6 + - - -
150H THR* 4.9 2.4 + - - +
151H SER* 5.4 1.0 + - - -
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Residues in contact with TYR 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LEU* 3.9 8.7 - - + +
21G GLY* 3.5 24.7 - - - +
43G LEU* 3.7 19.1 - - - +
47G GLU* 2.9 32.3 + - + -
52G VAL* 3.7 20.1 - - + +
54G GLN* 1.3 78.6 - - - +
56G ALA* 1.3 62.8 + - - +
19H GLU 3.3 16.5 - - - +
20H ASN* 3.6 5.4 + - - +
21H GLY* 3.1 14.6 + - - +
22H ARG* 3.5 50.8 + - + +
56H ALA 3.4 3.1 - - - +
57H ALA* 3.8 27.1 - - + -
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Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G GLN* 3.6 10.8 - - - +
55G TYR* 1.3 75.5 - - - +
57G ALA* 1.3 61.8 + - - +
58G LEU* 3.7 6.5 + - + +
18H GLN 3.1 23.1 - - - +
21H GLY* 3.7 9.8 - - - +
55H TYR* 3.5 2.2 - - - -
56H ALA* 2.9 34.2 + - - +
58H LEU* 4.1 9.9 - - + -
150H THR* 3.8 17.7 - - - +
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Residues in contact with ALA 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ALA* 1.3 73.8 - - - +
58G LEU* 1.3 63.5 + - - +
59G LEU* 4.0 8.7 + - + -
17H LEU* 2.9 34.2 + - + +
18H GLN* 3.7 22.4 - - - +
21H GLY* 3.8 2.0 - - - -
52H VAL* 4.2 11.9 - - + -
54H GLN 3.5 5.6 - - - -
55H TYR* 3.6 26.0 - - + -
150H THR* 4.9 2.6 + - - +
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Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ALA* 4.2 12.1 - - + +
57G ALA* 1.3 76.8 - - - +
59G LEU* 1.3 61.2 + - - +
150G THR* 3.9 29.6 - - + +
52H VAL* 3.8 2.4 - - - -
53H ARG* 2.9 51.5 + - - +
54H GLN* 2.6 37.6 + - + +
56H ALA* 4.0 14.6 - - + -
58H LEU* 5.0 1.3 - - + -
150H THR* 3.5 42.6 - - + +
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ALA* 4.0 10.7 + - + -
58G LEU* 1.3 79.9 - - - +
60G SER* 1.3 61.9 + - - +
61G PRO* 3.3 9.7 - - - +
64G VAL* 4.7 2.9 - - + -
14H LEU* 3.9 31.6 - - + +
18H GLN* 3.4 35.0 + - + +
51H ILE* 3.1 21.1 - - + +
52H VAL* 3.7 25.4 - - + -
53H ARG* 3.2 18.8 + - - -
150H THR 5.6 1.4 + - - -
152H LEU* 3.8 19.9 - - + +
154H LEU* 4.4 13.7 - - + -
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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