Contacts of the strand formed by residues 52 - 59 (chain H) in PDB entry 2P6T
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G ALA* 4.5 6.3 - - + -
58G LEU 4.3 2.0 - - - +
59G LEU* 3.3 23.6 - - + -
14H LEU* 3.5 17.0 - - + -
17H LEU* 5.5 1.8 - - + -
43H LEU* 4.9 4.3 - - + -
46H LEU* 4.2 14.2 + - + -
47H GLU* 4.2 26.8 - - + +
50H GLY* 4.5 3.8 - - - -
51H ILE* 1.3 75.0 - - + +
53H ARG* 1.3 61.5 + - - +
54H GLN* 4.2 14.8 - - - +
55H TYR* 3.8 39.7 - - + +
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Residues in contact with ARG 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G LEU* 3.0 55.2 + - - +
59G LEU 3.3 21.4 + - - -
60G SER* 4.2 18.5 - - - +
61G PRO* 4.6 6.1 - - - +
148G HIS* 3.7 37.7 + - - -
50H GLY* 4.9 4.3 - - - +
51H ILE 3.4 2.2 + - - -
52H VAL* 1.3 73.8 - - - +
54H GLN* 1.3 73.7 + - - +
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Residues in contact with GLN 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLN 5.1 0.7 - - - -
19G GLU* 3.0 47.0 + - - +
57G ALA* 3.6 1.4 - - - -
58G LEU* 2.6 59.8 + - + +
149G THR* 5.5 4.2 + - - -
150G THR* 5.1 2.1 + - - -
52H VAL* 3.4 5.5 - - - +
53H ARG* 1.3 92.6 + - - +
55H TYR* 1.3 76.8 + - - +
56H ALA* 4.8 3.9 - - - +
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Residues in contact with TYR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G GLU 3.2 15.6 - - - +
20G ASN* 3.8 1.0 - - - -
21G GLY 3.0 16.5 + - - +
22G ARG* 3.8 38.8 - - + +
56G ALA 3.4 4.0 - - - +
57G ALA* 3.8 29.2 - - + -
17H LEU* 4.3 7.9 - - + +
21H GLY* 3.5 25.6 - - - +
43H LEU* 3.3 33.8 - - - +
47H GLU* 3.4 32.3 + - - +
52H VAL* 3.8 14.7 - - + +
54H GLN* 1.3 77.5 - - - +
56H ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLN 3.2 20.6 - - - +
21G GLY* 4.0 8.4 - - - +
55G TYR* 3.6 2.4 - - - +
56G ALA* 2.9 32.5 + - - +
58G LEU* 3.7 17.0 - - + -
150G THR* 3.6 20.4 - - - +
54H GLN* 4.2 4.2 - - + -
55H TYR* 1.3 75.4 - - - +
57H ALA* 1.3 62.5 + - - +
58H LEU* 3.8 7.6 + - + +
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Residues in contact with ALA 57 (chain H).
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* 3.1 42.7 + - + +
18G GLN* 3.4 27.8 + - + +
21G GLY* 3.9 0.4 - - - -
52G VAL* 4.3 9.9 - - + -
54G GLN 3.8 4.3 - - - -
55G TYR* 4.0 18.8 - - + -
150G THR* 4.9 2.9 + - - +
56H ALA* 1.3 73.0 - - - +
58H LEU* 1.3 64.9 + - - +
59H LEU* 4.9 4.5 - - + -
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Residues in contact with LEU 58 (chain H).
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* 3.6 3.8 - - - -
53G ARG* 3.0 54.0 + - - +
54G GLN* 2.7 31.4 + - - +
56G ALA* 4.2 13.5 - - + -
58G LEU* 5.1 2.2 - - + -
150G THR* 3.6 39.5 - - + +
56H ALA* 4.3 11.4 - - + +
57H ALA* 1.3 77.7 - - - +
59H LEU* 1.3 63.3 + - - +
148H HIS* 6.3 0.4 - - - +
150H THR* 3.7 29.8 - - + +
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Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.4 26.7 - - + -
18G GLN* 2.9 43.7 + - + +
51G ILE* 3.1 14.1 - - + +
52G VAL* 3.2 36.6 - - + -
53G ARG* 3.5 13.8 + - - -
150G THR 5.5 2.0 + - - -
152G LEU* 4.4 15.1 - - + +
154G LEU* 4.3 16.6 - - + -
57H ALA* 4.0 4.0 + - + -
58H LEU* 1.3 76.2 - - - +
60H SER* 1.3 61.3 + - - +
61H PRO* 3.4 10.7 - - - +
64H VAL* 4.9 6.5 - - + -
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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