Contacts of the strand formed by residues 49 - 55 (chain D) in PDB entry 4QPL
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 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B SER* 3.2 32.8 - - - +
36B THR* 4.0 26.2 - - + +
36D THR* 3.7 25.8 - - + -
37D ILE 3.7 2.5 - - - +
38D MET* 4.0 8.3 - - + -
48D GLY* 1.3 73.9 - - - +
50D PHE* 1.3 62.9 + - - +
51D PHE* 3.7 27.6 - - + -
71D THR* 3.8 8.3 + - - +
146D ALA* 2.8 27.8 + - - +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D THR* 3.3 4.5 - - - +
37D ILE* 2.8 55.3 + - + +
39D GLY* 4.2 6.3 - - - -
45D TYR* 3.9 36.3 - + + -
48D GLY* 3.7 22.2 - - - -
49D VAL* 1.3 73.8 - - - +
51D PHE* 1.3 62.4 + - - +
52D LEU* 3.6 4.8 - - + +
69D PHE* 3.8 23.1 - + + -
71D THR* 3.5 18.4 - - + -
72D LYS 4.1 4.0 - - - -
73D ILE* 3.7 33.0 - - + -
110D LEU* 5.3 3.4 - - + -
142D THR* 4.1 9.0 - - + -
146D ALA* 3.6 21.5 - - + -
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 4.0 31.6 - + - -
34D GLN* 3.9 19.3 - - - +
35D ALA 3.4 3.1 - - - -
36D THR* 3.5 34.1 - - + -
49D VAL* 3.7 23.8 - - + -
50D PHE* 1.3 71.9 - - - +
52D LEU* 1.3 62.1 + - - +
69D PHE* 3.7 1.7 - - - +
70D THR* 2.8 44.0 + - - +
71D THR* 2.8 20.2 + - - +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLN* 3.5 11.0 + - - +
35D ALA* 2.9 40.3 + - + +
37D ILE* 4.1 24.9 - - + +
50D PHE 3.6 17.7 - - - +
51D PHE* 1.3 81.9 - - - +
53D THR* 1.3 66.7 + - - +
67D ILE* 3.8 23.8 - - + -
68D ALA 3.1 13.0 - - - +
69D PHE* 4.1 29.4 - - + -
70D THR* 4.2 1.6 - - - +
84D ILE* 4.5 0.2 - - + -
103D LEU* 4.4 8.3 - - + -
106D ILE* 4.1 17.3 - - + -
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 4.5 11.4 - - - +
33D TRP 3.6 6.1 - - - +
34D GLN* 4.8 8.5 - - + +
52D LEU* 1.3 75.2 - - - +
54D VAL* 1.3 64.3 + - - +
55D HIS* 4.2 21.7 + - + -
66D LYS 3.7 1.1 + - - +
67D ILE* 3.3 6.4 - - - +
68D ALA* 2.9 38.1 + - - +
70D THR* 3.5 24.5 - - + +
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PHE 3.7 0.5 - - - +
32D HIS* 3.3 7.1 - - - -
33D TRP* 2.8 53.4 + - + +
35D ALA* 4.5 20.2 - - + -
52D LEU 5.3 0.2 - - - -
53D THR* 1.3 79.0 - - - +
55D HIS* 1.3 62.5 + - - +
56D PHE* 3.8 29.8 - - + -
65D PRO* 4.1 10.8 - - + -
66D LYS 3.4 3.1 - - - -
67D ILE* 4.0 28.0 - - + -
99D VAL* 4.4 14.8 - - + -
103D LEU* 5.8 0.9 - - + -
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Residues in contact with HIS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PHE 3.4 5.6 - - - +
32D HIS* 3.3 49.2 + + + -
53D THR* 4.2 19.5 + - + -
54D VAL* 1.3 74.1 - - - +
56D PHE* 1.3 64.9 + - - +
57D PRO* 3.9 1.0 - - - +
65D PRO* 3.6 1.0 - - - +
66D LYS* 2.8 54.2 + - + +
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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