Contacts of the strand formed by residues 51 - 57 (chain F) in PDB entry 4DHZ
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 THR 51 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F VAL* 3.5 23.9 - - - +
39F ILE 3.8 3.6 - - - -
40F ALA* 4.2 11.0 - - + +
49F GLY 5.1 2.7 - - - +
50F GLY* 1.3 78.6 - - - +
52F PHE* 1.3 62.1 + - - +
53F LYS* 4.2 0.9 + - - +
73F THR* 3.8 11.1 + - - +
148F ALA* 3.2 22.1 + - - +
150F ASN* 4.5 15.3 + - - +
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Residues in contact with PHE 52 (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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38F VAL* 3.5 3.5 - - - +
39F ILE* 2.8 48.9 + - + +
41F GLY* 3.7 18.4 - - - -
47F PHE* 3.5 31.2 - + + -
50F GLY 3.7 15.3 - - - -
51F THR* 1.3 72.4 - - - +
53F LYS* 1.3 62.4 + - - +
54F LEU* 3.7 6.7 - - + +
71F PHE* 3.9 19.7 - + + -
73F THR* 3.4 25.4 - - + -
74F LYS 4.5 2.0 - - - -
75F ILE* 3.9 29.2 - - + -
112F LEU* 4.8 11.7 - - + -
144F THR* 4.5 4.9 - - + -
148F ALA* 3.7 23.6 - - + -
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Residues in contact with LYS 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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37F VAL 3.2 9.0 - - - +
38F VAL* 4.4 10.0 - - + +
51F THR* 4.2 1.2 + - - -
52F PHE* 1.3 71.5 - - - +
54F LEU* 1.3 65.1 + - - +
55F GLU* 5.4 1.6 - - - +
71F PHE* 3.9 0.3 - - - -
72F MET* 2.9 75.2 + - + +
73F THR* 2.8 27.2 + - - +
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Residues in contact with LEU 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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35F PHE 3.8 0.2 - - - +
37F VAL* 2.5 50.0 + - + +
39F ILE* 3.7 23.3 - - + -
52F PHE* 3.7 12.3 - - + +
53F LYS* 1.3 84.0 - - - +
55F GLU* 1.3 71.5 + - - +
69F VAL* 4.0 12.1 - - + -
70F ARG 3.5 10.8 - - - +
71F PHE* 3.6 49.1 - - + -
72F MET 4.3 0.9 - - - +
86F ILE* 3.9 16.2 - - + -
105F LEU* 6.0 1.6 - - + -
108F ILE* 4.1 7.4 - - + -
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Residues in contact with GLU 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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34F TYR* 2.6 42.2 + - + +
35F PHE 3.6 3.6 - - - +
36F HIS* 3.2 27.3 + - - +
53F LYS* 5.4 1.9 - - - +
54F LEU* 1.3 84.7 + - - +
56F LEU* 1.3 60.8 + - - +
68F LYS 3.6 1.4 - - - +
69F VAL* 3.4 5.9 - - - +
70F ARG* 3.0 52.5 + - - +
72F MET* 3.5 39.9 - - + +
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Residues in contact with LEU 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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33F ARG 3.8 0.2 - - - +
34F TYR* 3.8 4.8 - - - -
35F PHE* 2.9 54.5 + - + +
37F VAL* 4.6 7.4 - - + -
54F LEU 4.2 0.4 - - - -
55F GLU* 1.3 74.8 - - - +
57F PHE* 1.3 62.6 + - - +
58F LEU* 3.8 19.5 - - + -
67F PRO* 4.0 12.8 - - + -
68F LYS 3.3 4.3 - - - +
69F VAL* 3.9 23.8 - - + -
101F ILE* 3.7 44.9 - - + -
104F VAL* 4.3 12.6 - - + -
105F LEU* 4.5 9.6 - - + -
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Residues in contact with PHE 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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31F ASN* 4.6 13.2 - - - -
33F ARG* 3.3 39.3 - - + -
34F TYR* 4.3 19.1 - + + -
56F LEU* 1.3 75.4 - - - +
58F LEU* 1.3 82.0 + - - +
59F PRO* 3.5 12.1 - - + +
60F GLU 5.4 0.2 - - - -
67F PRO* 3.4 6.4 - - - +
68F LYS* 2.8 53.1 + - + +
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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