Contacts of the strand formed by residues 38 - 44 (chain H) in PDB entry 6PB4
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 38 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H GLU* 1.3 93.6 + - - +
39H LEU* 1.3 60.6 + - - +
40H TYR* 3.4 37.1 + - + +
82H ARG* 3.6 17.4 + - - +
96H GLU* 4.2 3.8 - - + -
97H ILE 3.3 30.7 - - - +
98H SER* 3.6 6.9 - - - +
99H TYR* 3.2 17.6 + - - -
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Residues in contact with LEU 39 (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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38H THR* 1.3 67.5 - - - +
40H TYR* 1.3 69.4 + - - +
69H PHE* 4.3 13.0 - - + -
70H ILE 3.3 17.0 - - - +
71H GLY 3.1 26.7 - - - +
72H GLU* 3.7 14.6 - - + -
75H LEU* 4.5 5.8 - - + -
97H ILE* 2.4 65.3 + - + +
99H TYR* 3.1 14.7 - - + -
102H PHE* 3.4 51.1 - - + -
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Residues in contact with TYR 40 (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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23H TYR* 5.0 5.0 + + - -
29H LEU* 4.6 29.6 - - + -
30H ILE* 5.0 12.6 - - + -
38H THR* 3.4 35.4 + - + +
39H LEU* 1.3 85.9 - - - +
41H TYR* 1.3 62.3 + - - +
69H PHE* 3.3 14.3 - - - -
70H ILE* 3.0 48.0 + - + +
82H ARG* 5.3 3.8 - - - -
94H VAL* 3.8 13.0 - - + -
95H ALA 3.2 8.3 - - - +
96H GLU* 3.5 33.7 + - + -
97H ILE* 4.6 1.8 - - - -
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Residues in contact with TYR 41 (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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11H LEU* 3.6 32.6 - - + +
14H PHE* 4.9 4.3 - + + -
15H LEU* 4.1 19.3 - - + -
40H TYR* 1.3 79.1 - - - +
42H ILE* 1.3 70.1 + - - +
43H VAL* 3.0 11.9 + - - -
67H GLY* 3.3 42.7 + - - -
68H ASP 3.0 19.1 - - - -
69H PHE* 3.4 46.4 - + + +
70H ILE* 4.9 0.9 - - - +
94H VAL* 3.3 6.3 - - - -
95H ALA* 2.9 38.8 + - + -
97H ILE* 4.9 0.2 - - + -
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Residues in contact with ILE 42 (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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41H TYR* 1.3 74.8 - - - +
43H VAL* 1.3 64.4 + - - +
44H LYS 3.2 23.8 - - - +
45H GLY 3.3 9.0 - - - +
47H VAL* 4.2 17.0 - - + -
64H LEU* 3.1 45.1 - - + +
65H ASN 3.2 18.2 - - - +
66H GLN* 3.3 19.9 - - - +
67H GLY 3.2 19.9 + - - -
68H ASP* 2.9 16.5 + - + +
69H PHE 6.2 0.2 - - - -
70H ILE* 5.8 8.3 - - + -
92H CYS* 4.9 3.8 - - + -
93H GLU 3.8 3.1 - - - +
94H VAL* 4.8 5.8 - - + +
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Residues in contact with VAL 43 (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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11H LEU* 5.9 0.9 - - + -
15H LEU* 3.8 40.6 - - + -
20H ILE* 4.3 9.6 - - + -
41H TYR* 3.0 9.3 + - + +
42H ILE* 1.3 73.5 - - - +
44H LYS* 1.3 56.8 + - - +
66H GLN* 3.6 11.3 - - - +
67H GLY 5.2 0.2 + - - -
93H GLU* 2.7 36.3 + - + +
94H VAL 4.0 2.0 - - - -
95H ALA* 3.5 25.1 - - + +
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Residues in contact with LYS 44 (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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22H LYS* 5.0 4.0 - - - +
42H ILE* 3.2 10.6 - - - +
43H VAL* 1.3 78.1 - - - +
45H GLY* 1.3 65.9 + - - +
66H GLN* 3.4 16.6 - - - +
90H THR* 6.2 1.3 - - - -
91H ALA* 3.3 25.6 - - - +
92H CYS* 3.1 8.3 - - - +
93H GLU* 2.9 50.8 + - + +
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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