Contacts of the strand formed by residues 70 - 76 (chain D) in PDB entry 4FPR
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 MET 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C THR* 3.4 11.6 + - - +
52D THR* 4.1 20.5 - - + +
55D LEU* 3.6 41.7 - - - +
56D ILE* 3.8 19.7 - - + +
66D TRP* 3.6 40.2 - - + +
67D GLY 3.7 11.2 - - - +
68D ILE 3.3 5.7 + - - -
69D ASP* 1.3 80.0 + - - +
71D THR* 1.3 71.9 + - - +
94D ILE* 4.0 18.8 - - + -
95D THR 3.1 6.3 - - - +
96D ALA* 3.8 11.0 - - + -
131D TRP* 4.2 6.5 - - + -
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Residues in contact with THR 71 (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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41C LYS* 4.0 29.2 - - + +
42C THR* 4.2 4.3 - - - +
45C LEU* 4.1 22.0 - - + -
74C VAL* 6.1 1.1 - - + -
49D ASN* 5.8 0.2 - - - -
52D THR* 4.9 1.8 - - - -
70D MET* 1.3 80.5 - - - +
72D ALA* 1.3 60.8 + - - +
73D LYS* 5.9 2.8 - - - +
93D LYS 3.8 0.9 - - - +
94D ILE* 3.4 4.0 - - - -
95D THR* 2.8 40.1 + - - -
97D HIS* 2.6 32.2 + - + +
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Residues in contact with ALA 72 (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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45C LEU* 4.7 12.2 - - - +
72C ALA 5.2 4.0 - - - +
45D LEU* 4.0 10.1 - - + +
48D CYS* 3.8 19.7 - - - -
49D ASN* 3.4 23.9 + - - +
52D THR* 3.3 24.4 + - - +
71D THR* 1.3 75.5 - - - +
73D LYS* 1.3 67.8 + - - +
93D LYS 3.5 4.3 - - - -
94D ILE* 4.4 2.5 - - + +
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Residues in contact with LYS 73 (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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72C ALA 5.7 0.7 - - - +
73C LYS* 4.1 43.7 - - + +
45D LEU* 4.1 6.3 - - - -
48D CYS* 3.6 4.6 - - - -
71D THR* 5.9 2.7 - - - +
72D ALA* 1.3 78.0 - - - +
74D VAL* 1.3 62.7 + - - +
75D GLN* 6.2 1.6 - - + -
93D LYS* 2.9 54.7 + - + +
95D THR* 5.5 6.7 + - - +
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Residues in contact with VAL 74 (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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71C THR* 6.0 2.0 - - + -
73C LYS* 5.9 3.1 - - - -
41D LYS* 4.4 9.2 - - + +
44D ALA* 4.2 15.0 - - + +
45D LEU* 3.6 36.0 - - + +
48D CYS* 4.3 10.1 - - + -
73D LYS* 1.3 78.6 - - - +
75D GLN* 1.3 73.2 + - - +
76D CYS* 4.2 7.4 - - - -
90D CYS* 4.0 21.5 - - + -
91D THR 3.2 15.9 - - - +
92D CYS* 4.6 0.7 - - + -
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Residues in contact with GLN 75 (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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136A LYS* 3.4 28.9 - - + +
73C LYS* 5.4 7.3 + - - +
73D LYS* 6.2 1.6 - - + -
74D VAL* 1.3 82.9 - - - +
76D CYS* 1.3 62.9 + - - +
90D CYS* 3.3 1.7 - - - -
91D THR* 2.8 34.2 + - - +
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Residues in contact with CYS 76 (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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136A LYS* 3.6 9.3 - - - +
39D PRO* 5.3 2.7 - - - -
40D THR 6.3 0.4 - - - -
41D LYS* 3.9 29.2 + - - +
44D ALA* 3.6 21.3 - - - -
74D VAL* 4.2 4.9 - - - -
75D GLN* 1.3 76.1 - - - +
77D ALA* 1.3 72.6 - - - +
78D PRO* 3.6 3.6 - - - +
88D VAL* 4.3 3.4 - - + -
89D LEU 3.5 3.8 - - - -
90D CYS* 2.0 45.5 - - - -
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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