Contacts of the strand formed by residues 150 - 156 (chain D) in PDB entry 5FJV
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 PRO 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C VAL* 5.2 1.6 - - + -
129C PHE* 3.5 32.1 - - + -
178C TRP* 3.5 39.7 - - + +
83D VAL 3.4 9.4 - - - +
84D TRP* 4.5 1.8 - - + +
131D VAL* 4.9 2.3 - - - +
132D THR 5.3 0.5 + - - -
133D HIS* 4.2 24.0 + - + +
135D THR* 3.3 27.1 - - + -
148D VAL 3.5 0.4 - - - -
149D PRO* 1.3 89.3 - - + +
151D ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 151 (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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129C PHE* 4.1 2.9 - - - -
82D ASN* 3.3 2.3 - - - +
83D VAL* 2.7 45.5 + - + +
85D LEU* 5.1 2.2 - - + -
130D ALA 5.1 1.1 - - - +
131D VAL* 4.6 15.0 - - + -
132D THR 5.6 0.4 - - - +
149D PRO 4.7 2.7 - - - +
150D PRO* 1.3 76.7 - - - +
152D ILE* 1.3 64.6 + - - +
153D TYR* 3.6 35.4 + - + +
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Residues in contact with ILE 152 (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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124C ASN* 3.6 36.1 - - - +
125C ALA 3.8 11.2 - - - +
126C ASP* 3.9 14.4 - - + +
129C PHE* 3.9 11.7 - - + -
70D ILE* 3.9 16.6 - - + -
80D THR* 4.4 8.3 - - + -
81D THR 3.3 9.0 - - - +
82D ASN* 3.4 20.4 - - + +
128D GLU* 4.8 14.9 + - - +
151D ALA* 1.3 70.3 - - - +
153D TYR* 1.3 67.0 + - - +
154D LYS* 4.2 17.4 + - - +
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Residues in contact with TYR 153 (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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79D MET 3.7 0.7 - - - +
80D THR* 3.3 4.5 - - - +
81D THR* 2.8 41.1 + - - +
83D VAL* 3.9 21.3 - - + -
85D LEU* 3.5 22.6 - - + +
119D ILE 5.4 1.0 + - - -
120D VAL 5.7 0.2 - - - -
121D LEU* 3.4 22.6 + - + -
125D ALA* 4.4 0.7 - - + -
128D GLU* 3.1 29.4 - - + +
129D PHE 3.6 14.5 + - - -
130D ALA* 3.9 17.8 - - - -
131D VAL 4.0 0.7 + - - -
151D ALA* 3.6 22.5 - - + +
152D ILE* 1.3 75.3 - - - +
154D LYS* 1.3 63.0 + - - +
155D SER* 3.9 0.4 - - - -
173D MET* 3.6 28.3 - - + -
175D PHE* 3.6 23.5 - + - -
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Residues in contact with LYS 154 (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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126C ASP* 5.9 2.2 + - - +
78D MET* 5.0 9.0 - - + -
79D MET 3.6 4.0 - - - -
80D THR* 3.4 23.1 - - + +
121D LEU* 4.4 1.6 - - - +
124D ASN 2.6 27.3 - - - +
125D ALA* 3.7 7.6 - - - +
126D ASP* 3.7 16.3 + - + +
127D GLY* 4.0 34.2 - - - +
128D GLU* 5.6 1.8 - - - +
152D ILE* 4.2 17.3 + - - +
153D TYR* 1.3 74.5 - - - +
155D SER* 1.3 54.4 + - - +
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Residues in contact with SER 155 (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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78D MET* 3.1 6.2 - - - +
79D MET* 2.7 60.2 + - - +
81D THR* 5.4 0.2 - - - -
121D LEU* 5.0 1.8 - - - -
123D ASN* 3.2 11.1 + - - -
124D ASN 4.0 3.4 - - - -
153D TYR 4.9 0.2 - - - -
154D LYS* 1.3 75.2 - - - +
156D SER* 1.3 63.4 + - - +
157D CYS* 3.8 1.0 - - - -
172D LYS 3.2 23.6 + - - -
173D MET* 4.0 21.4 - - - +
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Residues in contact with SER 156 (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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77D GLN 4.7 0.2 - - - -
78D MET* 3.9 10.3 - - - -
123D ASN* 2.6 27.9 + - - -
124D ASN* 3.9 6.8 - - - +
155D SER* 1.3 84.2 + - - +
157D CYS* 1.3 64.6 + - - +
171D CYS* 3.9 3.3 - - - -
172D LYS* 3.9 13.7 + - - +
68E GLN* 2.8 31.8 + - - -
201E GLU* 4.8 2.3 + - - +
203E GLY* 5.8 1.3 - - - -
204E GLU* 4.0 13.7 - - - -
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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