Contacts of the strand formed by residues 82 - 90 (chain D) in PDB entry 3F5O
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 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ILE* 4.7 12.3 - - + -
81D GLY* 1.3 79.7 - - - +
83D SER* 1.3 63.5 + - - +
84D VAL* 3.9 0.2 - - - +
136D LYS* 3.2 5.3 - - - +
137D HIS* 2.8 57.5 + - + +
139D GLY 5.8 2.7 - - - -
149D UOC 3.7 17.3 - - + -
150D COA 3.9 41.7 - - + +
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Residues in contact with SER 83 (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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57C GLY* 5.3 0.4 - - - -
90C TYR* 3.3 32.5 - - - +
65D ASP* 3.7 12.1 + - - -
82D VAL* 1.3 71.9 - - - +
84D VAL* 1.3 61.0 + - - +
134D HIS* 2.7 35.9 + - - -
135D THR 3.9 1.3 - - - -
136D LYS* 3.5 4.2 - - - +
150D COA 3.2 44.1 + - - +
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 6.1 0.9 - - + -
113B LEU* 3.9 16.8 - - + -
115B PHE* 3.5 26.2 - - + -
135B THR* 4.0 5.8 - - + -
89C THR* 3.4 5.4 - - - +
90C TYR* 2.9 31.0 + - - -
83D SER* 1.3 75.8 - - - +
85D ASP* 1.3 72.8 + - - +
113D LEU* 4.5 3.1 - - + -
135D THR* 2.8 21.9 + - + +
136D LYS 4.1 2.0 - - - -
137D HIS* 3.6 39.7 - - + +
150D COA 4.1 4.9 - - + -
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Residues in contact with ASP 85 (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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85B ASP* 3.7 34.8 - - - +
87B ASN* 4.8 7.1 + - - -
133B ARG* 4.7 1.2 + - - -
135B THR* 2.7 32.6 + - - -
88C ILE 3.4 4.9 - - - +
89C THR* 2.6 25.8 + - - -
90C TYR* 4.8 1.1 - - - -
84D VAL* 1.3 93.3 - - - +
86D MET* 1.3 62.1 + - - +
87D ASN* 6.0 1.3 - - - +
133D ARG 4.0 0.5 - - - +
134D HIS* 3.5 3.9 - - - -
135D THR* 2.9 31.0 + - - +
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Residues in contact with MET 86 (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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57C GLY 4.5 2.2 - - - +
61C ALA* 4.3 2.2 - - + -
87C ASN* 3.2 2.8 - - - +
88C ILE* 2.8 50.2 + - + +
90C TYR* 3.5 29.3 - - + +
61D ALA* 3.8 32.8 - - + +
64D VAL* 3.7 26.2 - - + -
65D ASP* 4.0 19.1 - - + +
85D ASP* 1.3 77.0 - - - +
87D ASN* 1.3 70.6 + - - +
88D ILE* 4.1 5.4 - - + -
133D ARG 3.3 11.9 - - - +
134D HIS* 4.1 14.4 - - + -
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Residues in contact with ASN 87 (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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87A ASN* 3.4 36.5 - - + +
89A THR* 4.8 2.2 + - - -
133A ARG* 2.9 35.2 + - - +
85B ASP* 4.8 5.9 + - - -
87B ASN* 6.2 0.2 - - + -
86C MET 3.3 10.5 - - - +
87C ASN* 4.0 11.4 - - + -
85D ASP* 6.0 1.4 - - - +
86D MET* 1.3 76.3 - - - +
88D ILE* 1.3 68.4 + - - +
132D GLY* 3.0 22.9 - - - -
133D ARG* 3.0 31.1 + - - +
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Residues in contact with ILE 88 (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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133A ARG* 4.2 0.4 - - - -
85C ASP* 3.5 3.6 - - - +
86C MET* 2.8 48.4 + - + +
88C ILE* 4.2 4.7 - - + -
60D THR* 4.0 14.1 - - + -
61D ALA* 3.8 32.5 - - + -
64D VAL* 4.4 13.0 - - + -
86D MET* 4.1 19.1 - - + -
87D ASN* 1.3 81.2 - - - +
89D THR* 1.3 71.9 + - - +
90D TYR* 3.5 38.1 - - + +
130D ALA* 4.2 2.5 - - + -
131D GLN 3.4 12.1 - - - +
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Residues in contact with THR 89 (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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87A ASN* 4.7 0.2 + - - -
115A PHE* 3.3 37.2 - - + -
133A ARG* 2.8 40.2 + - - +
135A THR* 3.9 3.3 + - - +
84C VAL 3.4 4.3 - - - +
85C ASP* 2.6 24.6 + - - +
88D ILE* 1.3 71.9 - - - +
90D TYR* 1.3 63.0 + - - +
91D MET* 3.6 13.1 + - + +
130D ALA* 3.1 7.3 - - - +
131D GLN 2.8 31.1 + - - -
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Residues in contact with TYR 90 (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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115A PHE* 3.8 8.9 - - - -
65C ASP* 5.0 0.4 + - - -
83C SER* 3.3 38.2 - - - +
84C VAL* 2.9 24.2 + - - +
86C MET* 3.5 30.6 - - + +
150C COA 3.1 39.9 + - - +
57D GLY* 2.8 42.1 + - - -
60D THR* 3.7 22.7 - - + -
61D ALA 4.4 0.2 + - - -
88D ILE* 3.5 31.8 - - + +
89D THR* 1.3 72.0 - - - +
91D MET* 1.3 60.4 + - - +
92D SER 3.8 0.7 - - - +
129D ILE* 3.8 5.6 - - + +
130D ALA* 4.4 3.1 - - + -
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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