Contacts of the strand formed by residues 82 - 90 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C GLY* 1.3 80.6 - - - +
83C SER* 1.3 63.4 + - - +
84C VAL* 3.7 0.5 - - - +
136C LYS* 3.2 5.4 - - - -
137C HIS* 2.8 55.1 + - + +
149C UOC 3.6 14.8 - - + -
150C COA 3.9 40.2 - - + +
52D ILE* 4.2 16.2 - - + -
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASP* 3.6 12.9 + - - -
82C VAL* 1.3 71.3 - - - +
84C VAL* 1.3 59.2 + - - +
134C HIS* 2.7 35.5 + - - -
135C THR 3.8 1.8 - - - -
136C LYS* 3.6 4.3 - - - +
150C COA 3.1 53.0 + - - +
57D GLY* 5.2 0.4 - - - -
90D TYR* 3.3 28.4 - - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 5.9 0.4 - - + -
113A LEU* 3.9 20.0 - - + -
115A PHE* 3.7 21.1 - - + -
135A THR* 4.1 6.3 - - + -
82C VAL 3.7 0.2 - - - +
83C SER* 1.3 77.7 - - - +
85C ASP* 1.3 80.0 + - + +
113C LEU* 4.8 2.7 - - + -
135C THR* 2.9 18.9 + - + +
136C LYS 4.1 1.6 - - - -
137C HIS* 3.5 40.4 - - + +
150C COA 3.9 6.7 - - + -
89D THR* 3.4 1.9 - - - +
90D TYR* 2.9 32.0 + - - -
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.6 36.0 - - + +
87A ASN* 4.8 6.6 + - - -
133A ARG* 4.7 0.9 + - - -
135A THR* 2.8 31.2 + - - -
84C VAL* 1.3 94.9 - - - +
86C MET* 1.3 61.5 + - - +
87C ASN* 6.0 1.6 - - - +
133C ARG 4.6 0.4 - - - -
134C HIS* 3.4 4.4 - - - -
135C THR* 2.8 31.1 + - - +
88D ILE 3.5 4.5 - - - +
89D THR* 2.6 27.5 + - - +
90D TYR* 4.6 1.8 - - - -
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Residues in contact with MET 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ALA* 3.7 42.0 - - + +
64C VAL* 3.8 19.7 - - + -
65C ASP* 4.0 17.9 - - + +
85C ASP* 1.3 77.3 - - - +
87C ASN* 1.3 71.7 + - - +
88C ILE* 4.1 5.2 - - + -
133C ARG 3.3 11.9 - - - +
134C HIS* 4.1 14.6 - - + -
57D GLY 4.6 2.7 - - - +
61D ALA* 4.3 3.6 - - + -
87D ASN* 3.3 3.3 - - - +
88D ILE* 2.8 44.9 + - + +
90D TYR* 3.5 29.8 - - + +
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 4.8 5.9 + - - -
87B ASN* 3.5 28.2 + - + +
89B THR* 4.8 2.0 + - - -
133B ARG* 2.9 36.3 + - - +
85C ASP* 6.0 1.6 - - - +
86C MET* 1.3 78.0 - - - +
88C ILE* 1.3 67.6 + - - +
132C GLY* 3.0 4.3 - - - -
133C ARG* 3.0 60.3 + - - +
86D MET 3.2 10.8 - - - +
87D ASN* 4.0 11.7 - - + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 4.2 0.7 - - - -
60C THR* 4.0 13.7 - - + -
61C ALA* 3.7 34.3 - - + -
64C VAL* 4.5 12.1 - - + -
86C MET* 4.1 16.6 - - + -
87C ASN* 1.3 81.6 - - - +
89C THR* 1.3 70.5 + - - +
90C TYR* 3.6 32.3 - - + +
130C ALA* 4.3 3.1 - - + -
131C GLN 3.4 11.7 - - - +
85D ASP* 3.4 4.2 - - - +
86D MET* 2.8 55.5 + - + +
88D ILE* 4.2 5.2 - - + -
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASN* 4.8 0.2 + - - -
115B PHE* 3.2 37.5 - - + -
133B ARG* 2.8 43.3 + - + +
135B THR* 4.0 2.6 + - - +
88C ILE* 1.3 71.4 - - - +
90C TYR* 1.3 62.8 + - - +
91C MET* 3.7 10.8 - - + +
130C ALA* 3.1 8.3 - - - +
131C GLN 2.8 31.5 + - - -
84D VAL 3.4 7.0 - - - +
85D ASP* 2.6 20.7 + - - +
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 3.9 8.8 - - - -
57C GLY* 2.8 42.9 + - - -
60C THR* 3.7 23.8 - - + -
88C ILE* 3.6 31.5 - - + +
89C THR* 1.3 73.4 - - - +
91C MET* 1.3 59.9 + - - +
92C SER 3.7 0.7 - - - +
129C ILE* 3.8 5.4 - - + +
130C ALA* 4.4 4.0 - - + -
65D ASP* 5.5 0.2 - - - -
83D SER* 3.3 39.4 - - - +
84D VAL* 2.9 23.2 + - - +
86D MET* 3.5 29.1 - - + +
150D COA 3.1 39.9 + - - +
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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