Contacts of the strand formed by residues 99 - 106 (chain C) in PDB entry 3BRW
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 HIS 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.8 25.0 - - + +
99B HIS 5.6 1.7 - - - +
90C TYR* 2.7 27.7 + + - -
94C PHE* 3.2 48.6 + + + +
97C LYS 2.8 25.9 + - - +
98C GLU* 1.3 74.6 - - - +
100C PHE* 1.3 73.8 + - - +
101C ASN* 3.2 30.2 + - - -
116C LEU 3.6 12.8 - - - +
117C LYS* 4.1 5.6 - - + +
178C SER* 4.2 1.1 - - - -
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Residues in contact with PHE 100 (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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101B ASN* 6.2 1.8 - - - -
172B VAL 3.5 23.3 - - - -
173B LEU* 3.9 13.2 - - + -
174B TYR 4.1 7.0 - - - -
175B PRO* 3.8 38.4 - - + -
177B ALA* 5.8 1.3 - - + -
98C GLU* 5.4 7.0 - - + -
99C HIS* 1.3 86.0 - - - +
101C ASN* 1.3 67.6 + - - +
102C TYR* 3.6 31.4 - + + -
114C PHE 3.9 0.3 - - - +
115C SER* 3.5 0.3 - - - -
116C LEU* 2.9 54.2 + - + +
117C LYS* 5.8 0.9 - - - -
118C TYR* 6.1 1.6 - - + -
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Residues in contact with ASN 101 (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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90C TYR* 3.7 1.2 + - - -
99C HIS* 3.2 28.3 + - - -
100C PHE* 1.3 80.2 - - - +
102C TYR* 1.3 58.9 + - - +
113C VAL* 5.7 1.3 - - + +
114C PHE 3.4 2.7 - - - +
115C SER* 2.6 30.1 + - - -
171C PRO* 3.6 2.6 - - - +
172C VAL* 2.7 55.7 + - + +
177C ALA* 5.0 4.0 - - - +
178C SER* 4.9 5.9 - - - +
181C ILE* 3.6 24.2 - - + +
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Residues in contact with TYR 102 (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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173B LEU* 3.4 50.7 + - + +
408B MET* 4.3 5.6 - - + +
409B MET* 4.6 4.0 - - - -
100C PHE* 3.6 28.0 - + + -
101C ASN* 1.3 78.9 - - - +
103C TYR* 1.3 61.9 + - - +
113C VAL* 3.6 3.8 - - - +
114C PHE* 2.7 45.4 + + + +
116C LEU* 3.7 23.1 - - + +
153C VAL* 3.7 29.6 - - + -
169C PHE* 3.7 23.3 - - + -
170C TYR 3.2 7.0 - - - +
171C PRO* 3.7 28.7 - - + -
172C VAL* 4.3 1.3 - - - -
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Residues in contact with TYR 103 (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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102C TYR* 1.3 75.3 - - - +
104C SER* 1.3 61.8 + - - +
112C LEU 3.2 13.9 - - - +
113C VAL* 4.7 6.7 - - + -
169C PHE* 3.8 3.8 - - - -
170C TYR* 2.8 79.7 + + + +
171C PRO 3.9 12.1 + - - -
172C VAL* 3.8 18.4 - - + -
398C TYR* 3.5 31.9 - + + -
401C LEU* 4.5 12.3 - - + -
402C HIS* 3.1 54.6 + + + -
405C SER* 4.8 5.0 - - - -
406C GLN* 5.4 2.1 + - - +
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Residues in contact with SER 104 (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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103C TYR* 1.3 79.3 - - - +
105C LEU* 1.3 60.0 + - - +
106C ASP 3.9 0.2 - - - -
111C HIS 3.8 0.2 - - - -
112C LEU* 2.9 36.2 + - - +
166C VAL* 3.0 35.6 - - - +
168C ARG 3.2 11.5 + - - -
169C PHE* 3.4 25.9 - - - -
170C TYR* 5.0 5.8 - - - -
398C TYR* 3.6 10.7 - - - -
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Residues in contact with LEU 105 (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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104C SER* 1.3 74.4 + - - +
106C ASP* 1.3 66.8 + - - +
107C THR* 3.8 6.5 + - + +
110C GLY* 3.5 25.8 - - - +
111C HIS* 3.9 24.9 - - + +
166C VAL* 3.6 15.8 - - - +
170C TYR* 5.9 1.6 - - - -
398C TYR* 3.6 18.7 + - + +
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Residues in contact with ASP 106 (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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104C SER 3.8 1.6 + - - -
105C LEU* 1.3 74.9 - - - +
107C THR* 1.3 71.4 + - - +
108C ALA* 3.0 14.4 + - - +
109C LEU* 3.5 35.8 + - + +
110C GLY* 2.8 44.2 + - - +
112C LEU* 4.2 14.5 - - + +
163C ASP 3.9 1.7 - - - +
164C VAL* 3.8 3.8 - - - +
165C ASN* 2.7 45.7 + - - +
166C VAL* 4.9 2.9 - - + -
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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