Contacts of the strand formed by residues 100 - 106 (chain A) 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 PHE 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU* 6.0 1.3 - - + -
99A HIS* 1.3 86.9 - - - +
101A ASN* 1.3 68.1 + - - +
102A TYR* 3.4 34.3 - + + -
114A PHE 4.1 0.3 - - - +
115A SER* 3.3 0.9 - - - -
116A LEU* 2.9 52.9 + - + +
117A LYS* 5.9 0.4 - - - -
118A TYR* 6.0 6.3 - - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.7 1.9 + - - -
99A HIS* 3.0 34.8 + - - -
100A PHE* 1.3 75.0 - - - +
102A TYR* 1.3 60.2 + - - +
113A VAL* 6.0 2.0 - - + -
114A PHE 3.7 3.8 - - - +
115A SER* 2.9 25.0 + - - +
171A PRO* 3.8 1.2 - - - +
172A VAL* 2.8 51.2 + - + +
177A ALA* 5.0 4.2 - - - +
178A SER* 4.8 6.9 - - - +
181A ILE* 3.5 27.9 - - + +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 3.4 41.3 - + + +
101A ASN* 1.3 76.4 - - - +
103A TYR* 1.3 62.5 + - - +
112A LEU 3.9 0.2 - - - +
113A VAL* 3.7 3.3 - - - +
114A PHE* 2.8 41.5 + + + +
116A LEU* 3.7 22.9 - - + +
153A VAL* 3.6 31.2 - - + +
156A MET* 6.1 0.6 - - + +
169A PHE* 3.8 26.4 - - + -
170A TYR 3.3 9.2 - - - +
171A PRO* 3.7 33.2 - - + -
172A VAL* 4.3 2.7 - - - -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 1.3 74.7 - - - +
104A SER* 1.3 60.2 + - - +
112A LEU 3.1 13.5 - - - +
113A VAL* 4.8 6.1 - - + -
169A PHE* 3.7 3.6 - - - -
170A TYR* 2.9 70.4 + + + +
171A PRO 3.8 13.2 - - - -
172A VAL* 3.7 18.6 - - + -
398A TYR* 3.6 32.5 - + + -
401A LEU* 4.1 15.4 + - + -
402A HIS* 3.2 54.5 + + + -
405A SER* 4.4 4.7 - - - -
406A GLN* 4.5 9.2 + - - +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 1.3 78.4 - - - +
105A LEU* 1.3 64.8 + - - +
106A ASP 3.9 0.7 - - - -
111A HIS 4.1 0.2 - - - -
112A LEU* 3.1 32.3 + - - +
166A VAL* 3.0 18.2 - - - +
168A ARG 2.6 25.4 + - - -
169A PHE* 3.5 25.6 - - - -
170A TYR* 4.5 10.5 - - - -
398A TYR* 3.4 13.6 - - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A SER* 1.3 76.9 + - - +
106A ASP* 1.3 65.8 + - - +
107A THR* 3.8 14.6 + - + +
110A GLY 4.4 9.9 - - - +
111A HIS* 4.0 26.9 - - + +
166A VAL* 3.5 16.0 - - - +
170A TYR* 5.7 1.8 - - - -
398A TYR* 3.6 21.7 + - + +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A SER 3.9 2.4 - - - -
105A LEU* 1.3 74.8 - - - +
107A THR* 1.3 60.5 + - - +
108A ALA* 3.1 26.2 + - - +
109A LEU* 3.2 35.5 + - + +
110A GLY* 2.8 43.9 + - - +
112A LEU* 4.1 11.6 - - + +
163A ASP 4.0 0.3 - - - +
164A VAL* 4.3 0.2 - - - -
165A ASN* 3.1 33.2 + - - +
166A VAL* 3.7 17.4 - - + +
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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