Contacts of the strand formed by residues 121 - 126 (chain G) in PDB entry 3BZE
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 LYS 121 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ALA* 3.3 4.7 - - - +
118G TYR* 3.0 31.0 + - - +
119G ASP* 4.2 2.5 - - + +
120G GLY* 1.3 80.2 - - - +
122G ASP* 1.3 91.0 + - - +
123G TYR* 4.1 0.7 - - - +
136G VAL* 2.6 38.6 + - - +
137G ASP* 4.1 16.8 - - - +
1H ILE* 3.8 22.9 - - + -
60H TRP* 4.4 0.4 - - - -
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Residues in contact with ASP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G GLN* 4.9 6.1 + - - +
116G PHE 4.0 5.4 - - - -
121G LYS* 1.3 103.9 + - - +
123G TYR* 1.3 59.3 + - - +
125G THR* 4.5 9.4 + - - +
136G VAL* 3.6 30.8 - - + +
137G ASP* 4.4 2.1 - - - +
60H TRP* 2.8 36.5 + - - +
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Residues in contact with TYR 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G LEU* 3.5 19.2 - - + +
84G TYR* 3.5 8.8 - - - -
85G TYR* 3.4 37.2 - + - -
95G LEU* 6.0 0.2 - - + -
116G PHE* 2.9 23.4 + - + +
117G ALA* 4.0 2.0 - - - -
118G TYR* 3.9 26.5 - - + +
121G LYS 3.3 0.6 + - - +
122G ASP* 1.3 76.5 - - - +
124G LEU* 1.3 68.6 + - + +
136G VAL* 2.8 26.8 + - - -
137G ASP* 4.8 2.5 - - + -
140G ALA* 3.3 46.3 - - + +
143G SER* 2.8 33.9 + - - -
9S LEU* 4.2 18.4 - - + -
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G GLN* 3.5 3.3 - - - +
116G PHE* 2.8 38.9 + - + +
123G TYR* 1.3 90.7 - - + +
125G THR* 1.3 63.9 + - - +
133G TRP* 4.1 17.9 - - + -
134G THR 3.6 22.9 - - - +
135G ALA* 3.8 7.6 - - - +
140G ALA 4.2 3.8 - - - +
143G SER* 4.4 5.2 - - - +
144G GLU* 3.8 23.8 - - + +
147G SER* 4.1 9.6 - - - +
7S LEU* 3.8 29.4 - - + -
9S LEU* 3.9 15.7 - - + -
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Residues in contact with THR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G GLU 4.0 3.6 - - - +
115G GLN* 2.8 31.0 + - - +
116G PHE 5.3 0.5 + - - -
122G ASP* 4.5 6.2 + - - +
124G LEU* 1.3 77.4 + - - +
126G LEU* 1.3 76.2 + - - +
127G ASN* 3.7 2.4 + - - +
133G TRP* 3.3 8.2 - - - -
134G THR* 2.8 47.3 + - - -
136G VAL* 3.6 15.7 - - - +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G TYR* 5.8 1.6 - - - +
114G GLU* 3.0 32.1 + - + +
125G THR* 1.3 87.6 - - - +
127G ASN* 1.3 68.7 + - - +
128G GLU 3.8 0.2 + - - -
130G LEU* 3.3 47.4 - - + +
132G SER 3.4 17.7 - - - +
133G TRP* 3.5 33.5 - - + -
153G ALA* 4.2 7.4 - - + -
156G GLN* 4.6 11.0 - - + -
160G LEU* 3.8 16.2 - - + -
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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