Contacts of the strand formed by residues 115 - 120 (chain B) in PDB entry 1Z09
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 GLY 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.3 5.9 - - - +
114B GLN* 1.3 82.0 - - - +
116B ILE* 1.3 64.0 + - - -
129B THR* 4.2 4.0 - - - -
130B MET* 3.4 23.1 - - - -
187B ILE* 2.6 37.2 + - - +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 5.2 9.6 - - + +
107B LEU* 4.7 7.2 - - + +
108B GLN* 3.3 54.1 - - - +
113B VAL* 5.0 7.4 - - + -
115B GLY* 1.3 78.6 - - - +
117B ILE* 1.3 68.2 + - - +
118B VAL* 4.2 13.7 - - + -
128B SER* 3.1 5.4 - - - -
129B THR* 2.9 46.2 + - + +
130B MET* 4.3 1.5 + - - +
184B LEU* 5.2 9.2 - - + -
185B ILE 4.1 6.1 - - - +
186B VAL* 5.2 7.2 - - + -
187B ILE 4.3 9.6 - - - +
188B GLN* 5.7 1.8 - - + +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 1.3 80.1 - - - +
118B VAL* 1.3 62.6 + - - +
119B VAL* 3.7 12.2 + - + +
125B PRO* 3.7 25.6 - - + -
127B LYS 3.7 3.4 - - - +
128B SER* 4.4 4.0 - - - -
130B MET* 3.3 38.4 - - + -
135B THR* 3.8 18.8 - - + +
138B TYR* 3.8 15.7 - - + -
139B ALA* 4.0 11.4 - - + +
184B LEU* 3.3 4.0 - - - +
185B ILE* 3.0 44.2 + - + +
187B ILE* 4.0 9.0 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 5.0 4.7 - - - +
104B LEU* 3.2 40.4 - - + -
116B ILE* 4.9 9.4 - - + +
117B ILE* 1.3 72.5 - - - +
119B VAL* 1.3 66.7 + - - +
125B PRO* 2.9 8.3 - - - +
126B ILE* 2.8 34.0 + - + -
127B LYS* 2.8 37.0 + - + +
128B SER* 5.4 0.4 - - - -
182B TYR* 5.5 9.9 - - + -
183B PHE 4.8 1.8 - - - +
184B LEU* 3.7 10.1 - - + -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 3.7 25.3 + - + +
118B VAL* 1.3 82.8 - - - +
120B ASN* 1.3 63.1 + - - +
123B GLY* 2.7 39.7 - - - +
124B ILE 3.6 3.1 - - - +
125B PRO* 3.8 6.7 - - + -
139B ALA* 4.6 8.3 - - + +
143B HIS* 4.5 1.8 - - + -
182B TYR* 4.4 2.4 - - - +
183B PHE* 2.5 74.3 + - + +
184B LEU* 5.1 0.7 - - - -
185B ILE* 4.8 9.2 - - + -
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL 4.3 0.2 + - - -
119B VAL* 1.3 70.7 - - - +
121B THR* 1.3 58.7 + - - +
122B GLU* 2.8 43.3 + - - +
123B GLY 3.1 5.2 + - - -
124B ILE* 2.4 27.7 + - - +
126B ILE* 3.1 43.0 - - + +
181B ASP 4.1 0.7 - - - -
182B TYR* 3.2 20.6 - - + -
183B PHE* 2.7 29.2 - - - -
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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