Contacts of the strand formed by residues 128 - 136 (chain B) in PDB entry 1YBY
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 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 3.6 13.0 - - - +
127B ASN* 1.3 95.0 - - + +
129B VAL* 1.3 68.6 + - - +
130B GLU* 6.4 0.2 - - + -
173B ARG* 4.3 22.0 - - + +
174B ILE 3.3 13.9 - - - +
175B ASP* 3.4 33.4 - - + -
176B THR* 4.8 0.4 - - - +
177B ARG* 3.9 9.9 - - - -
182B MSE 4.0 26.0 - - + -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.5 33.4 - - + +
105B VAL* 4.5 8.1 - - + -
106B LYS* 6.6 0.2 - - - -
109B GLU* 6.3 2.2 - - + -
126B PRO* 4.0 15.5 - - + -
128B PHE* 1.3 80.1 - - - +
130B GLU* 1.3 65.8 + - - +
131B LEU* 4.1 11.4 - - + -
172B ILE 3.7 0.2 - - - +
173B ARG* 3.3 5.9 - - - +
174B ILE* 2.9 49.9 + - + +
176B THR* 3.7 18.6 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 3.7 17.5 + - - -
128B PHE* 6.4 0.2 - - + -
129B VAL* 1.3 79.8 - - - +
131B LEU* 1.3 69.0 + - - +
155B GLU* 4.4 0.5 - - - +
171B ILE* 4.0 17.4 - - + +
172B ILE 3.2 5.6 - - - +
173B ARG* 2.6 39.3 + - + +
185B VAL* 3.9 20.3 - - - +
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Residues in contact with LEU 131 (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 PHE* 3.4 35.7 - - + +
106B LYS* 3.6 32.3 - - + -
129B VAL* 4.1 7.0 - - + -
130B GLU* 1.3 82.2 - - - +
132B GLU* 1.3 62.2 + - - +
154B VAL* 3.6 32.8 - - + -
155B GLU* 3.4 14.8 - - + +
156B THR* 4.0 6.7 - - + -
171B ILE* 4.0 4.9 - - - +
172B ILE* 2.9 36.4 + - - +
174B ILE* 3.7 21.8 - - + -
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Residues in contact with GLU 132 (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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131B LEU* 1.3 71.1 - - - +
133B VAL* 1.3 72.1 + - - +
134B THR* 3.5 12.0 + - + +
154B VAL* 3.3 4.2 - - - +
155B GLU* 2.8 51.4 + - + +
168B LYS* 5.7 0.9 - - - +
169B GLY* 3.4 28.1 + - - +
170B ASP 3.3 11.2 - - - +
171B ILE* 3.6 15.7 - - + +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 1.3 75.9 - - - +
134B THR* 1.3 61.8 + - - +
135B ASP 4.1 2.9 - - - +
136B THR* 4.0 20.2 - - + -
152B ALA* 4.0 20.2 - - + -
153B ILE 3.6 12.1 - - - +
154B VAL* 4.2 4.7 - - + -
166B VAL* 3.8 24.7 - - + -
167B ASN 3.8 12.1 - - - +
168B LYS* 3.4 4.4 - - - +
169B GLY 2.8 30.5 + - - -
170B ASP 2.9 19.3 + - - +
172B ILE* 4.1 23.8 - - + -
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Residues in contact with THR 134 (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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132B GLU* 3.5 16.8 + - - +
133B VAL* 1.3 76.8 - - - +
135B ASP* 1.3 75.6 + - - +
153B ILE* 2.9 23.1 + - - +
154B VAL 3.4 12.0 + - - -
155B GLU* 3.7 28.2 - - + -
168B LYS* 3.1 27.1 + - - +
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Residues in contact with ASP 135 (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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127A ASN* 4.1 23.1 + - - +
128A PHE* 5.0 1.8 - - - -
133B VAL* 3.7 2.1 - - - -
134B THR* 1.3 88.0 + - - +
136B THR* 1.3 66.4 + - - +
152B ALA* 3.4 1.4 - - - +
153B ILE* 2.9 42.4 + - + +
168B LYS* 3.8 20.3 + - - +
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Residues in contact with THR 136 (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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128A PHE* 5.8 2.0 - - - -
133B VAL* 4.0 6.3 - - + -
135B ASP* 1.3 80.3 + - - +
137B GLU* 1.3 64.4 + - - +
138B PRO* 3.2 9.9 - - - +
150B LYS* 3.4 20.1 - - - +
151B PRO 2.7 25.7 + - - -
152B ALA* 3.7 10.2 - - + +
166B VAL 3.5 24.0 - - - +
167B ASN* 3.8 2.9 - - - -
168B LYS* 3.8 26.2 + - - +
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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