Contacts of the strand formed by residues 128 - 136 (chain B) in PDB entry 1H5Y
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 THR 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PHE* 5.7 0.5 - - - -
103B VAL 4.3 1.6 - - - -
105B VAL* 5.4 1.3 - - + -
116B VAL* 4.0 26.0 - - + +
119B LEU* 3.5 50.5 + - + +
120B ALA 3.5 1.3 + - - -
123B PHE* 5.0 1.4 - - - +
124B GLY 3.0 13.4 + - - -
125B SER* 3.0 14.4 + - - +
126B GLN 3.3 0.6 - - - -
127B SER* 1.3 75.3 + - - +
129B VAL* 1.3 66.5 + - - +
167B GLY 4.4 4.5 - - - +
168B ALA* 3.6 3.7 - - - -
169B GLY* 2.7 30.0 + - - -
170B GLU* 3.6 2.6 + - - -
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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
----------------------------------------------------------
81B LEU* 4.4 12.8 - - + -
102B LYS* 4.1 25.6 - - + -
103B VAL 3.2 13.4 + - - +
104B SER* 3.2 20.2 - - - +
105B VAL* 3.0 26.0 + - - +
126B GLN 5.4 0.9 - - - +
127B SER 5.0 0.4 - - - -
128B THR* 1.3 76.6 - - - +
130B VAL* 1.3 72.6 + - - +
170B GLU* 3.5 40.2 - - + +
171B ILE 4.8 0.2 - - - -
172B LEU* 4.0 19.1 - - + +
202B ILE* 5.3 0.2 - - + -
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Residues in contact with VAL 130 (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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105B VAL* 3.4 15.3 - - + +
106B ASN* 5.1 0.7 - - - -
109B ALA* 4.8 2.7 - - + -
116B VAL* 3.8 29.6 - - + -
128B THR* 4.3 1.1 + - + -
129B VAL* 1.3 79.1 - - - +
131B ALA* 1.3 72.4 + - - +
132B ILE* 3.7 15.6 + - + -
159B TRP* 4.2 9.2 - - + +
163B VAL* 3.8 34.8 - - + -
168B ALA* 3.9 10.8 - - + -
170B GLU 3.1 9.9 + - - +
171B ILE* 3.4 9.3 - - + +
172B LEU 3.0 19.9 + - - -
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Residues in contact with ALA 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 SER* 3.3 18.6 + - - +
105B VAL 3.0 8.5 + - - +
106B ASN* 3.1 29.7 - - + +
130B VAL* 1.3 75.3 - - - +
132B ILE* 1.3 63.9 + - - +
133B ASP* 5.3 0.2 - - - +
159B TRP* 5.2 1.2 + - - -
172B LEU* 3.2 21.3 - - + +
401B GOL 3.5 34.3 - - - +
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Residues in contact with ILE 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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106B ASN* 4.8 0.9 - - - -
130B VAL* 3.9 12.1 - - + -
131B ALA* 1.3 78.6 - - - +
133B ASP* 1.3 65.0 + - - +
143B VAL* 4.0 28.9 - - + -
156B ALA* 4.2 16.4 - - + +
159B TRP* 3.7 25.8 - - + +
160B ALA* 4.0 26.5 - - + +
163B VAL* 4.8 0.9 - - + -
171B ILE* 3.9 24.2 - - + -
172B LEU 2.8 9.7 + - - +
173B LEU* 3.5 16.6 - - + +
174B THR 2.9 25.1 + - - +
193B VAL* 5.7 0.4 - - + -
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Residues in contact with ASP 133 (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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106B ASN* 3.3 13.5 + - - +
131B ALA* 4.1 1.3 + - - +
132B ILE* 1.3 72.9 + - - +
134B ALA* 1.3 58.7 + - - +
143B VAL* 3.5 6.0 - - - +
144B TYR 2.9 41.7 + - - +
147B GLY* 4.8 0.5 - - - -
148B GLY* 4.3 6.4 + - - -
172B LEU 5.3 0.2 - - - +
174B THR* 3.2 16.0 + - - +
176B ILE* 3.8 17.7 - - + -
401B GOL 2.5 49.5 + - - -
501B GOL 3.8 16.1 - - - -
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Residues in contact with ALA 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 ILE* 4.9 3.1 - - + -
133B ASP* 1.3 74.4 - - - +
135B LYS* 1.3 59.5 + - - +
141B TYR* 4.4 4.7 - - + -
142B GLU 3.2 13.7 - - - +
156B ALA* 4.0 25.8 - - + -
173B LEU* 5.0 1.1 - - + -
174B THR 3.0 8.3 + - - +
175B SER* 3.5 4.2 - - - -
176B ILE* 2.7 34.9 + - - +
189B LEU* 4.1 23.9 - - + +
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Residues in contact with LYS 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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134B ALA* 1.3 77.0 - - - +
136B TRP* 1.3 72.7 + - - +
137B ASN* 3.5 3.2 + - + -
141B TYR* 4.1 6.3 - - - -
142B GLU* 3.0 28.9 + - - +
144B TYR* 3.5 46.8 + - + +
148B GLY 5.0 2.4 + - - -
176B ILE* 3.9 29.2 - - + +
177B ASP* 3.4 21.3 - - - +
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Residues in contact with TRP 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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135B LYS* 1.3 82.2 - - - +
137B ASN* 1.3 59.4 + - - +
138B GLY* 3.3 43.6 + - - +
139B GLU 3.3 17.9 - - - -
140B TYR* 3.2 32.5 - - - -
141B TYR* 3.7 35.6 - + + +
177B ASP* 2.9 19.3 + - - +
186B ASP* 5.5 0.4 - - - +
192B ARG* 3.8 27.4 - - - -
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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