Contacts of the strand formed by residues 127 - 132 (chain B) in PDB entry 1H48
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 VAL 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA* 4.1 3.4 - - - +
91B LEU* 5.0 0.2 - - + -
94B VAL* 3.7 18.4 - - + -
96B VAL* 6.0 0.2 - - + -
113B ARG* 2.8 51.0 + - + +
116B ILE* 3.7 40.6 - - + -
117B ALA* 4.1 8.7 - - + -
122B CYS* 3.8 25.1 - - - -
123B HIS 4.2 2.9 - - - +
124B MET 3.1 6.6 + - - +
125B ASP 3.3 1.0 - - - -
126B ASP* 1.3 85.4 - - - +
128B ASN* 1.3 69.8 + - - +
129B VAL* 4.5 0.2 - - + -
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Residues in contact with ASN 128 (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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50A GLY* 3.3 25.6 - - - +
53A ALA* 3.2 14.6 - - + -
55A GLY* 2.9 46.4 + - - -
94B VAL 3.1 10.5 + - - +
95B ASP* 2.6 29.1 + - - +
96B VAL* 3.0 23.2 + - - +
113B ARG* 4.4 5.6 + - - +
127B VAL* 1.3 75.4 - - - +
129B VAL* 1.3 73.7 + - - +
130B LYS* 3.6 5.7 - - - +
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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
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55A GLY* 4.5 6.9 - - - +
56A ASP* 4.7 0.5 - - - +
40B ALA* 6.0 0.4 - - + -
96B VAL* 3.4 24.7 - - + +
98B ILE* 3.7 28.9 - - + -
109B ILE* 3.5 32.3 - - + +
112B MET* 3.9 17.5 - - + -
113B ARG* 4.3 17.2 - - + +
116B ILE* 4.0 24.7 - - + -
127B VAL* 4.5 2.7 - - + -
128B ASN* 1.3 86.6 + - - +
130B LYS* 1.3 66.6 + - - +
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Residues in contact with LYS 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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5A HIS 2.6 30.0 + - - +
6A GLY* 5.1 0.4 - - - -
7A PHE 5.9 0.2 - - - +
46A ASP* 3.7 31.4 - - + +
55A GLY 3.8 3.4 - - - +
56A ASP* 3.1 35.4 - - + +
95B ASP* 2.9 33.0 + - - -
96B VAL 2.9 13.1 + - - +
97B THR* 2.8 29.7 + - + +
98B ILE* 2.9 29.1 + - - +
109B ILE* 4.0 6.3 - - - -
128B ASN* 3.6 7.2 - - - +
129B VAL* 1.3 76.5 - - - +
131B ALA* 1.3 64.3 + - - +
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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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46A ASP* 5.0 1.7 - - - +
56A ASP* 3.4 8.2 + - - +
97B THR* 5.3 0.2 - - - -
98B ILE* 3.3 10.3 - - + +
105B MET* 3.7 31.0 - - + -
109B ILE* 4.2 5.7 - - + +
130B LYS* 1.3 81.1 - - - +
132B THR* 1.3 65.6 + - - +
901B C5P 3.0 47.5 + - + +
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Residues in contact with THR 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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7A PHE* 3.5 40.8 + - + +
8A ASP* 3.7 13.0 + - - -
46A ASP* 5.1 6.3 - - - -
97B THR* 4.3 7.6 - - + -
98B ILE 2.9 12.2 + - - +
99B ILE* 3.4 10.3 - - + -
100B ALA 3.1 23.4 + - - +
130B LYS* 6.3 0.2 - - - -
131B ALA* 1.3 76.5 - - - +
133B THR* 1.3 66.5 + - - +
901B C5P 3.0 31.7 + - - -
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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