Contacts of the strand formed by residues 124 - 130 (chain B) in PDB entry 5C16
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 SER 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B ASP* 5.1 14.8 - - - -
113B VAL 3.6 4.9 - - - -
114B MET* 3.8 14.5 - - - +
123B VAL* 1.3 78.6 - - - +
125B GLY* 1.3 58.9 + - - +
136B PHE* 3.7 0.7 - - - -
138B ASN* 3.1 35.5 + - - +
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Residues in contact with GLY 125 (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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111B LYS 3.5 0.3 - - - -
112B ASP* 3.0 9.3 + - - +
113B VAL* 2.9 32.3 + - - +
124B SER* 1.3 77.4 - - - +
126B THR* 1.3 64.7 + - - -
127B LEU 3.9 0.2 + - - -
136B PHE* 3.5 12.3 - - - -
137B LYS 3.1 13.5 - - - -
138B ASN* 4.4 2.0 - - - -
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Residues in contact with THR 126 (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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109B ILE* 3.7 25.8 - - + -
110B VAL 3.2 10.1 - - - +
111B LYS* 3.2 28.6 - - + +
125B GLY* 1.3 74.2 - - - -
127B LEU* 1.3 60.1 + - - +
128B THR* 3.8 10.1 + - - +
135B TYR* 3.5 3.1 - - - +
136B PHE* 3.2 5.6 - - - -
137B LYS* 2.8 36.8 + - - +
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Residues in contact with LEU 127 (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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108B ALA 4.4 0.3 - - - -
109B ILE* 3.3 2.5 - - - -
110B VAL* 2.4 54.8 + - + +
113B VAL* 4.0 18.8 - - + -
125B GLY 3.9 1.4 + - - -
126B THR* 1.3 65.5 - - - +
128B THR* 1.3 60.4 + - - +
129B VAL* 4.0 13.1 + - + +
134B LEU* 3.8 25.4 - - + -
135B TYR 3.5 12.6 - - - +
136B PHE* 4.3 13.9 - - + -
184B LEU* 3.8 28.0 - - + -
196B ILE* 3.7 38.1 - - + -
200B LEU* 5.4 0.4 - - + -
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Residues in contact with THR 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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98B ALA* 3.9 30.0 - - + +
106B ILE* 4.0 18.2 - - + -
108B ALA 3.4 13.5 - - - +
109B ILE* 3.9 16.5 - - + +
126B THR* 3.8 14.2 + - - +
127B LEU* 1.3 74.4 + - - +
129B VAL* 1.3 61.1 + - - +
130B THR* 3.9 11.5 + - + +
133B LYS 3.8 1.0 - - - +
134B LEU* 3.7 2.1 - - - +
135B TYR* 2.6 47.7 + - - +
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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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106B ILE* 4.1 0.5 - - - +
107B LYS* 2.9 24.4 + - + +
108B ALA* 2.9 28.9 + - + +
127B LEU* 4.0 13.6 + - + +
128B THR* 1.3 73.6 - - - +
130B THR* 1.3 74.6 + - - +
133B LYS 3.7 4.5 - - - +
134B LEU* 3.5 20.4 - - + -
151B LEU* 4.5 4.9 - - + -
196B ILE* 5.4 4.7 - - + +
199B ASN* 4.2 28.0 - - + +
200B LEU* 3.8 19.7 - - + -
203B HIS* 4.6 4.7 - - - +
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Residues in contact with THR 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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98B ALA* 6.0 0.7 - - + -
100B LEU* 3.9 18.2 - - + -
104B GLU* 2.6 31.9 + - - +
105B SER 3.5 15.7 - - - +
106B ILE* 4.4 3.8 - - - -
107B LYS* 3.9 5.4 - - - +
128B THR* 4.3 16.4 - - + +
129B VAL* 1.3 84.3 - - - +
131B ASP* 1.3 57.1 + - - +
132B PHE 3.0 3.5 + - - -
133B LYS* 2.8 38.7 + - + +
135B TYR* 5.8 0.2 - - + -
151B LEU* 3.3 21.3 - - - +
203B HIS* 4.0 3.1 - - - +
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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