Contacts of the strand formed by residues 115 - 120 (chain B) in PDB entry 4I9X
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B TYR 3.4 9.2 + - - +
114B ALA* 1.3 79.0 - - - +
116B TRP* 1.3 71.0 + - - +
117B ASN* 5.0 4.3 + - - -
129B LEU* 3.5 4.5 - - - +
130B THR* 2.8 48.9 + - - +
304B NA 4.0 10.1 - - - -
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Residues in contact with TRP 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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93B LEU* 3.6 30.3 - - + -
95B LEU* 3.9 26.8 - - + +
100B GLY 4.9 4.3 + - - -
102B ARG* 3.8 37.5 - - + +
105B ASN* 3.6 27.4 - - - -
114B ALA* 4.0 15.9 - - + -
115B THR* 1.3 82.6 - - - +
117B ASN* 1.3 73.0 + - - +
118B PHE* 6.0 0.4 - - + -
128B SER 3.1 19.1 - - - +
129B LEU* 4.5 3.1 - - + -
130B THR 4.8 0.2 - - - +
304B NA 3.5 24.1 - - - -
78C GLU* 6.2 1.6 - - + -
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Residues in contact with ASN 117 (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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95B LEU* 4.6 4.0 - - - +
115B THR* 5.0 4.2 + - - -
116B TRP* 1.3 87.9 + - - +
118B PHE* 1.3 64.4 + - - +
119B SER* 5.7 2.0 - - - +
126B ILE 4.5 0.7 - - - -
127B PHE* 3.3 5.0 - - - +
128B SER* 3.1 42.5 + - - +
130B THR* 4.4 11.3 + - - -
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Residues in contact with PHE 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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77B VAL* 4.8 8.1 - - + -
95B LEU* 4.4 8.5 - - + -
96B ASP 4.0 3.8 - - - -
97B ALA* 3.4 27.1 - - - -
98B VAL 3.8 10.5 - - - -
99B LYS 3.7 17.3 - - - -
100B GLY* 3.4 35.4 - - - +
116B TRP* 6.0 0.9 - - + -
117B ASN* 1.3 78.3 - - - +
119B SER* 1.3 76.3 + - - +
120B GLN* 4.2 7.9 - - + -
125B GLN* 3.6 27.4 - - + -
126B ILE 3.4 6.5 - - - -
127B PHE* 4.1 17.0 - + + -
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Residues in contact with SER 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 ASN* 5.7 2.3 - - - +
118B PHE* 1.3 80.8 + - - +
120B GLN* 1.3 60.9 + - - +
121B LEU* 3.7 18.9 + - - +
125B GLN* 3.3 9.7 - - - +
126B ILE* 2.8 39.7 + - - +
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Residues in contact with GLN 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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64A THR* 5.3 0.5 + - - -
71B THR* 4.5 0.2 + - - -
97B ALA 5.1 0.3 - - - +
98B VAL* 3.8 18.2 - - - +
118B PHE* 4.2 8.6 - - + -
119B SER* 1.3 73.1 - - - +
121B LEU* 1.3 63.0 + - - +
122B HIS* 2.8 34.1 + - + +
124B GLY 3.3 2.6 + - - -
125B GLN* 2.6 41.7 + - - +
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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