Contacts of the strand formed by residues 115 - 121 (chain J) in PDB entry 3IT8
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 GLY 115 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111J GLU* 4.2 2.2 - - - -
112J THR* 2.8 33.0 + - - +
113J ALA 3.3 1.2 - - - -
114J ASN* 1.3 80.2 - - - +
116J PRO* 1.3 79.3 - - - +
117J LEU* 4.2 1.0 - - - +
243J TYR* 4.9 0.9 - - - -
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Residues in contact with PRO 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J GLU* 3.9 9.0 - - + -
115J GLY* 1.3 84.2 - - - +
117J LEU* 1.3 62.8 + - - +
130J MET* 3.6 27.4 - - + -
131J THR* 3.7 20.4 + - - +
242J ASN* 4.0 27.6 - - + +
243J TYR* 3.1 38.5 - - + +
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Residues in contact with LEU 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ILE* 4.1 21.1 - - + -
86J THR* 5.8 5.2 - - + -
91J LEU* 4.5 0.2 - - + -
110J VAL* 2.9 29.0 + - + +
111J GLU* 4.4 3.8 - - - -
112J THR* 4.1 16.6 - - - +
115J GLY 3.4 3.1 + - - +
116J PRO* 1.3 75.3 - - - +
118J ALA* 1.3 60.4 + - - +
129J LYS* 3.9 3.3 - - - -
130J MET* 3.1 24.9 + - - +
131J THR* 4.4 1.7 + - - -
134J GLY 4.2 9.0 - - - +
135J PHE* 3.7 29.7 - - + +
136J PRO* 4.2 12.3 - - + -
141J LEU* 4.0 22.4 - - + -
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Residues in contact with ALA 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J TYR* 3.2 1.7 - - - -
110J VAL* 2.7 34.7 + - + +
117J LEU* 1.3 81.6 - - + +
119J ARG* 1.3 58.3 + - - +
127J PHE* 3.7 24.6 - - + -
128J THR 3.5 6.1 - - - +
130J MET* 3.3 6.3 - - - +
135J PHE* 3.7 28.3 - - + -
141J LEU* 4.2 10.8 - - + -
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Residues in contact with ARG 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J GLY 4.4 4.5 - - - +
109J TYR* 3.8 6.5 - - + -
118J ALA* 1.3 73.6 - - - +
120J TYR* 1.3 67.3 + - - +
121J HIS* 3.5 33.1 + - + +
127J PHE* 3.3 2.8 - - - -
128J THR* 2.7 39.5 + - - +
129J LYS 4.4 3.8 + - - -
130J MET* 3.4 38.4 - - + +
242J ASN 2.9 25.5 + - - -
243J TYR* 3.7 0.2 - - - +
244J GLU* 3.3 28.3 + - - +
247J GLU* 2.8 41.6 + - - +
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Residues in contact with TYR 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J GLY 2.8 21.3 + - - +
119J ARG* 1.3 76.6 - - - +
121J HIS* 1.3 73.2 + - - +
122J THR* 4.2 8.3 - - - -
125J LYS* 3.6 25.3 - - - +
126J ARG* 3.7 28.9 - - - -
127J PHE* 3.7 28.8 - + + -
148J TRP* 4.1 12.3 - + - -
151J VAL* 5.2 1.3 - - + -
152J LYS* 3.8 22.2 + - + +
155J LEU* 3.9 12.6 - - + -
156J GLY* 3.4 33.6 - - - -
159J GLU* 3.1 36.9 - - - +
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Residues in contact with HIS 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J ARG* 3.5 33.3 + - - -
120J TYR* 1.3 76.2 + - - +
122J THR* 1.3 61.0 + - - +
123J GLY 3.2 1.8 - - - +
124J ASP* 3.6 25.1 - - - +
125J LYS* 2.9 31.0 + - - -
126J ARG 3.0 14.1 + - - +
128J THR* 3.0 38.2 + - + +
159J GLU* 5.0 0.2 - - - -
244J GLU* 4.8 8.7 - - - -
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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