Contacts of the strand formed by residues 117 - 122 (chain B) in PDB entry 3I7I
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 ASN 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B LYS* 3.2 28.7 - - - +
116B MET* 1.3 88.4 - - - +
118B LEU* 1.3 61.6 + - - +
119B THR* 5.9 0.4 - - - +
152B ASN* 3.7 15.5 - - + +
154B THR* 6.3 3.1 - - + -
162B ASP* 4.4 1.6 - - - +
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Residues in contact with LEU 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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113B TRP* 3.6 47.6 - - + +
115B LYS* 3.4 36.8 - - + +
116B MET 4.7 3.1 - - - +
117B ASN* 1.3 83.8 - - - +
119B THR* 1.3 65.5 + - - +
151B LEU* 4.7 6.5 - - + -
152B ASN 2.8 15.5 + - - +
153B PHE* 3.3 30.8 - - + -
154B THR* 2.9 25.5 + - - +
162B ASP* 3.9 11.7 - - + +
163B ILE* 4.8 7.0 - - + -
228B LEU* 4.2 4.9 - - + -
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Residues in contact with THR 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 5.9 0.2 - - - +
118B LEU* 1.3 76.5 - - - +
120B TYR* 1.3 63.0 + - - +
153B PHE* 6.0 0.2 - - - -
154B THR* 3.0 24.9 - - - +
156B LEU* 3.7 31.1 - - + +
160B ILE 4.7 0.3 + - - -
161B ALA* 3.7 5.7 - - - -
162B ASP* 3.1 32.6 + - - +
163B ILE* 2.9 24.0 + - - +
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Residues in contact with TYR 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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119B THR* 1.3 74.8 - - - +
121B ARG* 1.3 63.5 + - - +
122B ILE* 4.3 12.3 - - + -
135B GLU 5.0 1.9 + - - -
138B PHE* 4.8 3.6 - - + -
139B LYS* 4.2 24.3 + - - +
142B PHE* 3.4 42.0 - + + -
153B PHE* 4.1 19.7 - + + -
154B THR* 3.0 18.4 + - - -
155B ARG* 3.1 48.1 - - + +
156B LEU 2.8 22.9 + - - -
161B ALA* 3.6 5.4 - - - -
163B ILE* 3.2 26.7 - - + +
165B ILE* 3.9 10.3 - - + -
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Residues in contact with ARG 121 (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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120B TYR* 1.3 76.0 - - - +
122B ILE* 1.3 71.8 + - - +
123B VAL* 3.5 28.6 + - - +
155B ARG* 4.8 0.2 - - - -
156B LEU* 3.6 18.6 - - + +
157B HIS 3.7 14.5 + - - +
158B ASP* 3.8 15.7 - - - +
159B GLY* 3.3 33.6 + - - +
161B ALA* 3.6 14.9 - - + +
163B ILE 3.1 6.9 + - - -
164B MET* 3.6 26.9 - - + +
165B ILE* 2.8 30.5 + - - +
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Residues in contact with ILE 122 (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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120B TYR* 4.3 17.7 - - + -
121B ARG* 1.3 78.5 + - - +
123B VAL* 1.3 62.7 + - - +
124B ASN 3.4 21.3 - - - +
125B TYR* 3.6 34.8 + - + +
134B VAL* 4.5 0.7 - - + -
135B GLU* 4.0 25.6 - - + +
138B PHE* 3.6 39.3 - - + -
155B ARG* 4.2 17.0 + - - +
156B LEU 4.4 2.6 + - - -
157B HIS* 5.4 1.7 - - - +
165B ILE* 3.8 11.4 - - + +
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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