Contacts of the strand formed by residues 114 - 118 (chain N) in PDB entry 3INU
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 114 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132M SER* 4.7 14.3 + - - -
112N ALA 4.7 2.1 + - - -
113N PRO* 1.3 72.3 - - - +
115N VAL* 1.3 60.3 + - - +
116N PHE* 3.8 25.0 - - - -
135N LEU 3.3 4.2 - - - +
136N LEU* 3.5 0.5 - - - -
137N ASN* 2.9 41.9 + - - +
138N ASN* 5.7 0.7 - - - +
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Residues in contact with VAL 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N PRO* 3.9 20.4 + - + +
114N SER* 1.3 75.1 - - - +
116N PHE* 1.3 74.2 + - - +
134N CYS* 3.9 25.4 - - - -
135N LEU 3.4 3.4 - - - +
136N LEU* 4.6 2.2 - - + -
194N CYS* 4.4 0.9 - - + -
196N VAL* 4.0 25.4 - - + -
201N LEU* 5.5 0.2 - - + -
205N VAL* 4.1 23.1 - - + -
207N LYS* 3.3 47.5 - - + +
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Residues in contact with PHE 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M LYS 4.4 3.4 - - - -
130M SER* 3.3 47.1 - - - +
131M THR 4.1 1.6 - - - -
132M SER* 4.2 18.6 - - - -
137M THR* 5.0 4.0 - - - -
138M ALA 5.2 1.1 - - - -
139M ALA* 3.8 15.9 - - + -
192M THR* 5.1 3.6 - - + -
114N SER* 3.8 34.8 - - - -
115N VAL* 1.3 84.1 - - - +
117N ILE* 1.3 60.6 + - - +
118N PHE* 4.1 17.9 - - + -
133N VAL 3.9 0.3 - - - +
134N CYS* 3.3 5.9 - - - -
135N LEU* 2.8 56.2 + - + +
137N ASN* 4.2 14.4 - - + -
207N LYS* 4.9 1.1 - - - -
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Residues in contact with ILE 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M SER* 4.7 3.8 + - - -
129M LYS* 4.0 31.8 + - + +
130M SER* 3.9 9.4 + - - -
116N PHE* 1.3 74.5 - - - +
118N PHE* 1.3 76.5 + - - +
119N PRO* 4.2 4.9 - - + +
132N VAL* 3.7 25.6 - - + -
133N VAL 3.5 2.9 - - - +
148N TRP* 4.1 15.9 - - + -
192N TYR 4.5 2.0 - - - +
194N CYS* 3.6 14.1 - - + -
207N LYS* 3.5 35.0 - - + +
208N SER 4.2 10.1 - - - +
209N PHE* 3.8 20.2 - - + -
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Residues in contact with PHE 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M LEU* 3.6 55.0 - - + -
125M ALA 3.2 29.2 - - - -
130M SER* 4.0 9.0 - - - -
139M ALA* 3.4 32.3 - - + -
140M LEU* 4.4 3.6 - - - -
190M VAL* 5.4 4.3 - - + -
116N PHE* 4.1 18.4 - - + -
117N ILE* 1.3 80.3 - - - +
119N PRO* 1.3 72.2 - - + +
131N SER 4.2 0.7 - - - +
132N VAL* 3.4 8.0 - - - +
133N VAL* 2.7 47.3 + - + +
135N LEU* 4.3 15.0 - - + -
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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