Contacts of the strand formed by residues 111 - 115 (chain D) in PDB entry 3IU3
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 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C SER* 4.1 16.7 + - - -
137C THR* 6.2 0.3 - - - -
109D ALA 3.8 1.4 + - - -
110D PRO* 1.3 73.0 - - - +
112D VAL* 1.3 60.1 + - - +
113D PHE* 3.6 28.2 - - - -
132D LEU 3.3 4.7 - - - +
133D LEU* 3.4 3.1 - - - -
134D ASN* 2.8 40.0 + - - +
135D ASN* 5.9 0.5 - - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR 4.8 0.3 - - - +
134C SER* 5.2 3.4 - - - -
110D PRO* 4.2 14.8 - - + +
111D SER* 1.3 78.2 - - - +
113D PHE* 1.3 70.3 + - - +
131D CYS* 4.2 12.6 - - - -
132D LEU 3.5 4.0 - - - +
133D LEU* 4.6 2.2 - - + -
193D VAL* 3.9 37.7 - - + -
198D LEU* 4.8 7.6 - - + -
202D VAL* 5.4 9.9 - - + -
204D LYS* 3.3 50.4 + - + +
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LYS 3.8 3.1 - - - -
132C SER* 3.3 38.1 - - - -
133C THR* 3.6 1.8 - - - -
134C SER* 3.6 31.6 - - - -
137C THR* 4.3 15.3 - - + -
139C ALA* 3.6 18.8 - - + -
185C THR* 4.5 3.8 - - + -
111D SER* 3.6 30.1 - - - -
112D VAL* 1.3 78.8 - - - +
114D ILE* 1.3 62.5 + - - +
115D PHE* 4.2 12.6 - - + -
130D VAL 4.7 0.2 - - - -
131D CYS* 3.5 9.3 - - - -
132D LEU* 2.9 53.9 + - + +
134D ASN* 3.8 14.4 - - + -
204D LYS* 4.9 0.9 - - - -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C SER* 4.8 1.0 + - - -
131C LYS* 3.2 45.1 + - + +
132C SER* 3.7 8.8 - - - -
113D PHE* 1.3 76.2 - - - +
115D PHE* 1.3 70.7 + - - +
116D PRO* 3.9 5.0 - - + +
129D VAL* 4.2 7.0 - - + -
130D VAL 3.4 11.9 - - - +
131D CYS* 4.6 3.6 - - - -
145D TRP* 4.3 11.7 - - + -
189D TYR 4.2 7.0 - - - +
191D CYS* 3.9 13.9 - - + +
204D LYS* 3.6 33.2 - - + +
205D SER 4.6 2.0 - - - +
206D PHE* 3.8 31.9 - - + -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.5 53.8 - - + -
127C ALA 3.5 16.8 - - - +
132C SER* 3.6 13.2 - - - -
139C ALA* 3.2 39.7 - - + -
140C LEU* 4.0 5.2 - - - -
183C VAL* 4.9 3.4 - - + -
113D PHE* 4.2 15.0 - - + -
114D ILE* 1.3 79.0 - - - +
116D PRO* 1.3 70.5 - - + +
128D SER 4.2 1.0 - - - +
129D VAL* 3.6 8.1 - - - +
130D VAL* 2.8 51.2 + - + +
132D LEU* 4.3 16.8 - - + -
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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
------------------------------------------------------------
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