Contacts of the strand formed by residues 108 - 115 (chain D) in PDB entry 1U5Y
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 VAL 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ILE* 4.4 20.6 - - + -
207B VAL* 4.2 11.4 - - + -
241B LEU* 4.6 2.5 - - + -
106D HIS* 3.3 17.2 + - + +
107D SER* 1.3 80.3 + - - +
109D LEU* 1.3 68.3 + - - +
133D LEU* 4.1 31.0 - - + -
134D ARG* 3.3 4.0 + - - +
135D ARG* 2.8 45.2 + - + +
139D LEU* 4.5 4.3 - - - -
238D PHE 3.3 14.8 - - - +
239D VAL* 4.3 15.7 - - + -
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Residues in contact with LEU 109 (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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207B VAL* 6.0 0.2 - - - +
108D VAL* 1.3 77.6 - - - +
110D HIS* 1.3 60.7 + - - +
111D LEU* 3.9 32.6 - - + +
131D PRO* 4.0 11.4 - - + -
133D LEU 3.4 14.6 - - - +
134D ARG* 3.6 40.8 - - + +
139D LEU* 3.8 42.8 - - + +
140D GLU 4.2 3.1 - - - +
141D ALA 4.4 6.1 - - - +
146D VAL* 4.6 5.8 - - + -
157D TYR* 4.6 0.7 + - - -
237D GLY* 3.2 3.6 - - - -
238D PHE* 2.9 32.8 + - + +
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Residues in contact with HIS 110 (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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184B LEU 5.1 0.4 + - - -
207B VAL* 3.5 23.6 - - + +
208B PHE* 3.6 28.7 - + - -
109D LEU* 1.3 73.8 - - - +
111D LEU* 1.3 61.6 + - - +
112D VAL* 4.6 5.6 - - + +
131D PRO* 3.5 2.9 - - - +
132D VAL* 3.0 41.0 + - + +
133D LEU* 3.1 24.3 + - + +
157D TYR* 2.8 27.4 + + - +
231D PRO 5.2 1.2 + - - -
235D PHE* 3.5 45.6 - + + +
236D LEU 3.4 8.6 + - - -
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Residues in contact with LEU 111 (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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109D LEU* 3.9 31.9 - - + +
110D HIS* 1.3 80.0 - - - +
112D VAL* 1.3 64.2 + - - +
129D TRP* 3.8 26.7 - - + -
130D GLN 3.3 8.1 - - - +
131D PRO* 4.2 8.1 - - + -
141D ALA* 3.7 30.7 - - + -
146D VAL* 4.0 8.5 - - + -
235D PHE* 3.3 9.7 - - - +
236D LEU* 2.7 52.2 + - + +
238D PHE* 4.0 18.2 - - + -
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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
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110D HIS* 4.6 6.3 - - - +
111D LEU* 1.3 79.7 - - - +
113D PRO* 1.3 78.4 - - + +
129D TRP* 3.7 5.4 - - - -
130D GLN* 2.8 35.9 + - + +
132D VAL* 3.7 38.4 - - + -
231D PRO* 3.5 41.3 - - + +
234D THR 4.2 0.4 - - - -
235D PHE* 4.3 4.5 - - + -
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Residues in contact with PRO 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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112D VAL* 1.3 96.2 - - + +
114D VAL* 1.3 59.3 + - - +
127D VAL* 3.5 18.6 - - + -
128D MET 3.5 7.9 - - - +
129D TRP* 3.9 4.5 - - + -
130D GLN* 5.2 0.7 - - - +
228D SER 4.2 0.2 - - - +
229D LEU* 3.9 43.6 - - + +
231D PRO* 4.2 2.4 - - + +
234D THR* 3.0 46.0 - - + +
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Residues in contact with VAL 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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113D PRO* 1.3 75.7 - - - +
115D ASN* 1.3 68.7 + - + +
128D MET* 2.9 43.5 + - + +
129D TRP 4.2 1.8 - - - +
130D GLN* 3.8 26.2 - - + +
229D LEU* 4.0 13.9 - - - +
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Residues in contact with ASN 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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114D VAL* 1.3 84.7 - - + +
116D ILE* 1.3 78.7 + - - +
117D THR* 5.1 0.6 + - - -
127D VAL* 3.3 11.6 - - - +
128D MET* 3.0 58.6 + - - +
229D LEU* 4.2 13.4 - - + +
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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