Contacts of the strand formed by residues 126 - 136 (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 THR 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C PHE* 5.3 2.1 - - - -
145C LYS* 4.1 20.8 - - - +
146C ASP* 5.4 2.3 + - - +
121D GLN* 2.9 44.7 + - - +
122D LEU* 4.0 4.2 + - - +
124D SER* 3.7 7.3 - - - -
125D GLY* 1.3 81.2 - - - +
127D ALA* 1.3 63.8 + - - +
177D THR* 5.2 7.4 - - + -
178D LEU 3.7 8.1 - - - +
179D SER* 5.4 1.8 - - - -
180D LYS* 4.7 2.3 - - - +
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Residues in contact with ALA 127 (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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117D PRO* 4.0 15.0 - - + -
121D GLN* 4.0 3.6 - - - -
122D LEU* 4.5 6.3 - - + -
126D THR* 1.3 77.2 - - - +
128D SER* 1.3 62.4 + - - +
129D VAL* 4.1 1.0 - - - +
176D LEU 3.5 2.1 - - - +
177D THR* 3.4 2.3 - - - +
178D LEU* 2.8 46.1 + - + +
180D LYS* 5.0 2.7 - - - -
183D TYR* 4.0 34.3 - - + -
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 5.6 1.9 - - - +
143C LEU* 3.7 19.5 - - - +
145C LYS* 4.3 7.8 + - - +
115D PHE 4.2 1.6 - - - +
116D PRO 4.5 0.2 - - - -
117D PRO* 3.8 18.7 - - - +
121D GLN* 3.2 29.0 + - - +
127D ALA* 1.3 70.5 - - - +
129D VAL* 1.3 63.6 + - - +
130D VAL* 3.8 5.7 + - - +
175D THR* 4.0 13.9 - - - +
176D LEU 3.4 3.4 - - - -
177D THR* 3.5 26.2 + - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ILE* 4.2 5.2 - - + -
115D PHE 3.6 7.4 - - - +
117D PRO* 3.8 25.4 - - + -
127D ALA 5.4 1.1 - - - +
128D SER* 1.3 71.9 - - - +
130D VAL* 1.3 61.5 + - - +
145D TRP* 3.6 27.3 - - + -
175D THR* 3.5 1.2 - - - -
176D LEU* 2.7 53.4 + - + +
178D LEU* 6.4 0.2 - - + -
183D TYR* 4.1 15.9 - - + -
189D TYR* 4.6 12.1 - - + -
206D PHE* 3.7 26.9 - - + -
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 3.7 33.0 - - + -
143C LEU* 4.4 15.3 - - + -
181C SER* 4.4 11.7 - - - +
183C VAL* 5.9 2.0 - - + -
114D ILE* 3.4 4.1 - - - +
115D PHE* 2.8 53.0 + - + -
128D SER 4.3 7.4 - - - +
129D VAL* 1.3 74.8 - - - +
131D CYS* 1.3 67.8 + - - +
132D LEU* 4.8 2.7 - - + +
145D TRP* 4.3 1.8 - - - -
173D SER* 4.9 8.1 - - - -
174D SER 3.6 5.2 - - - +
175D THR* 4.0 23.1 - - + +
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Residues in contact with CYS 131 (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* 4.2 13.5 - - - -
113D PHE 3.5 14.1 - - - -
114D ILE* 4.6 3.1 - - + +
130D VAL* 1.3 73.2 - - - +
132D LEU* 1.3 61.1 + - - +
133D LEU* 4.1 8.9 + - - +
145D TRP* 3.5 19.9 - - + -
172D LEU 3.9 0.3 - - - +
173D SER* 3.4 4.0 - - - -
174D SER* 2.8 42.8 + - - +
191D CYS* 2.0 50.3 - - + -
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Residues in contact with LEU 132 (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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139C ALA* 4.2 8.3 - - + -
168C PHE* 3.4 38.1 - - + -
183C VAL* 3.4 33.7 - - + -
185C THR* 5.3 0.2 - - + -
111D SER 3.3 5.5 - - - +
112D VAL* 3.5 2.6 - - - +
113D PHE* 2.9 65.1 + - + +
115D PHE* 4.3 14.6 - - + -
130D VAL* 4.2 3.9 + - + -
131D CYS* 1.3 73.2 - - - +
133D LEU* 1.3 64.9 + - - +
134D ASN* 4.1 16.6 - - - +
172D LEU 3.6 7.2 - - - +
173D SER* 4.6 1.8 - - - +
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Residues in contact with LEU 133 (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 PRO* 4.2 16.2 - - + -
111D SER 3.4 4.0 - - - +
112D VAL* 4.6 4.0 - - + -
131D CYS* 4.3 12.6 - - - +
132D LEU* 1.3 76.6 - - - +
134D ASN* 1.3 60.6 + - - +
136D PHE* 3.3 21.1 - - + -
141D ALA* 4.3 20.0 - - + -
143D VAL* 3.7 30.1 - - + -
171D SER* 3.3 1.7 - - - -
172D LEU* 2.7 50.2 + - + +
193D VAL* 3.5 39.5 - - + -
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Residues in contact with ASN 134 (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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166C HIS* 3.5 16.3 + - - -
183C VAL* 4.7 2.2 - - - +
185C THR* 3.5 29.1 + - - +
109D ALA 4.4 0.2 - - - +
110D PRO* 3.4 2.0 - - - +
111D SER* 2.8 37.1 + - - +
113D PHE* 3.8 23.1 - - + -
132D LEU* 4.1 16.9 - - + +
133D LEU* 1.3 72.5 - - - +
135D ASN* 1.3 90.2 + - - +
136D PHE* 3.7 1.6 - - - -
171D SER* 3.2 19.4 + - - -
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Residues in contact with ASN 135 (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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164C GLY* 6.2 1.4 - - - -
166C HIS* 3.1 32.8 + - - -
185C THR* 5.5 2.0 + - - -
108D ALA* 4.2 4.9 - - - +
109D ALA 3.6 11.3 - - - +
111D SER* 5.9 0.4 - - - +
134D ASN* 1.3 89.1 + - - +
136D PHE* 1.3 57.6 + - - +
167D ASP* 3.2 23.4 + - - +
169D THR* 3.8 21.9 + - + +
170D TYR 3.3 7.2 + - - -
171D SER* 3.1 8.7 + - - -
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Residues in contact with PHE 136 (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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108D ALA* 3.1 13.9 - - - +
110D PRO* 3.6 32.5 - - + -
133D LEU* 3.3 35.2 - - + -
135D ASN* 1.3 73.9 - - - +
137D TYR* 1.3 62.6 + - - +
138D PRO 3.2 27.8 - - - -
139D ARG 3.6 15.0 - - - -
141D ALA* 4.2 7.9 - - + -
160D VAL* 5.1 1.8 - - + -
169D THR* 3.5 4.3 - - - -
170D TYR* 2.8 59.5 + - + -
171D SER 4.4 0.2 - - - -
172D LEU* 3.8 31.0 - - + -
195D HIS* 3.5 9.6 - + - +
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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