Contacts of the strand formed by residues 134 - 142 (chain D) in PDB entry 2Q5E
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 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ILE 3.5 1.0 - - - +
130D GLU* 4.0 1.8 - - - -
131D ILE 2.6 37.9 + - - +
132D GLU* 3.4 14.4 - - + +
133D GLY* 1.3 80.9 - - - +
135D THR* 1.3 61.3 + - - +
136D HIS* 3.2 23.8 + - - +
195G HIS* 6.0 1.6 - - + -
220G PRO* 4.4 7.5 - - - +
221G ALA* 4.4 10.2 + - + -
224G ILE* 3.8 36.1 - - + +
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Residues in contact with THR 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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128D PRO* 3.6 31.0 - - + -
129D ILE 3.4 7.9 - - - +
130D GLU* 4.1 9.7 - - - +
133D GLY 5.2 1.2 + - - -
134D THR* 1.3 73.8 + - - +
136D HIS* 1.3 65.9 + - - +
137D GLN* 4.9 4.1 - - + +
220G PRO* 3.5 19.0 + - - +
223G TYR* 4.3 9.4 + - + -
224G ILE* 5.6 4.7 + - - +
227G PRO* 3.6 36.4 - - + +
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Residues in contact with HIS 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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117D PHE* 3.8 24.1 - - + +
128D PRO* 3.3 2.1 - - - +
129D ILE* 2.5 43.0 + - - +
131D ILE* 4.1 20.0 + - + +
134D THR* 3.2 32.6 + - - +
135D THR* 1.3 74.6 - - - +
137D GLN* 1.3 61.5 + - - +
138D VAL 3.9 0.2 + - - -
194F PHE* 3.5 46.1 - + + +
195F HIS* 5.8 0.4 - - - -
196F GLN 5.7 3.2 + - - -
220G PRO* 3.7 28.1 - - + +
221G ALA 5.7 1.1 - - - -
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Residues in contact with GLN 137 (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 PHE* 3.8 17.7 - - - +
126D ILE* 3.3 16.8 - - + +
127D VAL 3.5 2.5 - - - -
128D PRO* 3.4 38.6 - - - +
135D THR* 4.9 4.0 - - + +
136D HIS* 1.3 74.4 - - - +
138D VAL* 1.3 61.9 - - - +
139D TYR* 3.2 39.2 + - + +
220G PRO* 5.8 0.6 - - - +
223G TYR* 5.3 3.8 - - + +
227G PRO 5.9 1.9 + - - -
232G PRO* 3.9 21.0 - - + +
269G ARG* 2.8 32.7 + - - +
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Residues in contact with VAL 138 (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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115D SER* 3.7 28.3 - - - +
116D SER 3.5 4.3 - - - +
117D PHE* 3.1 43.7 - - + -
125D PHE 3.9 0.7 - - - +
126D ILE* 3.3 5.5 - - - -
127D VAL* 2.6 40.8 + - + +
129D ILE* 4.1 21.5 - - + -
137D GLN* 1.3 72.1 - - - +
139D TYR* 1.3 63.9 + - - +
140D VAL* 3.9 8.6 + - + +
169D TYR* 4.0 15.5 - - + -
173D VAL* 5.4 1.3 - - + -
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Residues in contact with TYR 139 (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 HIS 3.8 1.2 - - - +
115D SER* 3.2 3.1 - - - -
116D SER* 2.6 49.7 + - - +
117D PHE 4.2 0.9 - - - -
118D LYS 3.6 9.9 - - - +
119D PRO* 3.2 45.8 - - + +
120D ILE* 3.5 39.5 - - + +
123D ALA* 4.4 4.3 - - + -
125D PHE 3.8 2.5 - - - -
126D ILE* 3.9 31.9 - - + -
137D GLN* 3.2 45.7 + - + +
138D VAL* 1.3 72.3 - - - +
140D VAL* 1.3 59.9 + - - +
141D LEU* 4.3 0.3 + - - +
232G PRO* 3.8 14.6 + - - +
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Residues in contact with VAL 140 (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 VAL* 3.9 29.8 - - + -
114D HIS 3.5 5.6 - - - +
115D SER* 3.7 16.4 - - - +
123D ALA* 3.8 2.0 - - - +
124D ASP* 2.9 26.7 + - - +
125D PHE* 3.0 47.5 + - + +
127D VAL* 4.4 3.1 - - + -
138D VAL* 4.1 14.8 - - + +
139D TYR* 1.3 78.1 - - - +
141D LEU* 1.3 66.2 + - - +
173D VAL* 4.2 20.2 - - + -
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Residues in contact with LEU 141 (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 VAL* 3.3 3.5 - - - +
114D HIS* 2.9 40.5 + - + +
120D ILE* 3.9 22.2 - - + -
123D ALA* 3.8 27.4 - - - +
124D ASP* 3.4 8.7 - - - +
139D TYR 5.6 0.2 - - - +
140D VAL* 1.3 76.7 - - - +
142D LYS* 1.3 62.5 + - - +
236D TRP* 3.5 14.9 - - + -
237D PHE 4.1 15.5 - - - +
238D ASP* 4.5 16.4 - - + +
240D MET* 5.6 9.6 - - + -
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Residues in contact with LYS 142 (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 LEU 4.2 4.9 - - - -
113D VAL* 4.4 3.6 - - - -
124D ASP* 2.9 34.4 + - + +
125D PHE* 3.8 33.1 - - + -
141D LEU* 1.3 71.4 - - - +
143D ARG* 1.3 69.6 + - - +
144D PRO* 3.8 0.7 - - - +
146D VAL* 3.9 13.9 - - + -
147D ASP* 2.6 39.8 + - - -
177D LEU* 4.3 7.4 + - + -
179D ARG* 3.5 14.8 - - - +
236D TRP* 3.0 15.9 - - - -
240D MET* 4.4 9.7 - - - +
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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