Contacts of the strand formed by residues 125 - 135 (chain D) in PDB entry 1XU2
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 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ILE* 4.3 12.6 - - + -
117D THR 3.4 13.7 - - - +
118D SER* 3.4 3.0 + - - -
124D VAL* 1.3 71.9 + - - +
126D GLU* 1.3 70.9 + - - +
219D LYS* 3.8 0.3 - - - -
220D ILE* 2.9 39.1 + - - +
222D ARG 2.8 20.2 + - - -
224D ASN* 3.1 10.0 + - - -
225D ALA* 3.1 36.1 + - + +
227D LEU* 4.1 15.7 - - + -
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Residues in contact with GLU 126 (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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116D ILE* 3.4 8.7 - - - +
117D THR* 2.9 40.8 + - + +
124D VAL* 4.1 8.2 - - + +
125D THR* 1.3 79.0 - - - +
127D VAL* 1.3 65.7 + - - +
144D ASP* 3.2 40.3 - - + +
145D ILE* 4.9 0.7 - - - +
217D THR* 4.6 8.1 - - - +
218D VAL 3.8 17.2 - - - +
219D LYS* 3.7 32.8 - - + +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PRO* 3.6 29.8 - - + -
115D ASN 3.6 7.2 - - - +
116D ILE* 4.3 3.6 - - + -
126D GLU* 1.3 82.1 - - - +
128D MET* 1.3 77.9 + - - +
129D TRP* 3.5 36.1 + - + +
144D ASP* 3.1 23.6 - - - +
160D VAL* 6.0 1.3 - - + -
218D VAL* 4.4 6.9 + - + +
220D ILE* 4.8 10.1 - - + -
227D LEU* 4.3 26.2 - - + -
234D THR* 4.9 3.1 - - + -
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Residues in contact with MET 128 (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* 3.4 0.2 - - - +
114D VAL* 2.8 35.2 + - + -
115D ASN* 3.0 43.1 + - - +
117D THR* 4.8 15.5 - - + -
127D VAL* 1.3 81.4 - - - +
129D TRP* 1.3 56.9 + - - +
143D GLY* 3.6 20.9 - - - -
144D ASP* 3.5 27.6 - - - -
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Residues in contact with TRP 129 (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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111D LEU* 3.9 28.5 - - + -
112D VAL 3.5 20.9 - - - -
113D PRO* 3.8 14.8 - - + -
114D VAL* 3.7 7.2 - - - +
127D VAL* 3.5 39.4 + - + +
128D MET* 1.3 72.6 - - - +
130D GLN* 1.3 59.1 + - - +
131D PRO* 4.6 0.7 - - - +
141D ALA* 4.3 13.0 - - + +
143D GLY* 3.0 25.0 + - - +
144D ASP 4.1 13.4 + - - -
145D ILE 4.8 0.9 - - - -
146D VAL* 4.9 6.3 - - + -
158D SER* 5.9 0.7 - - - -
159D GLN 5.1 0.9 - - - -
160D VAL* 5.7 1.6 - - + -
218D VAL* 4.3 24.0 + - + +
234D THR* 4.1 15.7 - - + -
235D PHE* 3.8 31.4 - - - -
236D LEU* 3.8 34.9 - - + +
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Residues in contact with GLN 130 (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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111D LEU* 3.3 5.5 - - - -
112D VAL* 2.9 53.4 + - + +
113D PRO 3.0 24.2 + - - -
114D VAL* 3.6 19.1 - - + +
129D TRP* 1.3 73.2 - - - +
131D PRO* 1.3 72.0 - - + +
132D VAL* 3.6 9.7 + - + +
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Residues in contact with PRO 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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109D LEU* 3.9 26.0 - - + -
110D HIS 3.6 6.7 - - - +
111D LEU* 3.7 9.3 - - + -
129D TRP 4.6 1.8 - - - +
130D GLN* 1.3 90.8 - - + +
132D VAL* 1.3 63.4 + - - +
133D LEU 4.8 3.4 - - - +
134D ARG* 3.5 25.8 - - + +
141D ALA* 4.8 7.2 - - + +
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Residues in contact with VAL 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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110D HIS* 2.9 42.8 + - + +
112D VAL* 3.8 33.0 - - + -
130D GLN* 3.6 10.0 + - - +
131D PRO* 1.3 76.6 - - - +
133D LEU* 1.3 59.5 + - + +
231D PRO* 5.9 1.1 - - + -
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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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153B ILE* 4.1 20.6 - - + -
207B VAL* 3.6 36.1 - - + +
208B PHE* 3.9 4.0 - - + -
209B HIS* 3.8 36.6 - - + +
108D VAL* 4.0 13.0 - - + -
109D LEU* 3.3 10.2 - - - +
110D HIS* 2.9 39.8 + - + +
131D PRO* 5.2 0.7 - - - -
132D VAL* 1.3 81.9 - - + +
134D ARG* 1.3 70.2 + - - +
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Residues in contact with ARG 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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153B ILE* 5.6 0.2 - - - +
108D VAL 3.4 6.5 - - - +
109D LEU* 3.7 18.4 - - + +
131D PRO* 3.5 31.0 - - + +
133D LEU* 1.3 85.6 - - - +
135D ARG* 1.3 61.6 + - - +
136D GLY 3.5 22.6 + - - +
137D ARG* 5.1 17.0 - - - +
139D LEU 3.3 24.9 + - - -
140D GLU* 4.5 13.9 - - - +
141D ALA 5.5 1.8 - - - +
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Residues in contact with ARG 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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152B GLY* 5.9 0.8 - - - -
153B ILE* 3.7 44.8 - - + +
241B LEU* 3.1 38.4 + - - +
105D LYS* 3.3 48.9 - - - +
106D HIS 2.7 28.4 + - - +
107D SER* 3.3 6.8 + - - -
108D VAL* 3.0 35.2 + - + +
134D ARG* 1.3 74.3 - - - +
136D GLY* 1.3 70.5 + - - +
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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