Contacts of the strand formed by residues 125 - 135 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B ILE* 4.3 12.8 - - + -
117B THR 3.4 10.5 - - - +
118B SER* 3.3 3.8 + - - -
124B VAL* 1.3 71.7 - - - +
126B GLU* 1.3 69.9 + - - +
219B LYS* 3.8 0.3 - - - -
220B ILE* 2.9 39.0 + - - +
222B ARG 2.7 20.4 + - - -
224B ASN* 3.1 20.1 + - - -
225B ALA* 3.1 18.2 + - + +
227B LEU* 3.9 25.6 - - + -
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.2 9.0 - - - +
117B THR* 2.9 36.4 + - - +
124B VAL* 4.3 11.7 - - + +
125B THR* 1.3 78.7 - - - +
127B VAL* 1.3 65.4 + - - +
144B ASP* 3.7 41.1 - - + +
145B ILE* 4.7 3.5 - - - +
217B THR* 4.6 6.1 - - - +
218B VAL 3.6 17.5 - - - +
219B LYS* 3.6 32.8 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.7 24.5 - - + -
115B ASN 3.6 6.3 - - - +
116B ILE* 4.8 3.1 - - + -
126B GLU* 1.3 81.8 - - - +
128B MET* 1.3 73.4 + - - +
129B TRP* 3.2 46.3 + - + +
144B ASP* 3.0 23.2 + - - +
160B VAL* 6.0 0.9 - - + -
218B VAL* 4.5 5.8 + - + +
220B ILE* 4.7 9.0 - - + -
227B LEU* 4.1 31.4 - - + -
234B THR* 4.8 2.9 - - + -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 2.9 44.8 + - + +
115B ASN* 2.9 23.1 + - + +
117B THR* 4.2 24.0 - - + -
126B GLU 4.3 0.2 - - - -
127B VAL* 1.3 76.7 - - - +
129B TRP* 1.3 59.8 + - - +
143B GLY* 3.7 31.4 - - - +
144B ASP* 4.2 8.7 - - + +
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Residues in contact with TRP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.8 24.5 - - + -
112B VAL 3.6 25.6 - - - -
113B PRO* 3.9 12.6 - - + -
114B VAL* 3.9 4.0 - - - +
127B VAL* 3.2 45.2 + - + +
128B MET* 1.3 74.9 - - - +
130B GLN* 1.3 61.0 + - - +
131B PRO* 4.5 2.0 - - - +
141B ALA* 4.6 10.5 - - + +
143B GLY* 3.1 21.6 + - - +
144B ASP 4.0 14.6 + - - -
145B ILE* 4.6 1.1 - - - -
146B VAL* 5.0 5.8 - - + -
158B SER* 6.0 0.7 - - - -
159B GLN 5.0 0.4 - - - -
160B VAL* 5.8 1.8 - - + -
218B VAL* 4.4 24.8 + - + +
234B THR* 4.0 17.3 - - + -
235B PHE* 3.7 29.8 - - - -
236B LEU* 3.8 36.8 - - + +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.3 4.5 - - - -
112B VAL* 2.8 54.8 + - + +
113B PRO 3.4 20.4 + - - -
114B VAL* 4.0 19.7 - - + +
129B TRP* 1.3 74.7 - - - +
131B PRO* 1.3 70.7 - - + +
132B VAL* 3.6 9.0 + - + +
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.9 19.7 - - + -
110B HIS 3.6 7.4 - - - +
111B LEU* 3.7 17.2 - - + -
129B TRP 4.5 2.0 - - - +
130B GLN* 1.3 90.6 - - + +
132B VAL* 1.3 62.4 + - - +
133B LEU 4.8 1.6 - - - +
134B ARG* 3.9 32.3 - - + +
141B ALA* 4.7 9.2 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B HIS* 3.0 35.6 + - + +
112B VAL* 3.7 35.0 - - + -
130B GLN* 3.6 8.5 + - + +
131B PRO* 1.3 77.9 - - - +
133B LEU* 1.3 65.7 + - + +
231B PRO* 6.2 0.2 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 4.3 16.2 - - + -
207A VAL* 3.7 35.4 - - + +
208A PHE* 4.1 2.5 - - - -
209A HIS* 3.9 40.6 - - + +
108B VAL* 4.2 14.8 - - + -
109B LEU* 3.4 9.6 - - - +
110B HIS* 3.0 40.7 + - + +
131B PRO 3.7 0.9 - - - -
132B VAL* 1.3 82.4 - - + +
134B ARG* 1.3 70.2 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.6 7.2 - - - +
109B LEU* 3.8 19.0 - - + +
131B PRO* 3.9 29.3 - - + +
133B LEU* 1.3 83.3 - - - +
135B ARG* 1.3 64.6 + - - +
136B GLY 4.2 15.0 - - - +
139B LEU 4.9 11.0 + - - -
140B GLU* 5.8 4.6 - - - +
141B ALA* 5.7 5.5 - - - +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.8 31.6 - - + +
241A LEU* 3.3 41.8 + - - +
105B LYS* 4.3 12.5 - - - +
106B HIS* 2.9 36.8 + - - +
107B SER* 3.2 5.2 - - - -
108B VAL* 3.0 45.1 + - + +
134B ARG* 1.3 76.2 - - - +
136B GLY* 1.3 69.9 + - - +
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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