Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 1XUQ
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 GLY 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ARG* 4.1 4.3 - - - -
129B GLY 4.0 1.0 + - - -
130B SER* 1.3 76.7 - - - +
132B TRP* 1.3 65.2 + - - -
147B THR 3.1 13.2 - - - -
149B ASN 3.6 13.7 - - - -
166B VAL* 2.9 33.1 + - - +
167B TRP* 3.4 15.1 - - - +
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Residues in contact with TRP 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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82B ASN* 3.5 45.1 - - + +
83B HIS* 3.8 16.4 - + - -
85B PHE* 5.5 0.4 - + - -
86B PHE* 3.8 25.1 - + + -
127B ARG* 4.4 0.9 - - - +
131B GLY* 1.3 79.4 - - - -
133B ALA* 1.3 59.0 + - - +
134B TRP* 3.4 39.4 - + + +
146B SER* 3.1 8.9 - - - -
147B THR* 3.0 32.7 + - - +
149B ASN 3.4 15.6 + - - -
150B GLN* 2.9 21.3 + - - -
163B GLY 4.6 1.1 - - - -
164B LEU 3.3 14.4 - - - -
165B ASP* 3.4 54.4 + - + -
166B VAL* 3.9 5.4 - - - +
167B TRP* 4.0 0.6 - - - +
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Residues in contact with ALA 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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120B PHE* 3.6 25.6 - - + +
123B ALA* 4.5 2.2 - - + -
124B GLY* 3.9 32.3 - - - +
132B TRP* 1.3 74.6 - - - +
134B TRP* 1.3 62.3 + - - +
145B THR 3.7 7.4 - - - +
146B SER* 4.3 1.3 - - - +
163B GLY* 3.1 4.0 - - - -
164B LEU* 2.7 38.2 + - + +
166B VAL* 4.6 3.5 - - + +
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Residues in contact with TRP 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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82B ASN* 3.5 32.3 - - + -
85B PHE* 3.8 26.5 - + + -
120B PHE* 3.5 10.3 - - - -
132B TRP* 3.4 40.3 - + + +
133B ALA* 1.3 77.5 - - - +
135B LEU* 1.3 57.8 + - - +
136B VAL* 3.7 16.8 - - + -
144B VAL* 3.3 7.4 - - - +
145B THR* 2.9 45.7 + - - +
147B THR* 3.0 28.2 + - + -
153B PRO* 3.5 34.5 - - + +
160B PRO* 3.9 20.6 - - + -
162B ILE 3.4 18.8 - - - +
163B GLY* 3.8 9.0 - - - -
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Residues in contact with LEU 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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102B LEU* 4.4 8.7 - - + -
106B ILE* 4.3 20.4 - - + -
110B PHE* 3.9 19.7 - - + -
116B PHE* 3.9 35.7 - - + -
120B PHE* 3.7 2.0 - - - -
134B TRP* 1.3 71.6 - - - +
136B VAL* 1.3 62.9 + - - +
142B LEU* 4.0 20.2 - - + -
143B GLU 3.5 14.1 - - - +
144B VAL* 4.6 0.7 - - + +
160B PRO 3.8 0.2 - - - -
161B VAL* 2.8 44.0 + - + +
162B ILE* 2.9 30.1 + - + +
192B TRP* 5.0 2.0 - - + -
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Residues in contact with VAL 136 (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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134B TRP* 3.7 21.1 - - + -
135B LEU* 1.3 78.6 - - - +
137B VAL* 1.3 65.3 + - - +
142B LEU* 3.2 9.4 - - - +
143B GLU* 2.8 56.4 + - + +
145B THR* 4.1 15.9 - - + +
153B PRO* 3.9 25.8 - - + -
158B LYS* 4.1 20.2 - - + -
159B THR 3.2 13.7 - - - +
160B PRO* 4.1 4.5 - - + -
161B VAL* 4.3 2.9 - - - +
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Residues in contact with VAL 137 (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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136B VAL* 1.3 73.9 - - - +
138B ASN* 1.3 63.0 + - - +
139B ASN 4.6 1.6 - - - +
140B GLY* 3.8 30.3 - - - +
141B GLU 3.3 4.5 - - - +
142B LEU* 4.3 3.6 - - + -
157B GLY 4.6 1.0 - - - +
158B LYS* 3.6 2.4 - - - -
159B THR* 2.8 40.5 + - - +
161B VAL* 3.6 25.6 - - + -
199B TYR* 3.9 23.6 - - + -
202B ALA* 4.7 23.3 - - + +
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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