Contacts of the strand formed by residues 141 - 150 (chain B) in PDB entry 1UXU
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 ASN 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.6 8.5 - - - +
133B ASP* 2.7 54.2 + - + +
134B VAL* 4.8 0.6 - - - +
136B TYR 2.8 28.1 + - - -
137B PHE 4.0 1.2 + - - -
138B PRO* 3.2 30.5 - - - +
139B PHE 3.5 1.4 - - - +
140B ASP* 1.3 89.8 + - - +
142B GLN* 1.3 65.9 + - - +
178B TRP* 4.6 2.6 - - - -
207B LEU* 3.8 17.1 - - + +
208B LEU 3.1 13.8 - - - +
209B LYS* 4.2 0.2 - - - -
210B ARG* 4.8 2.5 + - - +
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Residues in contact with GLN 142 (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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45B MET* 4.0 25.4 - - - -
47B GLU* 3.1 26.7 + - - +
50B GLN* 2.8 44.1 + - - -
130B CYS* 3.6 5.2 - - - +
131B VAL 3.6 8.7 - - - -
132B VAL* 3.4 13.8 - - - +
141B ASN* 1.3 74.1 + - - +
143B GLN* 1.3 60.7 + - - +
144B CYS* 3.7 4.8 + - - -
178B TRP* 3.5 23.8 - - + -
206B LEU 3.6 2.3 - - - +
207B LEU* 3.7 3.8 - - - -
208B LEU* 2.9 40.6 + - + +
210B ARG* 4.8 1.4 - - - +
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Residues in contact with GLN 143 (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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130B CYS* 3.2 3.3 - - - -
131B VAL* 2.8 46.2 + - + +
133B ASP* 4.9 10.8 + - + +
141B ASN* 4.2 0.8 - - - +
142B GLN* 1.3 72.5 - - - +
144B CYS* 1.3 60.9 + - - +
145B ASN* 4.0 5.1 + - - +
205B THR* 3.6 30.2 - - + +
206B LEU 3.8 2.2 - - - -
207B LEU* 4.0 16.7 - - + +
2215B NAG 3.1 44.2 + - - +
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Residues in contact with CYS 144 (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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45B MET* 4.0 13.9 - - - -
52B LEU* 3.8 21.3 - - + -
128B SER* 5.4 1.3 - - - +
129B SER 4.4 0.7 - - - +
130B CYS* 2.1 49.1 - - - +
142B GLN* 4.2 5.6 - - - -
143B GLN* 1.3 72.9 - - - +
145B ASN* 1.3 66.4 + - - +
146B LEU* 3.7 3.2 + - - +
204B PHE 3.6 0.9 - - - +
206B LEU* 2.8 42.7 + - + +
208B LEU* 4.2 14.4 - - - -
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Residues in contact with ASN 145 (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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96B ASN* 2.8 27.5 + - - +
128B SER* 3.9 4.7 + - - -
129B SER 4.4 5.8 + - - +
143B GLN* 4.0 4.9 + - - -
144B CYS* 1.3 74.3 - - - +
146B LEU* 1.3 66.9 + - - +
147B THR* 4.6 4.2 + - - +
203B THR* 3.9 8.8 - - + +
204B PHE 3.4 1.5 - - - +
205B THR* 2.9 28.9 + - - +
2215B NAG 1.4 64.4 + - - +
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Residues in contact with LEU 146 (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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37B ILE* 5.2 0.2 - - + -
52B LEU* 4.5 12.3 - - + -
54B ALA* 5.5 0.7 - - + -
56B LEU* 4.4 23.8 - - + -
94B LEU* 4.0 9.9 - - + -
126B THR* 4.3 13.7 - - - +
128B SER* 3.3 28.7 - - - +
144B CYS 4.2 7.2 - - - +
145B ASN* 1.3 75.8 - - - +
147B THR* 1.3 61.2 + - - +
148B PHE* 3.7 21.0 - - + -
183B MET* 3.7 29.6 - - + -
202B VAL 3.7 1.9 - - - +
203B THR* 3.3 1.6 - - - -
204B PHE* 2.8 40.7 + - + +
206B LEU* 5.0 9.9 - - + -
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Residues in contact with THR 147 (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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94B LEU* 3.5 5.4 - - - +
95B TYR* 2.8 44.0 + - + -
96B ASN* 2.9 21.2 + - - +
145B ASN* 4.6 4.9 + - - +
146B LEU* 1.3 72.9 + - - +
148B PHE* 1.3 58.3 + - - +
201B ASP* 3.5 26.0 - - + +
202B VAL 3.5 2.7 - - - -
203B THR* 2.7 29.8 + - - +
1213B MLK 4.0 15.3 - - + +
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Residues in contact with PHE 148 (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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35B LEU* 3.8 20.9 - - + -
37B ILE* 3.6 28.5 - - + -
56B LEU* 3.9 17.3 - - + -
58B ILE* 4.1 22.0 - - + -
92B ILE* 4.0 8.5 - - + -
93B VAL* 3.3 19.5 - - - +
94B LEU* 3.8 26.0 - - + -
95B TYR* 4.1 4.7 - - - -
126B THR* 5.0 3.1 - - + -
146B LEU* 3.7 30.5 - - + -
147B THR* 1.3 73.3 - - - +
149B GLY* 1.3 58.7 + - - +
160B ILE* 4.0 3.1 - - - +
201B ASP* 3.2 5.5 - - - -
202B VAL* 2.8 36.1 + - + +
204B PHE* 3.9 17.0 - + - -
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Residues in contact with GLY 149 (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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92B ILE* 3.8 11.3 - - - +
93B VAL* 2.8 32.5 + - - +
95B TYR* 3.2 19.9 - - - -
148B PHE* 1.3 76.2 - - - +
150B SER* 1.3 65.9 + - - -
160B ILE* 4.3 8.7 - - - -
200B PRO 4.3 5.6 - - - -
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Residues in contact with SER 150 (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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90B PRO* 6.4 0.2 - - - -
91B ASP* 2.6 28.9 + - - -
92B ILE* 4.0 9.1 - - - +
95B TYR* 2.5 24.1 + - - -
149B GLY* 1.3 71.0 - - - -
151B TRP* 1.3 63.4 + - - +
153B TYR* 2.9 43.8 + - - +
158B VAL* 4.7 16.4 - - - -
160B ILE* 5.4 1.4 - - - +
200B PRO* 5.1 1.4 + - - +
1213B MLK 3.6 5.4 - - - +
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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