Contacts of the helix formed by residues 121 - 134 (chain B) in PDB entry 1UXI
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 PRO 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ARG* 3.6 25.3 - - + +
89B GLU* 4.2 16.4 - - + -
92B ILE* 3.7 37.5 - - + +
119B ASN 3.6 0.2 - - - -
120B ASN* 1.3 83.1 - - + +
122B LEU* 1.3 66.8 + - - +
123B ASP 3.6 1.6 - - - -
124B ALA* 3.4 21.1 + - + +
125B MET* 2.9 28.0 + - + +
175B HIS 5.9 0.9 - - - +
302B THR* 5.1 4.9 - - + -
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Residues in contact with LEU 122 (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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117B MET* 3.4 24.9 - - + +
118B VAL* 3.7 6.3 - - - +
119B ASN 3.3 6.7 - - - +
120B ASN* 3.0 20.2 - - - +
121B PRO* 1.3 68.7 - - - +
123B ASP* 1.3 65.7 + - - +
125B MET* 3.1 2.4 + - - +
126B THR* 2.8 37.5 + - - +
142B GLY* 4.0 1.3 - - - -
143B GLN 2.9 31.6 - - - +
144B ALA* 3.6 12.3 - - + -
175B HIS* 3.8 15.5 + - + +
251B ALA* 3.4 31.6 - - + -
1310B NAD 3.6 9.6 - - - +
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Residues in contact with ASP 123 (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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121B PRO 3.6 0.4 - - - -
122B LEU* 1.3 80.3 + - - +
124B ALA* 1.3 61.8 + - - +
126B THR* 3.4 1.9 + - - -
127B TYR* 3.1 23.6 + - - +
144B ALA* 5.6 0.7 - - - +
173B GLY 4.2 0.7 - - - +
174B GLY* 3.0 21.0 - - - -
175B HIS* 2.6 31.6 + - - +
251B ALA* 3.9 15.1 - - - +
264B TYR* 3.6 33.2 - - - +
266B GLY* 3.9 7.8 + - - -
299B VAL* 3.8 15.6 - - + +
302B THR* 5.5 0.7 - - - +
303B LEU* 5.0 2.2 - - - -
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Residues in contact with ALA 124 (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* 4.4 4.9 - - + -
121B PRO* 3.4 22.8 + - + +
122B LEU 3.3 0.4 - - - -
123B ASP* 1.3 79.1 - - - +
125B MET* 1.3 62.9 + - + +
127B TYR* 3.4 6.0 + - - +
128B LEU* 3.0 22.2 + - - +
302B THR* 3.5 26.3 + - - +
303B LEU* 4.3 8.3 - - + +
306B LEU* 3.2 25.5 - - + +
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Residues in contact with MET 125 (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* 4.2 15.5 - - + -
95B ASN* 3.5 21.5 - - - +
96B ALA* 3.9 13.2 - - + +
99B THR* 3.3 25.5 - - - +
117B MET* 3.9 17.7 - - + +
119B ASN* 3.6 21.5 - - + +
120B ASN 3.8 11.2 - - - +
121B PRO* 2.9 23.3 + - + +
122B LEU 3.7 0.2 - - - +
124B ALA* 1.3 83.3 - - + +
126B THR* 1.3 61.9 + - - +
128B LEU* 3.2 7.0 + - + +
129B ALA* 2.8 28.1 + - - +
306B LEU* 4.0 21.8 - - + -
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Residues in contact with THR 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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117B MET* 3.5 13.3 - - + +
122B LEU* 2.8 22.8 + - - +
123B ASP* 3.7 5.2 - - - -
125B MET* 1.3 76.2 - - - +
127B TYR* 1.3 64.3 + - - +
129B ALA* 3.0 5.4 + - - +
130B ALA* 3.0 21.3 + - - +
140B VAL* 3.7 8.2 - - + +
141B ILE* 3.5 29.2 - - - +
142B GLY* 3.4 20.7 - - - +
251B ALA* 4.2 1.3 - - - +
264B TYR* 3.6 29.6 - - + -
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Residues in contact with TYR 127 (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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123B ASP 3.1 14.6 + - - +
124B ALA* 3.5 12.1 - - - +
126B THR* 1.3 77.6 - - - +
128B LEU* 1.3 62.7 + - - +
130B ALA* 3.5 2.6 + - - +
131B GLU* 3.1 52.9 + - + +
253B TYR* 4.2 7.0 - + - -
262B ASP* 3.0 41.7 + - - -
263B ILE* 4.1 2.5 - - - -
264B TYR* 3.3 32.2 - + + -
303B LEU* 3.8 21.1 - - + -
306B LEU* 4.4 9.9 - - + -
307B LYS* 3.3 33.4 + - + -
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Residues in contact with LEU 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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96B ALA* 3.4 44.0 - - + +
99B THR* 4.0 16.8 - - + -
100B ARG* 3.4 28.3 - - - +
124B ALA 3.0 14.5 + - - +
125B MET* 3.2 12.8 + - + +
127B TYR* 1.3 77.9 - - - +
129B ALA* 1.3 57.2 + - - +
131B GLU* 3.4 19.1 - - - +
132B VAL* 2.8 50.5 + - + +
306B LEU* 4.1 14.6 - - + -
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Residues in contact with ALA 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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99B THR* 4.9 0.2 - - - -
103B ILE* 3.8 23.0 - - + +
115B ILE* 4.7 4.3 - - + -
117B MET* 3.6 23.3 - - + -
125B MET 2.8 13.4 + - - +
126B THR* 3.0 9.6 + - - +
128B LEU* 1.3 73.1 - - - +
130B ALA* 1.3 58.9 + - - +
131B GLU 3.0 0.9 - - - -
132B VAL 2.9 1.0 + - - -
133B SER* 2.7 39.9 + - - -
140B VAL* 3.9 11.9 - - + -
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Residues in contact with ALA 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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126B THR 3.0 6.9 + - - +
127B TYR 3.8 2.0 - - - +
129B ALA* 1.3 74.4 - - - +
131B GLU* 1.3 57.8 + - - +
133B SER* 3.4 5.5 + - - -
134B GLY* 2.9 29.1 + - - -
135B PHE 3.9 5.0 + - - +
137B LYS* 4.0 22.2 + - + +
140B VAL* 3.4 17.6 - - + +
264B TYR* 3.5 38.1 - - + +
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Residues in contact with GLU 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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100B ARG* 5.4 1.2 + - - -
127B TYR* 3.1 42.1 + - + +
128B LEU* 3.4 25.4 - - + +
130B ALA* 1.3 79.9 - - - +
132B VAL* 1.3 60.2 + - + +
134B GLY* 4.1 4.7 + - - -
137B LYS* 5.7 1.8 - - - +
306B LEU* 4.9 5.2 - - - +
307B LYS* 5.1 7.8 - - - +
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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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100B ARG* 4.1 24.7 - - + +
103B ILE* 3.6 22.2 - - + -
104B SER* 3.7 28.9 - - - +
107B ALA* 5.4 0.2 - - - +
128B LEU* 2.8 46.2 + - + +
131B GLU* 1.3 74.3 - - + +
133B SER* 1.3 65.8 + - - +
134B GLY* 4.7 0.2 - - - -
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Residues in contact with SER 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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103B ILE* 3.5 10.7 - - - +
107B ALA* 3.6 20.8 - - - +
115B ILE* 3.8 7.2 - - - -
129B ALA 2.7 22.8 + - - -
130B ALA* 3.4 6.6 + - - -
132B VAL* 1.3 73.8 - - - +
134B GLY* 1.3 63.3 + - - +
135B PHE* 3.0 44.2 + - - +
140B VAL* 3.7 3.3 - - - +
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Residues in contact with GLY 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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130B ALA 2.9 14.6 + - - -
131B GLU 4.1 4.2 + - - -
132B VAL 3.4 2.2 - - - -
133B SER* 1.3 78.1 - - - +
135B PHE* 1.3 64.8 + - - +
136B PRO* 4.5 1.2 - - - +
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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