Contacts of the helix formed by residues 141 - 155 (chain B) in PDB entry 2UUG
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 TRP 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.3 8.1 - + - -
23B THR* 4.0 18.6 - - + +
24B LEU* 3.6 26.7 - - + -
27B VAL* 4.1 16.0 - - + +
44B VAL* 4.2 4.9 - - + -
45B PHE* 4.0 16.8 - + - -
124B THR 3.2 14.6 - - - +
125B VAL* 3.5 32.3 - - + -
126B LEU* 3.4 40.6 - - + +
127B THR* 2.7 38.3 + - + +
136B HIS* 3.7 16.7 + - + +
139B LEU* 3.9 2.6 - - + +
140B GLY* 1.3 76.6 - - - +
142B GLU* 1.3 50.5 + - - +
144B PHE* 3.2 10.2 + + + +
145B THR* 2.8 41.2 + - - +
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Residues in contact with GLU 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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124B THR* 3.2 25.9 + - - -
125B VAL* 3.6 17.9 - - + +
134B HIS* 5.2 4.5 + - - -
137B ALA* 5.7 1.3 - - + -
138B SER* 5.1 13.7 - - - +
140B GLY 3.2 1.5 - - - +
141B TRP* 1.3 78.5 - - - +
143B THR* 1.3 58.2 + - - +
145B THR* 3.6 3.6 - - - -
146B ASP* 2.9 37.4 + - - +
167B HIS* 3.6 21.2 + - - -
171B LYS* 3.0 29.2 + - - -
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Residues in contact with THR 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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14B GLU* 4.7 3.4 - - - +
19B TYR* 3.7 32.2 + - + +
140B GLY* 3.2 14.9 + - - -
142B GLU* 1.3 79.3 - - - +
144B PHE* 1.3 58.1 + - - +
146B ASP* 3.3 9.3 - - + +
147B LYS* 3.1 26.2 + - - +
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Residues in contact with PHE 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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11B LEU* 3.8 41.1 - - + -
14B GLU* 4.3 11.9 - - + -
15B LYS* 5.1 6.3 - - + -
19B TYR* 3.5 16.5 + - - +
20B PHE* 3.8 37.7 - + + -
45B PHE* 4.0 24.0 - + - -
48B PHE* 4.0 18.6 - + - -
126B LEU* 4.0 15.5 - - + -
140B GLY 3.2 9.5 + - - +
141B TRP* 3.7 11.0 - + + +
143B THR* 1.3 76.0 - - - +
145B THR* 1.3 64.1 + - + +
146B ASP 3.1 1.8 - - - -
147B LYS* 3.2 6.2 + - - +
148B VAL* 3.1 34.0 + - + +
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Residues in contact with THR 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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122B LEU* 4.2 16.5 - - + +
123B ASN 3.4 21.8 - - - +
124B THR* 2.8 20.7 + - - +
126B LEU* 4.2 17.9 - - + -
141B TRP 2.8 28.8 + - - +
144B PHE* 1.3 77.3 - - + +
146B ASP* 1.3 62.4 + - - +
148B VAL* 3.4 10.3 + - - +
149B ILE* 3.2 28.3 + - - +
171B LYS* 2.9 22.5 + - - -
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Residues in contact with ASP 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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142B GLU* 2.9 25.4 + - - +
143B THR* 3.3 10.0 - - + +
145B THR* 1.3 77.9 + - - +
147B LYS* 1.3 64.1 + - - +
149B ILE* 3.2 8.8 + - - +
150B SER* 3.0 22.2 + - - -
171B LYS* 3.0 33.8 - - - +
174B ILE* 4.1 13.5 - - + +
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Residues in contact with LYS 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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10B VAL 5.9 1.1 - - - -
11B LEU* 5.0 2.0 - - + -
13B GLU* 6.4 1.8 - - - -
14B GLU* 3.5 44.4 - - + +
143B THR 3.1 10.6 + - - +
144B PHE* 3.3 10.8 - - + +
146B ASP* 1.3 80.7 - - - +
148B VAL* 1.3 55.5 + - - +
150B SER* 3.3 15.1 + - - -
151B LEU* 2.9 68.9 + - + +
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Residues in contact with VAL 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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7B TRP* 3.4 29.5 - - + -
11B LEU* 4.3 8.5 - - + -
48B PHE* 3.9 27.8 - - + -
120B LEU* 4.7 1.1 - - + -
122B LEU* 3.8 18.6 - - + -
144B PHE* 3.1 27.0 + - + +
145B THR* 3.4 15.7 - - - +
146B ASP 3.2 0.2 - - - -
147B LYS* 1.3 72.8 - - - +
149B ILE* 1.3 59.6 + - - +
151B LEU* 3.2 8.9 + - - +
152B ILE* 3.0 35.0 + - + +
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Residues in contact with ILE 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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59B VAL* 5.5 2.9 - - + -
61B LEU* 3.8 31.9 - - + -
122B LEU* 4.6 7.9 - - + -
145B THR* 3.2 15.9 + - - +
146B ASP* 3.2 8.4 + - - +
148B VAL* 1.3 76.1 - - + +
150B SER* 1.3 56.5 - - - +
152B ILE* 3.8 10.9 - - + +
153B ASN* 3.1 27.5 + - - +
161B PHE* 4.3 11.0 - - + -
171B LYS* 3.8 42.4 - - + +
174B ILE* 4.2 6.5 - - + -
175B ILE* 3.9 28.7 - - + -
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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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146B ASP 3.0 13.0 + - - -
147B LYS* 3.3 25.5 + - - +
148B VAL 3.1 0.2 - - - -
149B ILE* 1.3 78.2 - - - +
151B LEU* 1.3 63.3 + - - +
153B ASN* 3.5 9.6 + - - +
154B GLN* 3.3 22.7 + - - +
174B ILE* 4.2 16.9 - - - +
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Residues in contact with LEU 151 (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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7B TRP* 5.0 4.7 - - + -
10B VAL* 4.0 29.2 - - + +
11B LEU* 3.5 31.6 - - + -
14B GLU* 6.0 0.2 - - + -
53B LEU* 4.8 3.4 - - + +
147B LYS* 2.9 50.0 + - + +
148B VAL* 3.2 5.6 + - - +
150B SER* 1.3 75.9 - - - +
152B ILE* 1.3 65.8 + - - +
154B GLN* 4.5 9.6 - - - +
155B HIS* 3.0 52.6 + - + +
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Residues in contact with ILE 152 (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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7B TRP* 3.7 19.7 - - + -
53B LEU* 4.0 13.2 - - + -
56B VAL* 4.5 6.5 - - + -
59B VAL* 4.0 11.9 - - + -
120B LEU* 3.5 32.5 - - + -
122B LEU* 5.8 0.2 - - + -
148B VAL* 3.0 25.7 + - + +
149B ILE* 3.8 10.1 - - + +
151B LEU* 1.3 75.8 - - - +
153B ASN* 1.3 63.8 + - - +
156B ARG* 3.1 33.6 + - + +
159B VAL* 4.3 21.5 - - + -
161B PHE* 3.7 22.2 - - + -
180B HIS* 3.8 2.0 + - + -
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Residues in contact with ASN 153 (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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149B ILE 3.1 16.5 + - - +
150B SER* 3.5 9.1 + - - +
152B ILE* 1.3 81.6 - - - +
154B GLN* 1.3 59.8 + - - +
156B ARG 3.5 0.3 - - - +
161B PHE* 4.8 2.2 - - + -
174B ILE 3.5 23.3 + - - +
175B ILE* 3.3 8.4 - - + -
176B ASP* 3.0 30.5 + - - +
179B ARG* 2.9 27.0 + - - +
180B HIS* 2.9 36.0 + - + -
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B SER 3.3 13.3 + - - +
151B LEU* 4.0 11.7 - - - +
152B ILE 3.3 0.6 - - - -
153B ASN* 1.3 80.8 - - - +
155B HIS* 1.3 98.1 + - - +
156B ARG 3.3 1.3 + - - +
179B ARG* 3.6 24.1 + - - +
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Residues in contact with HIS 155 (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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5B LEU 6.1 1.3 - - - +
10B VAL* 3.5 33.3 - - + +
53B LEU* 4.5 15.2 - - + +
151B LEU* 3.0 32.7 + - + +
154B GLN* 1.3 106.7 + - - +
156B ARG* 1.3 65.3 + - - +
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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