Contacts of the helix formed by residues 169 - 179 (chain B) in PDB entry 1U5U
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 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.7 3.6 - - - -
23B ARG* 3.2 15.8 - - - +
27B GLU* 3.0 28.5 + - - +
145B TRP* 3.8 9.0 - - - -
166B VAL 3.2 14.6 - - - +
167B TYR 3.3 1.6 + - - -
168B LYS* 1.3 81.9 - - - +
170B PRO* 1.3 76.1 - - - +
171B TYR* 2.9 36.1 + - - +
172B TYR* 3.0 46.3 + - + +
173B TYR 3.4 0.3 + - - -
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Residues in contact with PRO 170 (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 GLY 4.9 0.2 - - - +
8B PHE* 3.4 12.8 - - + -
11B PHE* 3.5 28.4 - - + -
20B LEU* 3.8 25.8 - - + -
23B ARG* 3.6 34.3 - - + +
24B ILE* 4.4 9.2 - - + +
169B ASN* 1.3 89.5 - - - +
171B TYR* 1.3 67.6 + - + +
173B TYR* 3.5 3.8 + - + +
174B TYR* 2.9 30.1 + - - +
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Residues in contact with TYR 171 (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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8B PHE* 3.7 22.8 - + - -
24B ILE* 3.5 28.4 - - + +
27B GLU* 3.7 35.7 - - + -
28B HIS* 3.3 23.7 + - - -
143B ILE* 4.2 0.5 - - - +
145B TRP* 3.9 20.2 - + + -
169B ASN* 2.9 11.2 + - - +
170B PRO* 1.3 80.3 - - + +
172B TYR* 1.3 62.3 + - - +
174B TYR* 4.2 4.5 - + + -
175B ASN* 2.8 41.9 + - - +
288B HIS* 5.6 0.7 - - - -
290B GLY 3.5 19.1 - - - -
291B ILE* 3.3 20.1 - - + +
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Residues in contact with TYR 172 (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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143B ILE* 3.0 34.8 - - - +
145B TRP* 3.4 20.1 - + - -
149B SER* 3.3 23.2 - - - -
152B ASP* 2.6 35.1 + - + -
165B TYR* 3.4 56.7 - + + +
166B VAL* 4.3 2.9 - - - -
168B LYS* 4.0 8.7 - - + -
169B ASN* 3.0 34.9 + - + +
171B TYR* 1.3 75.3 - - - +
173B TYR* 1.3 64.3 + - - +
176B LEU* 3.0 29.6 + - - +
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Residues in contact with TYR 173 (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 GLY* 3.8 23.1 - - - +
10B ILE* 3.5 39.2 - - + +
11B PHE* 4.8 3.4 - - + -
166B VAL* 3.5 47.0 + - + +
167B TYR* 3.8 17.7 - + - -
169B ASN 3.4 3.2 + - - +
170B PRO* 3.7 8.7 - - + +
172B TYR* 1.3 82.7 - - - +
174B TYR* 1.3 61.8 + - - +
176B LEU* 3.7 1.4 - - - +
177B VAL* 3.1 29.5 + - + +
235B GLN 2.7 30.1 + - - -
236B ARG* 3.8 3.1 + - - -
238B ILE* 3.9 14.6 - - + -
239B TRP* 3.8 13.0 - - - -
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Residues in contact with TYR 174 (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 ASN* 2.8 65.3 + - + +
7B GLY* 4.1 5.3 - - - -
8B PHE* 3.4 53.8 - + + -
140B GLU* 3.9 16.5 + - - -
170B PRO 2.9 19.1 + - - +
171B TYR* 4.1 6.1 - + - +
173B TYR* 1.3 77.1 - - - +
175B ASN* 1.3 75.3 + - - +
177B VAL 3.4 1.6 + - - -
178B GLU* 3.2 19.9 + - + +
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Residues in contact with ASN 175 (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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140B GLU* 5.0 1.0 - - - +
141B ALA* 3.6 32.5 - - - +
142B ASN 3.0 20.9 + - - +
143B ILE* 3.5 13.7 - - + +
171B TYR* 2.8 31.0 + - - +
174B TYR* 1.3 90.1 - - - +
176B LEU* 1.3 60.6 + - - +
178B GLU* 3.3 12.0 + - - +
179B ALA* 3.0 27.9 + - - +
290B GLY* 3.2 23.8 + - - +
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Residues in contact with LEU 176 (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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143B ILE* 3.3 24.0 - - + +
153B PHE* 5.3 5.8 - - + -
156B VAL* 6.2 1.6 - - + -
162B ALA* 6.1 1.1 - - + -
165B TYR* 4.6 9.9 - - + -
166B VAL* 3.7 21.3 - - + -
172B TYR 3.0 20.2 + - - +
173B TYR 3.7 3.8 - - - +
175B ASN* 1.3 74.5 - - - +
177B VAL* 1.3 61.9 + - - +
179B ALA* 3.3 6.2 + - + -
180B LEU* 3.0 57.3 + - + +
238B ILE* 3.6 27.1 - - + -
241B PHE* 4.7 14.8 - - + -
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Residues in contact with VAL 177 (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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3B TRP* 3.7 15.3 - - + -
5B ASN* 3.3 34.5 - - - +
7B GLY* 4.5 0.7 - - - -
173B TYR* 3.1 26.9 + - + +
174B TYR 3.5 1.1 - - - +
175B ASN 3.2 0.2 - - - -
176B LEU* 1.3 79.2 - - - +
178B GLU* 1.3 61.3 + - - +
180B LEU* 3.8 15.2 + - - +
229B ARG* 4.2 5.7 + - - -
230B LEU* 5.2 6.5 + - + +
235B GLN* 3.5 39.0 - - + +
238B ILE* 3.8 19.5 - - + -
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Residues in contact with GLU 178 (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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3B TRP* 4.0 6.2 - - - -
5B ASN* 2.9 27.1 + - - +
139B GLY* 3.6 17.3 - - - -
140B GLU* 3.7 37.0 + - + +
141B ALA 5.1 0.4 - - - +
174B TYR* 3.2 27.1 + - + +
175B ASN* 3.5 14.8 - - + +
176B LEU 3.2 0.2 - - - -
177B VAL* 1.3 80.3 - - - +
179B ALA* 1.3 52.4 + - - +
181B ARG* 2.8 29.3 + - - -
223B GLU* 4.8 1.6 - - - +
229B ARG* 3.4 30.1 + - - +
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Residues in contact with ALA 179 (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 ALA* 3.5 17.9 - - + -
138B THR* 2.5 49.9 + - - +
139B GLY* 3.7 2.7 - - - -
141B ALA 5.6 0.9 - - - +
142B ASN* 6.1 2.7 - - - +
143B ILE* 5.7 4.5 - - + -
175B ASN 3.0 16.2 + - - +
176B LEU* 3.9 10.1 - - + +
178B GLU* 1.3 78.1 - - - +
180B LEU* 1.3 63.9 + - + +
181B ARG* 3.5 0.5 + - - -
195B GLN* 5.8 1.1 - - - +
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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