Contacts of the helix formed by residues 169 - 180 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.9 4.3 - - - -
23A ARG* 3.3 13.6 - - - +
27A GLU* 2.8 31.7 + - - +
145A TRP* 3.8 9.2 - - - -
166A VAL 3.2 13.2 - - - +
167A TYR 3.4 1.0 - - - -
168A LYS* 1.3 82.6 - - - +
170A PRO* 1.3 76.3 - - - +
171A TYR* 2.8 38.0 + - - +
172A TYR* 2.9 45.2 + - + +
173A TYR 3.5 0.3 + - - -
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 4.8 0.2 - - - +
8A PHE* 3.3 21.1 - - + -
11A PHE* 3.7 26.8 - - + -
20A LEU* 3.7 26.0 - - + -
23A ARG* 3.5 38.6 - - + -
24A ILE* 4.4 5.8 - - + -
169A ASN* 1.3 90.7 - - - +
171A TYR* 1.3 67.5 + - + +
173A TYR* 3.5 3.8 + - + +
174A TYR 3.0 22.3 + - - -
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.8 22.0 - + - -
24A ILE* 3.5 30.3 - - + +
27A GLU* 3.6 33.7 - - + -
28A HIS* 3.1 24.6 + - - -
143A ILE* 4.6 0.7 - - - +
145A TRP* 4.0 19.3 - + + -
169A ASN* 2.8 14.6 + - - +
170A PRO* 1.3 75.7 - - + +
172A TYR* 1.3 61.7 + - - +
174A TYR* 3.8 6.1 - + + -
175A ASN* 2.8 43.2 + - - +
288A HIS* 5.7 0.4 - - - -
290A GLY 3.7 17.9 - - - -
291A ILE* 3.5 20.9 - - + +
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.3 24.7 - - - +
145A TRP* 3.3 29.3 - + - -
149A SER* 3.4 20.6 - - - -
152A ASP* 2.6 34.4 + - + -
165A TYR* 3.3 60.2 - + + +
166A VAL* 4.1 4.0 - - - +
168A LYS* 4.0 9.6 - - + -
169A ASN* 2.9 33.1 + - + +
171A TYR* 1.3 76.5 - - - +
173A TYR* 1.3 57.3 + - - +
176A LEU* 2.9 34.0 + - - +
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 3.8 22.0 - - - +
10A ILE* 3.4 43.3 - - + +
11A PHE* 4.9 2.9 - - + -
166A VAL* 3.5 45.7 + - + +
167A TYR* 3.9 16.6 - + - -
169A ASN 3.5 2.0 + - - +
170A PRO* 3.8 8.5 - - + +
172A TYR* 1.3 81.1 - - - +
174A TYR* 1.3 62.2 + - - +
176A LEU* 3.3 2.4 + - - +
177A VAL* 3.1 30.4 + - + +
235A GLN 2.7 29.5 + - - -
236A ARG* 3.7 3.1 - - - -
238A ILE* 3.7 15.0 - - + -
239A TRP* 3.6 13.5 - - - -
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASN* 2.8 65.0 + - + +
7A GLY* 4.0 5.8 - - - -
8A PHE* 3.5 50.9 - + + -
140A GLU* 3.9 21.6 + - - -
170A PRO 3.0 18.4 + - - +
171A TYR* 4.1 6.1 - + - +
173A TYR* 1.3 78.9 - - - +
175A ASN* 1.3 74.6 + - - +
177A VAL 3.4 0.2 + - - -
178A GLU* 3.2 14.7 + - + +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 4.9 1.0 - - - +
141A ALA* 3.6 31.1 - - - +
142A ASN 2.8 25.6 + - - +
143A ILE* 3.5 9.7 - - + +
171A TYR* 2.8 33.2 + - - +
174A TYR* 1.3 91.3 - - - +
176A LEU* 1.3 60.0 + - - +
178A GLU* 3.3 10.4 + - - +
179A ALA* 3.0 27.4 + - - +
290A GLY* 3.2 24.2 + - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.4 22.2 - - + +
153A PHE* 5.3 5.2 - - + -
162A ALA* 6.1 1.3 - - + -
165A TYR* 4.6 10.5 - - + -
166A VAL* 3.5 27.4 - - + -
172A TYR 2.9 21.6 + - - +
173A TYR 3.6 4.5 - - - +
174A TYR 3.3 0.2 - - - -
175A ASN* 1.3 75.8 - - - +
177A VAL* 1.3 58.3 + - - +
179A ALA* 3.2 6.0 + - + +
180A LEU* 2.9 55.9 + - + +
238A ILE* 3.5 24.0 - - + -
241A PHE* 4.8 15.5 - - + -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TRP* 3.6 22.5 - - + -
5A ASN* 3.5 26.2 - - - +
7A GLY 4.6 0.4 - - - +
173A TYR* 3.1 26.5 + - + +
174A TYR 3.5 8.5 - - - +
176A LEU* 1.3 79.0 - - - +
178A GLU* 1.3 59.6 + - - +
179A ALA 3.4 0.3 + - - -
180A LEU* 3.6 15.9 + - - +
229A ARG* 4.3 5.0 + - - +
230A LEU* 5.2 7.0 + - + +
235A GLN* 3.6 31.9 - - + +
238A ILE* 3.6 20.4 - - + -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TRP* 3.6 14.0 - - - -
5A ASN* 2.8 23.1 + - - +
139A GLY* 3.6 19.2 - - - -
140A GLU* 3.7 38.1 + - + +
141A ALA 5.1 0.4 - - - +
174A TYR* 3.2 24.4 + - + +
175A ASN* 3.5 15.0 - - + +
176A LEU 3.2 0.2 - - - -
177A VAL* 1.3 79.0 - - - +
179A ALA* 1.3 52.9 + - - +
181A ARG* 2.5 30.8 + - - -
223A GLU* 5.4 0.3 - - - -
229A ARG* 3.4 27.5 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA* 3.4 18.5 - - + -
138A THR* 2.7 46.4 + - - +
139A GLY* 3.9 2.2 - - - -
141A ALA 5.7 1.1 - - - +
142A ASN* 6.1 3.1 - - - +
143A ILE* 5.3 4.9 - - + -
175A ASN 3.0 16.3 + - - +
176A LEU* 3.2 11.9 + - + +
178A GLU* 1.3 77.6 - - - +
180A LEU* 1.3 63.1 + - + +
181A ARG* 3.7 0.6 + - - -
195A GLN* 6.0 0.7 - - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 4.3 5.8 - - + -
115A ASP* 3.8 31.2 - - - +
116A ALA* 3.9 4.7 - - + +
176A LEU* 2.9 32.5 + - + +
177A VAL 3.6 7.4 + - - +
178A GLU 3.6 0.4 - - - -
179A ALA* 1.3 77.7 - - + +
181A ARG* 1.3 76.4 + - - +
182A ARG 4.3 0.2 - - - -
228A GLY 4.1 4.3 - - - +
229A ARG* 4.3 5.0 - - - -
230A LEU* 3.8 26.0 + - + -
238A ILE* 3.5 37.2 - - + +
241A PHE* 4.0 22.2 - - + -
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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