Contacts of the helix formed by residues 157 - 164 (chain A) in PDB entry 1U1H
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 GLY 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU 3.3 4.9 + - - -
156A VAL* 1.3 74.2 - - - +
158A PRO* 1.3 70.0 - - - +
159A VAL 3.4 2.5 - - - -
160A SER* 3.2 1.6 + - - -
161A TYR* 2.9 27.2 + - - +
188A TYR* 4.6 0.4 - - - -
205A LEU* 4.5 4.0 - - - -
206A ASP 2.7 17.4 + - - -
207A GLU* 3.2 22.4 - - - -
226A TYR* 4.4 1.6 - - - -
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Residues in contact with PRO 158 (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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157A GLY* 1.3 82.9 - - - +
159A VAL* 1.3 63.4 + - + +
161A TYR* 3.5 3.6 - - - +
162A LEU* 3.2 26.7 + - - +
181A LEU* 4.4 2.0 - - + -
184A ILE* 3.7 7.3 - - + +
185A LEU* 3.6 28.9 - - + -
188A TYR* 3.2 46.8 - - + +
205A LEU* 5.0 4.5 - - + -
207A GLU* 3.6 7.9 - - - +
225A ALA* 4.9 5.4 - - + -
226A TYR* 4.1 7.9 - - + +
229A LEU* 4.4 12.6 - - + -
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Residues in contact with VAL 159 (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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158A PRO* 1.3 74.6 - - + +
160A SER* 1.3 63.0 + - - +
162A LEU* 3.4 5.8 + - - +
163A LEU* 3.1 29.5 + - + +
178A LEU* 4.2 13.7 - - + -
181A LEU* 4.5 11.4 - - + +
207A GLU* 3.4 13.0 - - - +
221A ALA* 4.5 8.5 - - + +
222A PHE* 3.2 69.3 - - + +
225A ALA* 4.6 5.2 - - + -
226A TYR* 4.3 6.5 - - + -
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Residues in contact with SER 160 (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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156A VAL* 4.5 4.7 - - - -
157A GLY 3.2 4.2 + - - -
159A VAL* 1.3 74.3 - - - +
161A TYR* 1.3 67.4 + - - +
163A LEU* 3.2 1.2 + - - +
164A LEU* 3.0 33.1 + - - +
206A ASP 4.0 9.9 - - - -
207A GLU* 2.6 46.7 + - - +
208A PRO* 4.2 5.8 - - - -
209A VAL* 3.3 28.4 + - - +
222A PHE* 4.4 1.0 - - - -
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Residues in contact with TYR 161 (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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68A VAL* 4.1 9.2 - - + -
71A THR* 3.1 30.1 - - + -
72A THR* 3.0 29.5 + - - -
75A LEU* 3.5 26.6 - - + +
77A ALA* 4.1 13.9 - - - +
122A PRO* 3.4 32.3 - - + +
124A LEU* 3.9 20.5 - - + +
130A PHE* 5.1 0.9 - + - -
156A VAL* 4.1 10.3 - - + +
157A GLY 2.9 17.9 + - - +
158A PRO 3.5 7.2 - - - +
160A SER* 1.3 78.4 - - - +
162A LEU* 1.3 68.1 + - + +
164A LEU* 3.4 11.0 + - - +
165A SER* 2.8 20.7 + - - -
184A ILE* 4.5 5.4 - - + -
188A TYR* 3.9 8.1 - - - +
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Residues in contact with LEU 162 (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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124A LEU* 3.5 26.9 - - + -
158A PRO 3.2 5.4 + - - +
159A VAL 3.9 0.7 - - - +
160A SER 3.2 0.2 - - - -
161A TYR* 1.3 80.9 - - + +
163A LEU* 1.3 63.3 + - - +
164A LEU 3.0 4.5 - - - -
165A SER* 3.0 14.5 + - - -
177A LEU* 3.4 41.9 - - + +
178A LEU* 3.9 18.6 - - + -
180A LEU* 4.0 9.9 - - + -
181A LEU* 3.7 38.1 - - + +
184A ILE* 3.5 33.9 - - + -
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Residues in contact with LEU 163 (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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159A VAL* 3.1 34.5 + - + +
160A SER 3.2 3.8 + - - +
162A LEU* 1.3 76.7 - - - +
164A LEU* 1.3 61.1 + - - +
165A SER 3.3 4.7 - - - +
166A LYS* 4.7 4.3 + - - -
176A GLU* 5.6 2.0 - - - +
177A LEU* 5.1 5.8 - - + +
178A LEU* 3.8 31.2 - - + +
209A VAL* 3.5 35.7 - - + -
214A LEU* 4.4 9.4 - - + -
218A LYS* 4.3 24.0 - - + +
222A PHE* 4.2 8.5 - - + -
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Residues in contact with LEU 164 (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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68A VAL* 4.8 8.1 - - + -
112A TRP* 3.8 27.1 - - + -
113A PHE* 4.2 25.6 - - + +
119A TYR* 2.6 51.7 + - + +
121A VAL* 4.4 1.6 - - - +
122A PRO* 4.0 2.9 - - - +
156A VAL* 4.7 7.4 - - + -
160A SER* 3.0 35.2 + - - +
161A TYR* 3.8 9.0 - - - +
162A LEU 3.0 0.4 - - - -
163A LEU* 1.3 77.3 - - - +
165A SER* 1.3 63.5 + - - +
166A LYS* 3.7 6.8 + - - +
208A PRO* 5.3 0.7 - - + -
209A VAL* 4.2 8.7 - - + -
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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