Contacts of the helix formed by residues 157 - 164 (chain N) in PDB entry 5U07
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 ASP 157 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2N SER 4.3 3.4 + - - -
155N VAL* 3.6 3.7 + - - +
156N ALA* 1.3 77.6 - - - +
158N PRO* 1.3 72.0 - - - +
159N VAL* 3.8 9.4 + - - +
160N ARG* 2.8 61.0 + - - +
161N GLU* 3.8 6.4 + - - +
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Residues in contact with PRO 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N SER 4.3 6.1 - - - +
3N GLY 4.4 0.2 - - - -
4N PHE 4.2 20.6 - - - +
5N LEU* 3.8 27.2 - - + +
116N ALA* 4.1 7.2 - - + -
117N VAL 4.3 1.1 - - - +
118N THR* 3.2 29.4 - - + +
155N VAL* 3.7 24.9 - - + +
157N ASP* 1.3 86.6 - - - +
159N VAL* 1.3 59.6 + - + +
160N ARG 3.1 2.2 - - - -
161N GLU* 2.7 23.7 + - + +
162N LEU 2.9 10.6 + - - -
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Residues in contact with VAL 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N LYS* 6.3 1.1 - - + -
60N THR* 3.8 41.7 - - + +
116N ALA* 4.2 4.7 - - + +
118N THR* 4.3 17.0 - - - +
157N ASP* 3.5 9.1 - - - +
158N PRO* 1.3 75.2 - - + +
160N ARG* 1.3 63.0 + - - +
162N LEU* 3.1 15.1 + - + +
163N VAL* 3.0 34.5 + - + +
186N TYR* 4.8 10.1 - - + +
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Residues in contact with ARG 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157N ASP* 2.8 52.6 + - - +
158N PRO 3.1 0.4 - - - -
159N VAL* 1.3 77.6 - - - +
161N GLU* 1.3 63.6 + - - +
163N VAL* 3.4 6.8 + - - -
164N GLU* 3.1 47.3 + - - +
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Residues in contact with GLU 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N LEU* 4.0 8.3 - - + -
152N ARG* 3.4 18.0 + - - +
155N VAL* 4.7 6.1 - - + -
157N ASP 3.8 3.5 + - - +
158N PRO* 2.7 23.3 + - + +
160N ARG* 1.3 73.9 - - - +
162N LEU* 1.3 55.4 + - - -
164N GLU* 2.5 23.6 - - - +
165N ALA* 3.5 21.1 - - - +
166N VAL* 3.3 11.9 - - - +
245N TYR* 2.9 44.0 + - - +
248N GLN* 4.8 1.2 + - - -
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Residues in contact with LEU 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N LEU* 4.3 8.5 - - + +
60N THR* 4.1 15.5 - - + +
62N ARG* 3.4 38.8 + - + +
114N THR* 3.9 22.2 - - - +
116N ALA* 3.5 29.6 - - + -
158N PRO 2.9 7.2 + - - +
159N VAL* 3.1 19.2 + - + +
161N GLU* 1.3 74.7 - - - +
163N VAL* 1.3 80.3 + - + +
164N GLU* 3.0 4.8 + - - -
166N VAL* 4.6 8.6 - - + +
184N LEU* 3.4 26.9 - - + -
226N VAL* 5.0 0.7 - - - +
230N LEU* 4.9 1.0 - - - +
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Residues in contact with VAL 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N VAL* 3.0 26.1 + - + +
160N ARG* 3.4 6.0 + - - +
162N LEU* 1.3 87.1 - - + +
164N GLU* 1.3 75.7 + - - +
184N LEU* 5.5 1.8 - - + -
186N TYR* 5.3 7.0 - - - +
224N THR* 4.9 19.7 - - + -
225N GLU 5.0 4.7 - - - +
226N VAL* 3.6 24.6 - - + +
227N PRO* 3.7 8.7 - - + +
230N LEU* 4.2 0.3 - - - +
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Residues in contact with GLU 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N ARG* 3.1 34.7 - - - +
161N GLU* 2.5 30.6 - - - +
162N LEU 3.0 1.3 - - - -
163N VAL* 1.3 98.9 - - - +
165N ALA* 1.3 69.6 + - + +
166N VAL 3.3 2.9 - - - -
227N PRO* 4.1 18.5 - - + +
230N LEU* 3.7 9.0 - - + -
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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