Contacts of the helix formed by residues 152 - 161 (chain G) 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 PRO 152 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130G ILE* 4.8 4.3 - - + -
134G HIS* 3.9 25.6 - - + +
150G ILE 3.6 3.5 - - - +
151G LEU* 1.3 88.5 - - + +
153G ALA* 1.3 65.3 + - - +
154G ASP* 3.9 16.2 - - - +
155G ARG* 3.5 31.4 - - + +
156G ILE* 3.4 21.2 + - - +
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Residues in contact with ALA 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G SER 3.8 22.0 - - - +
94G VAL* 4.7 4.4 - - + +
95G GLY 6.1 0.2 - - - +
151G LEU 3.4 2.8 + - - +
152G PRO* 1.3 71.2 - - - +
154G ASP* 1.3 60.7 + - - +
156G ILE* 3.4 4.4 + - - +
157G THR* 2.8 38.1 + - - +
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Residues in contact with ASP 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G PRO* 3.9 7.4 - - - +
153G ALA* 1.3 79.5 - - - +
155G ARG* 1.3 93.6 + - - +
157G THR* 3.8 5.0 - - - -
158G GLU* 2.9 30.0 + - - +
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Residues in contact with ARG 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ILE* 4.2 27.7 - - + +
133G GLU* 2.2 41.5 + - - -
134G HIS* 4.2 8.3 + - - -
152G PRO* 3.5 26.9 + - + +
154G ASP* 1.3 99.2 + - - +
156G ILE* 1.3 63.3 + - + +
158G GLU* 3.2 6.4 + - - +
159G VAL* 2.9 27.9 + - - +
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G VAL* 3.9 21.5 - - + +
93G SER* 3.2 27.6 - - - +
94G VAL* 3.7 19.1 - - + -
127G LEU* 3.8 22.2 - - + -
130G ILE* 4.5 13.5 - - + -
151G LEU* 3.7 22.7 - - + -
152G PRO 3.4 13.2 + - - +
153G ALA 3.4 3.6 + - - +
154G ASP 3.4 0.6 - - - -
155G ARG* 1.3 75.2 - - - +
157G THR* 1.3 64.6 + - - +
159G VAL* 2.9 8.6 + - - +
160G LEU* 2.9 33.1 + - + +
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Residues in contact with THR 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G VAL* 4.5 9.9 - - - +
153G ALA* 2.8 20.4 + - - +
154G ASP* 3.9 5.4 - - - -
156G ILE* 1.3 77.1 - - - +
158G GLU* 1.3 62.9 + - - +
160G LEU* 3.4 9.6 + - - +
161G LYS* 3.3 26.6 + - - +
177G LEU* 4.6 14.2 - - + +
179G SER* 3.1 31.0 - - - +
180G THR* 4.7 4.7 - - + -
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Residues in contact with GLU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASP 2.9 18.3 + - - +
155G ARG* 3.6 6.9 - - - +
156G ILE 3.1 0.2 - - - -
157G THR* 1.3 77.2 - - - +
159G VAL* 1.3 72.5 + - - +
161G LYS* 3.3 27.0 + - + +
162G SER* 4.0 3.3 + - - -
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Residues in contact with VAL 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ALA* 3.8 22.0 - - + +
126G GLU* 4.6 11.4 - - + +
127G LEU* 3.6 33.9 - - + +
130G ILE* 3.6 23.6 - - + -
155G ARG 2.9 17.6 + - - +
156G ILE 2.9 6.5 + - - +
158G GLU* 1.3 80.7 - - - +
160G LEU* 1.3 61.4 + - - +
161G LYS 3.0 5.7 + - - -
162G SER* 3.1 23.4 + - - -
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Residues in contact with LEU 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G VAL* 5.2 5.2 - - + -
117G PHE* 4.8 13.5 - - + -
119G LEU* 3.6 32.4 - - + +
123G ALA* 6.1 0.7 - - + -
127G LEU* 3.8 22.9 - - + -
156G ILE* 2.9 34.9 + - + +
157G THR* 3.8 4.7 - - - +
158G GLU 3.3 0.2 - - - -
159G VAL* 1.3 77.0 - - + +
161G LYS* 1.3 57.7 + - - +
162G SER* 3.3 2.0 + - - -
172G ARG* 3.1 28.0 + - - +
174G LEU* 5.4 1.8 - - + -
177G LEU* 3.6 28.5 - - + -
180G THR* 3.7 20.5 - - + +
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Residues in contact with LYS 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G THR* 3.3 20.1 + - - +
158G GLU* 3.6 20.1 - - + +
159G VAL 3.0 1.6 - - - -
160G LEU* 1.3 78.3 - - - +
162G SER* 1.3 65.5 + - - +
163G ARG* 3.3 26.0 + - - +
172G ARG* 4.6 2.3 + - - +
179G SER* 3.8 42.7 - - - +
180G THR* 4.3 10.9 - - + +
182G VAL* 5.6 1.0 - - - +
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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