Contacts of the helix formed by residues 182 - 190 (chain F) in PDB entry 5X6E
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 HIS 182 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172F GLN* 6.2 0.2 - - - -
180F ILE* 3.7 2.8 - - + +
181F ALA* 1.3 106.7 + - + +
183F SER* 1.3 67.4 + - - +
184F SER* 3.3 1.8 - - - +
185F ALA* 3.0 17.2 + - + +
186F VAL* 3.2 16.2 + - - +
18H G 5.2 2.0 - - + -
19H T 3.9 51.9 + + + -
20H T 3.3 43.4 + - + -
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F MET* 4.9 2.4 - - - +
172F GLN* 5.1 24.1 + - - +
181F ALA 4.4 0.2 + - - -
182F HIS* 1.3 70.0 - - - +
184F SER* 1.3 53.1 + - - +
186F VAL* 3.4 8.7 + - - +
187F SER* 2.4 38.4 + - - -
8G G 5.4 4.7 - - - -
9G T 4.6 11.0 - - - -
20H T 5.9 1.2 - - - +
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Residues in contact with SER 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F HIS* 4.8 0.2 - - - +
183F SER* 1.3 77.4 - - - +
185F ALA* 1.3 57.6 + - - +
187F SER* 3.3 8.5 - - - -
188F ARG* 2.4 39.9 + - - +
9G T 4.6 2.2 - - - +
10G T 3.5 19.2 - - - +
11G A 4.0 5.8 - - - -
19H T 3.2 19.3 + - - +
20H T 2.9 37.3 + - - +
21H A 3.9 3.4 - - - -
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Residues in contact with ALA 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F ILE* 3.6 19.7 - - + -
182F HIS* 3.0 12.6 + - + +
184F SER* 1.3 80.6 + - - +
186F VAL* 1.3 61.5 + - - +
188F ARG* 3.1 16.4 + - - +
189F ILE* 3.1 32.2 + - + +
17H T 4.8 10.5 - - + +
18H G 5.4 1.3 - - + +
19H T 3.6 20.9 - - + -
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Residues in contact with VAL 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 4.5 14.6 - - + -
171F MET* 3.3 49.5 - - + +
172F GLN* 5.4 1.3 - - - +
174F LEU* 4.5 6.3 - - + -
175F GLY* 3.7 25.4 - - - +
180F ILE* 3.7 24.0 - - + +
182F HIS 3.2 18.8 + - - +
183F SER* 3.7 6.5 - - - +
185F ALA* 1.3 74.0 - - - +
187F SER* 1.3 59.1 + - - +
189F ILE* 3.7 8.8 + - + +
190F ILE* 3.6 11.1 + - - +
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Residues in contact with SER 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F MET* 4.3 12.2 - - - +
183F SER* 2.4 24.7 + - - -
184F SER* 3.3 10.3 - - - -
186F VAL* 1.3 74.7 - - - +
188F ARG* 1.3 52.9 + - - +
189F ILE 3.1 1.8 - - - -
190F ILE* 2.8 16.0 + - - +
191F SER* 2.4 35.1 + - - -
8G G 5.2 0.9 - - - +
9G T 3.0 26.4 - - - +
10G T 3.7 17.6 + - - +
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Residues in contact with ARG 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F SER 2.4 36.2 + - - +
185F ALA* 3.1 10.2 + - - +
187F SER* 1.3 67.5 - - - +
189F ILE* 1.3 65.6 + - + +
191F SER* 2.5 34.5 + - - +
192F LYS 5.0 0.3 - - - +
10G T 4.5 4.9 - - + +
11G A 4.7 2.0 - - - +
12G A 3.9 13.3 - - - +
13G C 6.0 0.7 - - - +
17H T 3.4 41.7 - - + +
18H G 2.4 41.3 + - - -
19H T 2.5 32.9 + - - +
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Residues in contact with ILE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LYS* 5.6 4.5 - - + -
140F LEU* 5.0 19.7 - - + -
143F ILE* 4.2 32.5 - - + -
180F ILE* 5.2 7.0 - - + -
185F ALA* 3.1 26.1 + - + +
186F VAL* 3.7 13.2 - - - +
187F SER 3.1 0.6 - - - -
188F ARG* 1.3 87.3 - - + +
190F ILE* 1.3 51.5 + - + +
191F SER 3.3 0.2 - - - -
192F LYS 3.3 3.8 - - - +
193F LEU* 2.7 52.7 + - + +
17H T 4.6 19.7 - - - +
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Residues in contact with ILE 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F MET* 3.8 23.6 - - + -
186F VAL 3.6 2.0 + - - +
187F SER* 2.8 14.9 + - - +
189F ILE* 1.3 76.6 - - + +
191F SER* 1.3 69.0 + - - +
192F LYS* 3.2 17.8 - - + +
193F LEU* 3.1 36.3 - - + +
199F ILE* 5.1 7.6 - - + -
201F TYR* 5.5 9.0 - - + -
206F PHE* 4.4 25.8 - - + -
9G T 3.7 26.4 - - - +
10G T 4.0 2.6 + - - -
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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