Contacts of the helix formed by residues 187 - 198 (chain F) in PDB entry 4U8T
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 SER 187 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F SER* 2.8 23.7 + - - -
186F SER* 1.3 87.6 - - - +
188F LEU* 1.3 63.3 + - - +
189F GLU* 3.2 17.8 + - - +
190F HIS* 3.4 36.9 + - - +
191F VAL* 3.8 1.9 + - - +
229F VAL* 4.3 4.0 - - - +
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Residues in contact with LEU 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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187F SER* 1.3 70.8 + - - +
189F GLU* 1.3 65.2 + - - +
191F VAL* 3.0 16.0 + - + -
192F LYS* 3.1 22.6 + - + +
229F VAL* 3.8 32.4 - - + +
234F ARG* 6.0 3.8 - - - +
236F CYS* 5.1 3.8 - - + -
323F PHE* 3.8 37.0 - - + +
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Residues in contact with GLU 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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187F SER* 3.1 9.1 + - - +
188F LEU* 1.3 79.2 - - - +
190F HIS* 1.3 64.8 + - + +
192F LYS* 3.3 26.7 + - - +
193F LYS* 2.8 64.0 + - + +
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Residues in contact with HIS 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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185F SER* 4.0 2.5 - - - +
186F SER* 5.7 0.2 - - - -
187F SER* 3.4 26.3 + - - +
188F LEU 3.2 0.6 - - - -
189F GLU* 1.3 86.4 - - + +
191F VAL* 1.3 58.6 + - - +
193F LYS* 3.4 3.0 + - + -
194F SER* 2.8 26.3 + - - -
200F TRP* 3.5 7.7 - - + -
254F TRP* 3.5 56.9 + + + +
260F TYR* 4.3 10.8 - + - -
0R 6MZ 2.8 42.1 + + - +
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Residues in contact with VAL 191 (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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185F SER* 3.7 29.6 - - - -
187F SER 3.8 6.1 - - - +
188F LEU* 3.0 11.7 + - + +
190F HIS* 1.3 73.2 - - - +
192F LYS* 1.3 65.7 + - - +
194F SER* 3.0 8.9 + - - -
195F PHE* 2.9 19.4 + - - +
200F TRP* 4.2 2.7 - - + -
227F PHE* 4.0 14.4 - - + -
228F SER 6.0 0.7 - - - -
229F VAL* 4.2 13.2 - - + -
236F CYS* 4.1 9.2 - - - -
268F TRP* 3.6 29.6 - - + -
323F PHE* 3.9 17.3 - - + -
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Residues in contact with LYS 192 (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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188F LEU* 3.1 20.1 + - + +
189F GLU* 3.6 33.6 - - - +
191F VAL* 1.3 76.9 - - - +
193F LYS* 1.3 58.8 + - + +
195F PHE* 2.9 18.7 + - - +
196F TYR* 3.0 37.8 + - + +
323F PHE* 3.6 46.7 - - + +
324F LEU* 5.1 0.4 - - + -
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Residues in contact with LYS 193 (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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189F GLU* 2.8 51.1 + - + +
190F HIS* 3.8 5.8 - - + +
192F LYS* 1.3 77.4 - - + +
194F SER* 1.3 62.8 + - - +
196F TYR* 4.4 7.0 - - + +
197F ASN* 2.9 42.5 + - - +
253F ILE* 3.0 44.4 - - + +
254F TRP* 4.3 6.7 - - + +
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Residues in contact with SER 194 (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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190F HIS 2.8 15.5 + - - -
191F VAL* 3.1 12.3 - - - -
193F LYS* 1.3 77.6 - - - +
195F PHE* 1.3 55.0 + - - +
198F GLY* 2.8 27.3 + - - +
199F ILE 3.0 22.1 + - - -
200F TRP* 3.5 25.6 - - - +
227F PHE* 4.3 0.2 - - - -
253F ILE* 5.5 0.2 - - - -
254F TRP* 4.6 2.0 - - - +
266F VAL* 4.0 3.8 - - - +
268F TRP* 3.2 26.0 + - - -
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Residues in contact with PHE 195 (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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167F ILE* 3.5 33.7 - - + -
191F VAL 2.9 5.5 + - - +
192F LYS 2.9 8.5 + - - +
194F SER* 1.3 78.8 - - - +
196F TYR* 1.3 88.9 + + - +
198F GLY* 3.9 4.3 + - - -
268F TRP* 3.3 36.2 - + + +
271F VAL* 4.0 13.0 - - + -
323F PHE* 4.0 21.1 - + + -
324F LEU* 3.9 19.1 - - + -
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Residues in contact with TYR 196 (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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192F LYS* 3.0 46.2 + - + +
193F LYS* 4.4 4.7 - - + -
195F PHE* 1.3 99.1 - + - +
197F ASN* 1.3 71.7 + - - +
324F LEU* 3.4 26.1 + - + +
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Residues in contact with ASN 197 (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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193F LYS* 2.9 33.1 + - - +
196F TYR* 1.3 87.5 - - - +
198F GLY* 1.3 65.2 + - - +
199F ILE* 3.3 13.8 + - + +
250F ASP* 5.5 1.4 - - - +
253F ILE* 3.8 36.9 - - + +
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Residues in contact with GLY 198 (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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194F SER 2.8 15.9 + - - -
195F PHE 3.9 3.5 + - - -
196F TYR 3.6 1.4 - - - -
197F ASN* 1.3 79.2 - - - +
199F ILE* 1.3 60.3 + - - +
265F LYS* 3.5 5.2 - - - +
266F VAL* 2.8 40.2 + - - +
268F TRP* 5.0 2.5 - - - -
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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