Contacts of the helix formed by residues 208 - 220 (chain X) in PDB entry 1UNF
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 ARG 208 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204X ASP 4.0 6.3 + - - -
205X PHE* 2.9 54.4 + - + +
206X GLN* 3.2 6.8 + - - -
207X ASN* 1.3 93.3 - - - +
209X ARG* 1.3 62.2 + - - +
210X PRO* 3.4 7.2 - - + -
211X ASP* 2.8 58.9 + - + +
212X TYR 3.2 10.0 + - - -
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Residues in contact with ARG 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X ALA 2.9 28.4 + - - -
137X ALA* 3.6 14.6 + - - +
139X GLN 2.7 23.4 + - - -
140X PHE* 5.0 0.2 - - - +
141X GLY 3.0 28.7 + - - +
196X VAL* 3.5 26.7 + - + +
198X GLU* 5.3 3.2 - - - +
201X TYR* 2.9 47.9 + - + +
207X ASN 2.8 12.5 + - - +
208X ARG* 1.3 68.3 - - - +
210X PRO* 1.3 71.3 - - + +
212X TYR* 3.4 6.2 + - + +
213X ILE* 3.0 42.4 + - + +
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Residues in contact with PRO 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X ALA* 4.6 16.6 - - + -
207X ASN 4.5 2.0 - - - +
208X ARG* 3.5 6.3 - - - -
209X ARG* 1.3 93.6 - - + +
211X ASP* 1.3 65.6 + - - +
213X ILE* 3.3 10.6 + - + +
214X SER* 3.0 24.7 + - - -
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Residues in contact with ASP 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205X PHE* 3.9 7.9 - - + -
208X ARG* 2.8 51.5 + - - +
210X PRO* 1.3 79.8 - - - +
212X TYR* 1.3 64.2 + - - +
214X SER* 3.2 7.4 + - - -
215X VAL* 3.0 30.0 + - + +
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Residues in contact with TYR 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X MET* 3.9 23.6 - - + -
98X PHE* 3.5 22.9 - - - -
194X ILE* 3.6 20.0 - - + +
195X ASP 2.8 29.1 + - - -
196X VAL* 4.4 3.6 - - + -
200X ALA* 3.5 9.3 - - + +
201X TYR* 3.4 42.0 - + + -
205X PHE* 3.5 36.3 - + + -
208X ARG 3.2 6.6 + - - +
209X ARG* 3.5 12.6 - - + +
211X ASP* 1.3 78.9 - - - +
213X ILE* 1.3 62.3 + - + +
215X VAL* 3.4 2.0 + - + +
216X PHE* 2.9 30.2 + + + +
220X LEU* 5.5 1.6 - - + -
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Residues in contact with ILE 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X PHE* 5.0 2.2 - - + -
133X LYS* 3.7 29.2 - - + +
136X ALA* 3.4 39.9 - - + -
137X ALA* 3.5 23.1 - - + +
194X ILE* 3.7 22.7 - - + -
196X VAL* 4.5 1.3 - - + -
209X ARG* 3.0 34.9 + - + +
210X PRO* 3.7 8.1 - - + +
212X TYR* 1.3 81.1 - - + +
214X SER* 1.3 62.3 + - - +
216X PHE* 3.3 2.9 - - - +
217X MET* 3.0 27.7 + - + +
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Residues in contact with SER 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X LYS* 3.5 30.1 + - - +
210X PRO 3.0 16.5 + - - -
211X ASP* 3.5 9.2 - - - -
213X ILE* 1.3 79.4 - - - +
215X VAL* 1.3 58.4 + - - +
217X MET* 3.3 4.0 + - - +
218X ASP* 2.8 32.7 + - - +
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Residues in contact with VAL 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X VAL* 2.7 44.4 - - + -
205X PHE* 4.1 24.5 - - + -
211X ASP* 3.0 21.6 + - + +
212X TYR* 3.8 3.8 - - + +
214X SER* 1.3 73.3 - - - +
216X PHE* 1.3 62.3 + - - +
218X ASP* 4.3 5.6 - - - +
219X LYS* 2.8 37.5 + - + +
220X LEU* 3.6 1.4 + - + +
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Residues in contact with PHE 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 3.7 16.6 - + - -
101X CYS* 4.5 5.2 - - + -
102X MET* 3.5 41.1 - - + -
132X PHE* 4.7 1.1 - + - -
192X LEU* 4.2 15.3 - - + -
193X THR 3.3 23.6 - - - -
194X ILE* 3.5 30.3 - - + -
212X TYR* 2.9 20.3 + + + +
213X ILE 3.3 9.0 - - - +
215X VAL* 1.3 76.3 - - - +
217X MET* 1.3 81.6 + - + +
220X LEU* 3.0 23.7 + - + +
221X VAL* 3.0 33.9 + - + -
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Residues in contact with MET 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X GLY* 3.4 6.1 - - - -
108X GLY 4.1 5.4 + - - +
125X PHE* 5.1 1.0 - - + -
128X PHE* 4.0 9.9 - - + -
129X LEU* 3.6 37.5 - - + -
132X PHE* 3.7 32.1 - - + -
133X LYS* 4.7 5.6 - - + -
192X LEU* 4.1 7.0 - - + -
213X ILE* 3.0 17.8 + - + +
214X SER 3.8 4.0 - - - +
216X PHE* 1.3 103.5 - - + +
218X ASP* 1.3 62.2 + - - +
221X VAL* 3.3 22.0 - - - +
223X TRP* 3.8 33.8 - - + -
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Residues in contact with ASP 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X GLY 4.0 1.7 - - - +
107X GLY* 3.3 12.0 - - - -
108X GLY 3.7 6.9 + - - +
214X SER* 2.8 21.4 + - - +
215X VAL* 3.3 6.0 + - - +
217X MET* 1.3 78.7 - - - +
219X LYS* 1.3 92.1 + - + +
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Residues in contact with LYS 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X VAL* 3.8 32.3 - - + -
103X LYS 4.1 0.9 - - - +
105X GLY* 4.4 2.9 + - - -
106X GLY 3.0 32.9 + - - +
215X VAL* 2.8 21.8 + - + +
217X MET 3.4 0.2 - - - -
218X ASP* 1.3 105.1 + - + +
220X LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X LEU* 4.3 27.4 - - + +
34X VAL* 3.8 37.5 - - + -
35X MET* 3.7 34.8 - - + -
102X MET* 3.0 24.2 - - + -
103X LYS 2.9 29.1 + - - +
106X GLY* 4.0 0.2 - - - -
107X GLY 3.9 0.4 - - - -
212X TYR* 5.5 1.8 - - + -
215X VAL* 4.1 0.4 - - + +
216X PHE* 3.0 27.1 + - + +
219X LYS* 1.3 85.6 - - + +
221X VAL* 1.3 68.0 + - - +
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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