Contacts of the helix formed by residues 204 - 215 (chain B) in PDB entry 1UK0
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B ALA* 3.4 31.8 + - - +
27B GLU* 5.2 5.3 + - - +
28B TYR* 3.1 32.5 + - - -
106B ASN* 3.2 25.7 + - - +
203B SER* 1.4 81.1 + - - +
205B THR* 1.3 60.0 + - + +
206B THR* 3.1 13.3 + - - +
207B ASN* 2.8 36.4 + - - +
208B PHE* 3.5 5.5 + - - -
246B TYR 3.6 7.4 - - - +
247B CYS 3.5 15.5 - - - +
248B HIS* 3.1 42.6 + - + +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 4.7 18.8 + - - -
15B ILE* 3.5 30.3 + - - +
20B SER* 4.9 9.5 + - - -
203B SER 5.5 0.2 - - - +
204B ARG* 1.3 76.9 - - + +
206B THR* 1.3 64.1 + - - +
207B ASN 3.4 0.3 + - - -
208B PHE* 3.9 13.7 - - - +
209B ALA 4.2 0.5 + - - -
247B CYS* 5.3 4.7 - - + +
249B THR* 5.8 0.9 - - + -
253B ASP* 4.5 16.5 + - - +
255B ILE 4.3 15.3 - - - +
256B GLY* 5.1 1.1 - - - -
257B LEU* 4.0 31.2 - - + +
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE 4.6 2.9 - - - +
17B ASP 4.5 2.0 - - - +
20B SER* 4.1 10.8 + - - +
21B MET* 3.4 58.1 - - + +
24B ALA* 4.7 2.9 - - - +
106B ASN 5.6 0.2 - - - -
109B ASP 3.7 0.9 - - - -
110B ILE* 3.2 36.7 + - - +
113B ALA* 3.6 18.2 - - - +
204B ARG* 3.1 13.7 + - - +
205B THR* 1.3 85.2 + - - +
207B ASN* 1.4 58.9 + - - +
209B ALA 4.9 0.2 - - - -
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Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP 4.3 0.9 - - - +
106B ASN* 3.4 33.8 + - - +
109B ASP* 2.7 39.2 + - - +
110B ILE 3.6 4.3 + - - -
203B SER* 3.8 17.5 + - - +
204B ARG* 2.8 24.8 + - - +
206B THR* 1.4 67.2 - - - +
208B PHE* 1.3 49.8 + - - +
209B ALA 3.4 2.2 - - - -
210B GLY* 2.4 33.6 + - - -
211B ILE* 2.7 15.2 + - + -
502B FRM 3.8 20.2 - - - -
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.6 22.9 - - + -
201B HIS 4.5 0.2 - - - -
203B SER* 3.4 24.7 - - - -
204B ARG 3.5 18.4 + - - -
205B THR 3.9 3.6 - - - +
207B ASN* 1.3 73.7 - - - +
209B ALA* 1.4 59.5 + - - +
211B ILE* 3.6 21.6 - - + +
212B LEU* 2.8 37.2 + - + +
257B LEU* 2.9 51.1 - - + -
258B ILE* 3.7 3.6 - - - -
259B LEU* 3.5 38.6 - - + -
341B LEU* 4.4 19.3 - - + -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.5 19.9 - - + +
16B PHE* 3.4 37.5 - - + -
113B ALA* 4.3 17.0 - - + -
116B LEU* 4.2 7.9 - - + -
136B LEU* 3.7 6.5 - - + +
205B THR 4.2 2.0 + - - -
206B THR 4.8 1.4 + - - -
207B ASN 3.1 2.8 + - - -
208B PHE* 1.4 75.6 - - - +
210B GLY* 1.3 58.1 + - - +
212B LEU 3.6 1.6 + - - -
213B SER* 2.9 28.5 + - - -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 4.0 15.6 - - - +
112B VAL* 3.7 20.0 - - - +
113B ALA 4.7 2.4 - - - +
206B THR 5.0 0.4 + - - -
207B ASN 2.4 19.2 + - - -
209B ALA* 1.3 71.1 - - - +
211B ILE* 1.4 51.6 + - - -
213B SER* 2.8 12.5 + - - -
214B GLN* 2.8 34.2 + - - +
217B ARG* 3.4 4.7 + - - -
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 3.7 12.8 - - - +
180B ARG* 3.1 3.6 - - - -
203B SER* 3.5 26.0 - - - +
207B ASN* 2.7 23.5 + - + +
208B PHE* 3.6 37.5 - - + +
210B GLY* 1.4 66.8 - - - +
212B LEU* 1.4 58.4 + - + +
213B SER 3.1 4.0 - - - -
215B GLY* 2.6 34.9 + - - +
216B LEU* 3.2 40.8 - - + +
217B ARG* 4.4 2.2 - - - +
259B LEU* 3.7 15.0 - - + -
338B LEU* 4.1 5.9 - - + +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.9 2.9 - - + -
15B ILE* 4.2 18.6 - - + -
136B LEU* 2.8 35.0 - - + +
138B THR* 3.6 16.5 + - + -
140B ILE* 4.4 18.2 - - + -
178B ILE* 4.6 15.9 - - + -
180B ARG* 3.7 10.4 - - + +
208B PHE* 2.8 30.7 + - + +
209B ALA 3.6 0.9 - - - -
211B ILE* 1.4 73.5 - - - +
213B SER* 1.3 53.0 - - - +
259B LEU* 4.9 2.2 - - + -
338B LEU* 4.6 14.4 - - + -
341B LEU* 3.8 32.1 - - + -
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 3.2 12.0 - - - +
116B LEU* 3.8 19.5 - - - -
135B LYS 4.6 4.0 - - - -
136B LEU 3.8 9.8 - - - +
137B LYS* 5.6 3.8 - - - +
180B ARG* 3.5 8.9 + - - -
209B ALA 2.9 11.2 + - - -
210B GLY* 2.8 31.2 + - - -
211B ILE 3.1 0.6 - - - -
212B LEU* 1.3 77.6 - - - +
214B GLN* 1.3 74.2 + - - +
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Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.8 15.9 - - - +
180B ARG* 3.0 20.9 + - - +
186B ARG* 4.8 4.3 + - - -
210B GLY 2.8 15.5 + - - +
213B SER* 1.3 95.8 + - - +
215B GLY* 1.4 66.3 - - - +
216B LEU 4.6 0.5 - - - +
217B ARG* 3.0 48.3 + - - +
333B ILE* 5.5 2.1 - - - +
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ARG* 3.0 18.4 - - - +
183B GLU* 6.0 0.4 - - - -
186B ARG* 5.9 1.8 - - - -
210B GLY 3.8 0.6 + - - -
211B ILE* 2.6 32.3 + - - -
214B GLN* 1.4 81.6 - - - +
216B LEU* 1.3 74.1 + - - -
217B ARG* 2.7 14.4 + - - -
338B LEU* 4.4 4.0 - - - -
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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