Contacts of the helix formed by residues 213 - 226 (chain A) in PDB entry 1UZL
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 THR 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE* 3.7 3.1 - - - -
187A ASP* 5.2 2.7 - - + -
210A ARG* 5.3 2.0 - - - +
211A VAL* 5.3 3.6 - - + +
212A GLY* 1.3 77.3 - - - -
214A PRO* 1.3 74.8 - - + +
215A ALA* 3.6 9.2 + - - +
216A GLU* 2.9 52.0 + - - +
217A VAL* 3.3 14.4 + - - +
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.7 5.8 - - - +
27A ILE* 4.3 20.5 - - + +
30A ALA* 3.7 23.5 - - + +
186A ILE* 3.7 10.5 - - + -
187A ASP* 3.4 28.0 - - + +
188A THR* 5.2 2.9 - - - -
213A THR* 1.3 88.2 - - - +
215A ALA* 1.3 57.0 + - - +
217A VAL* 3.1 6.4 + - + +
218A ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 4.4 3.9 - - + +
34A ARG* 5.0 2.1 + - - -
213A THR* 3.1 9.3 + - - +
214A PRO* 1.3 79.6 - - - +
216A GLU* 1.3 57.8 + - + +
218A ALA* 3.2 8.6 + - - +
219A GLY* 2.8 29.1 + - - -
9B ALA 4.1 31.2 - - - +
11B PRO* 6.4 0.7 - - + -
228B ASP* 5.0 1.6 - - - +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 5.8 0.2 - - + -
210A ARG* 2.9 36.6 + - - -
212A GLY* 3.2 4.8 - - - -
213A THR* 2.9 44.1 + - - +
215A ALA* 1.3 75.9 - - + +
217A VAL* 1.3 62.0 + - - +
219A GLY* 3.8 4.2 + - - -
220A VAL* 3.6 18.0 + - - +
239A VAL* 3.8 7.2 - - + +
228B ASP* 4.2 10.3 - - - +
230B SER* 2.9 28.5 + - - +
231B TYR* 3.7 20.3 - - + +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.1 29.6 - - + -
31A ILE* 4.6 7.6 - - + -
138A ILE* 4.8 2.7 - - + -
181A VAL* 4.0 23.1 - - + -
183A PRO* 4.3 13.5 - - + -
186A ILE* 3.7 36.1 - - + -
213A THR 3.3 5.4 + - - +
214A PRO 3.1 7.2 + - - +
216A GLU* 1.3 75.1 - - - +
218A ALA* 1.3 64.0 + - - +
220A VAL* 3.0 16.4 + - - +
221A VAL* 3.4 11.4 + - + +
239A VAL* 4.3 9.6 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.5 30.7 - - - +
31A ILE* 3.8 15.7 - - - +
34A ARG* 3.8 17.9 - - + +
35A LEU* 5.5 0.3 - - - +
214A PRO 2.9 13.8 + - - +
215A ALA* 3.2 11.6 + - - +
217A VAL* 1.3 75.9 - - - +
219A GLY* 1.3 56.5 + - - +
221A VAL* 3.3 3.2 + - - +
222A SER* 2.8 30.5 + - - -
9B ALA 6.3 0.4 - - - +
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.7 20.1 - - - +
215A ALA 2.8 16.2 + - - -
216A GLU 4.1 3.8 - - - -
217A VAL 3.2 0.6 - - - -
218A ALA* 1.3 77.6 - - - +
220A VAL* 1.3 60.2 + - - +
222A SER* 3.5 3.9 - - - -
223A PHE* 3.2 15.9 + - - +
223B PHE* 3.8 8.5 - - - -
228B ASP* 3.8 22.4 - - - +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 4.1 18.6 - - + -
216A GLU 3.6 13.5 - - - +
217A VAL 3.0 6.3 + - - +
219A GLY* 1.3 73.4 - - - +
221A VAL* 1.3 62.6 + - - +
223A PHE* 3.2 4.4 + - + +
224A LEU* 2.9 27.6 + - + +
237A ILE* 4.0 33.0 - - + -
239A VAL* 3.5 28.3 - - + -
223B PHE* 4.0 17.3 - - + -
228B ASP 4.6 3.1 - - - +
232B ILE* 3.9 16.4 - - + -
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.7 36.1 - - + -
35A LEU* 4.3 6.7 - - + -
86A VAL* 3.9 22.4 - - + -
136A ILE* 4.0 9.1 - - + +
138A ILE* 3.7 27.8 - - + -
181A VAL* 4.2 8.5 - - + -
217A VAL* 3.6 14.8 - - + +
218A ALA 3.3 5.6 + - - +
220A VAL* 1.3 74.9 - - - +
222A SER* 1.3 59.5 + - - +
224A LEU* 3.2 9.0 + - - +
225A ALA* 2.9 28.6 + - - +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.3 31.3 + - - -
35A LEU* 3.9 8.0 - - - +
38A ASP* 2.6 32.0 + - - +
40A HIS* 5.4 0.9 + - - -
218A ALA 2.8 17.9 + - - -
219A GLY 3.5 7.2 - - - -
221A VAL* 1.3 75.2 - - - +
223A PHE* 1.3 61.8 + - - +
225A ALA* 3.4 3.5 + - - +
226A SER* 3.1 23.0 + - - -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLY 3.2 2.4 + - - +
220A VAL* 3.2 9.4 + - + +
222A SER* 1.3 80.4 + - - +
224A LEU* 1.3 71.5 + - + +
226A SER* 2.6 35.5 + - - -
228A ASP* 3.9 23.1 - - + -
229A ALA* 3.4 8.2 - - + +
232A ILE* 3.4 35.4 - - + -
237A ILE* 4.6 6.7 - - + -
219B GLY 3.7 19.3 - - - -
220B VAL* 3.9 18.8 - - + -
223B PHE* 3.4 56.5 - + + -
237B ILE* 5.4 0.2 - - + -
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.1 15.6 - - - +
136A ILE* 3.9 29.7 - - + +
179A ASN* 4.0 37.5 + - + +
180A VAL 4.9 1.6 - - - +
181A VAL* 3.5 32.1 - - + -
220A VAL* 2.9 22.5 + - + +
221A VAL 3.2 1.5 + - - +
223A PHE* 1.3 89.2 - - + +
225A ALA* 1.3 59.2 + - - +
226A SER 4.1 0.2 - - - +
229A ALA* 3.5 19.8 - - + +
232A ILE* 4.5 6.3 - - + -
237A ILE* 4.0 23.6 - - + -
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 4.8 4.7 + - - +
35A LEU* 3.9 20.0 - - + -
40A HIS* 4.3 19.5 + - - +
84A VAL* 4.0 30.7 - - + +
132A PHE* 5.3 2.6 - - - -
134A ARG* 4.9 8.6 - - - +
136A ILE* 3.8 6.2 - - + +
221A VAL 2.9 16.9 + - - +
222A SER 3.7 5.2 - - - +
224A LEU* 1.3 76.5 - - - +
226A SER* 1.3 61.6 + - - +
227A GLU* 5.5 0.5 - - - +
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 6.0 3.4 - - - -
13A PHE* 6.3 4.5 - - - -
40A HIS* 5.3 4.7 - - - -
132A PHE* 6.1 0.5 - - - -
134A ARG* 4.9 6.9 + - - -
222A SER 3.1 11.9 + - - -
223A PHE* 2.6 25.7 + - - -
224A LEU 4.1 0.7 - - - +
225A ALA* 1.3 83.0 - - - +
227A GLU* 1.3 66.7 + - - +
228A ASP* 3.2 22.4 + - - +
229A ALA* 3.3 14.7 + - - +
230A SER 4.6 0.3 + - - -
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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