Contacts of the helix formed by residues 217 - 228 (chain B) in PDB entry 1UU1
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 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.9 1.2 - - - +
78B ASN* 3.8 4.3 - - - +
188B LEU* 4.6 4.6 - - - +
192B GLU* 3.7 37.5 + - - +
194B LEU 4.5 2.4 + - - -
216B ALA* 1.3 79.0 - - - +
218B GLU* 1.3 54.5 + - - +
219B LYS* 3.3 10.3 + - - +
220B PHE* 2.9 19.3 + - - +
221B ILE* 2.8 32.5 + - - +
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Residues in contact with GLU 218 (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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75B SER* 4.5 4.5 + - - -
77B ASN* 3.2 51.1 + - + +
78B ASN* 3.5 19.1 + - - +
217B SER* 1.3 73.2 - - - +
219B LYS* 1.3 59.1 + - - +
221B ILE* 3.9 0.3 - - - +
222B ASP* 2.8 32.6 + - - +
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Residues in contact with LYS 219 (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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6A LEU* 3.6 28.4 - - + +
7A ILE* 3.9 25.1 - - + +
9A LYS* 3.1 30.2 + - - +
192B GLU* 3.3 24.5 - - - +
217B SER* 3.1 8.8 + - - +
218B GLU* 1.3 80.1 - - - +
220B PHE* 1.3 61.3 + - - +
222B ASP* 4.5 1.1 - - - -
223B ALA* 3.1 18.2 + - - +
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Residues in contact with PHE 220 (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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7A ILE* 3.8 21.2 - - + +
92B MET* 3.9 21.3 - - + -
95B MET* 3.9 31.6 - - + -
96B PHE* 4.1 17.5 - + - -
169B PHE* 3.7 28.9 - + + -
195B ALA* 4.1 3.6 - - + -
214B VAL* 4.1 23.3 - - + -
216B ALA* 3.4 20.9 - - + -
217B SER* 2.9 18.7 + - - +
219B LYS* 1.3 74.3 - - - +
221B ILE* 1.3 59.5 + - + +
223B ALA* 2.7 8.6 + - - +
224B TYR* 2.7 49.4 + + + +
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Residues in contact with ILE 221 (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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76B LYS 5.3 0.2 - - - +
77B ASN* 3.4 20.6 - - - +
78B ASN 3.5 31.4 - - - +
79B VAL 3.9 13.9 - - - +
80B SER* 3.8 15.0 - - - +
214B VAL* 3.6 26.5 - - + +
216B ALA* 3.8 12.8 - - + +
217B SER 2.8 21.2 + - - +
218B GLU 3.9 0.4 - - - +
220B PHE* 1.3 76.4 - - + +
222B ASP* 1.3 57.7 + - - +
224B TYR* 3.3 4.4 + - + +
225B ASN* 2.8 44.4 + - - +
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Residues in contact with ASP 222 (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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9A LYS* 2.8 35.3 + - - +
13A PRO* 5.0 6.1 - - - +
14A TYR 5.5 1.0 + - - -
218B GLU 2.8 23.8 + - - +
219B LYS* 3.8 3.8 - - - +
221B ILE* 1.3 74.5 - - - +
223B ALA* 1.3 62.5 + - - +
225B ASN* 3.3 9.6 + - - +
226B ARG* 2.9 54.2 + - - +
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Residues in contact with ALA 223 (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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7A ILE* 3.8 26.5 - - + +
8A ALA 4.8 3.1 - - - +
9A LYS* 3.9 18.6 - - + +
95B MET* 4.7 5.8 - - - -
219B LYS 3.1 14.8 + - - +
220B PHE* 2.7 14.6 + - + +
222B ASP* 1.3 74.9 + - - +
224B TYR* 1.3 63.3 + - - +
226B ARG* 2.9 17.0 + - - +
227B VAL* 3.2 17.3 + - + +
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Residues in contact with TYR 224 (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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80B SER* 3.3 22.2 - - - -
81B VAL 2.7 20.6 + - - -
82B GLY* 3.7 3.6 - - - -
87B GLU* 4.4 2.9 + - - +
88B ILE* 3.6 28.2 + - + +
91B VAL* 3.1 34.9 - - + +
95B MET* 3.8 19.9 - - + -
214B VAL* 4.3 10.8 - - + -
220B PHE* 2.7 36.0 + + + +
221B ILE* 3.4 8.5 - - + +
223B ALA* 1.3 71.6 - - - +
225B ASN* 1.3 67.7 + - - +
227B VAL* 2.9 4.9 + - - +
228B ARG* 2.9 57.4 + - + +
232B ASN* 4.0 1.4 + - - -
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Residues in contact with ASN 225 (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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14A TYR* 3.5 41.8 - - + +
57B PRO* 5.5 0.5 - - - +
79B VAL 5.2 0.5 - - - +
80B SER* 2.8 19.7 + - - -
221B ILE* 2.8 34.3 + - - +
222B ASP* 3.5 9.7 - - - +
223B ALA 3.2 0.4 - - - -
224B TYR* 1.3 78.5 - - - +
226B ARG* 1.3 60.2 + - + +
227B VAL 3.3 0.2 - - - -
228B ARG* 2.7 46.3 + - - +
230B PRO* 5.8 1.0 - - - +
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Residues in contact with ARG 226 (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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9A LYS* 3.1 46.3 - - + +
11A ALA* 3.1 12.3 - - - +
12A TYR* 2.9 49.4 - - + +
13A PRO* 3.8 26.2 - - + +
14A TYR* 4.8 3.1 - - - +
111A ILE* 5.2 7.1 - - - +
115A ALA* 3.6 15.1 - - - +
222B ASP* 2.9 45.5 + - - +
223B ALA 2.9 8.1 + - - +
225B ASN* 1.3 79.1 - - + +
227B VAL* 1.3 63.7 + - + +
228B ARG 4.5 2.3 - - - +
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Residues in contact with VAL 227 (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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9A LYS* 5.9 5.4 - - + +
90A TYR* 2.5 40.5 + - - +
115A ALA* 3.6 32.5 - - - +
91B VAL* 4.4 13.0 - - + +
94B LEU* 4.5 7.2 - - + -
95B MET* 4.0 31.0 - - + -
223B ALA* 3.6 12.3 - - + +
224B TYR 2.9 7.2 + - - +
226B ARG* 1.3 84.7 - - + +
228B ARG* 1.3 58.3 + - - +
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Residues in contact with ARG 228 (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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14A TYR* 3.1 27.5 - - - -
90A TYR* 4.0 5.6 - - - -
112A PHE* 5.6 1.0 - - - -
57B PRO* 2.9 36.9 - - - +
80B SER* 3.4 3.2 + - - -
81B VAL 4.0 0.9 - - - -
87B GLU* 5.2 2.0 - - - +
91B VAL* 4.4 10.8 - - + -
224B TYR* 2.9 51.2 + - + +
225B ASN* 2.7 33.2 - - - +
226B ARG 4.5 2.3 - - - +
227B VAL* 1.3 81.8 - - - +
229B LEU* 1.3 85.2 + - - +
230B PRO* 3.0 23.7 + - - +
232B ASN* 3.1 22.9 - - - +
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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