Contacts of the helix formed by residues 217 - 228 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D ASN* 4.0 2.9 - - - +
169D PHE* 5.0 0.2 - - - -
188D LEU* 3.4 12.4 - - - +
192D GLU* 3.3 39.9 + - - -
194D LEU 4.4 1.2 + - - -
216D ALA* 1.3 80.1 - - - +
218D GLU* 1.3 65.7 + - - +
219D LYS* 3.8 8.8 + - - +
220D PHE* 3.2 20.6 + - - +
221D ILE* 3.1 18.4 + - - +
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Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D SER* 4.6 3.6 + - - -
77D ASN* 3.6 40.7 - - + +
78D ASN* 3.7 16.0 - - - +
217D SER* 1.3 72.7 - - - +
219D LYS* 1.3 57.5 + - - +
221D ILE* 3.5 1.9 + - - +
222D ASP* 2.9 29.6 + - - +
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Residues in contact with LYS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PRO 5.1 0.8 + - - -
4C LEU 5.0 4.9 - - - -
5C ASP* 2.7 43.5 + - - +
8C ALA* 5.7 0.7 - - - +
192D GLU* 6.5 0.9 - - - -
217D SER* 3.1 8.0 - - - +
218D GLU* 1.3 76.0 - - - +
220D PHE* 1.3 66.1 + - - +
222D ASP* 3.3 7.2 + - - +
223D ALA* 3.0 22.6 + - + +
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Residues in contact with PHE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D MET* 3.4 38.8 - - + -
95D MET* 3.5 26.0 - - + -
96D PHE* 4.2 11.0 - + - -
169D PHE* 3.6 34.3 - + + -
195D ALA* 4.4 1.1 - - + -
214D VAL* 4.1 13.7 - - + -
216D ALA* 3.5 20.9 - - + -
217D SER* 3.2 19.2 + - - +
219D LYS* 1.3 74.4 - - - +
221D ILE* 1.3 63.7 + - + +
223D ALA* 2.9 8.0 + - - +
224D TYR* 2.7 58.3 + + + +
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Residues in contact with ILE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LYS 5.5 0.2 - - - +
77D ASN* 3.3 28.3 - - - +
78D ASN 3.4 24.2 - - - +
79D VAL 4.1 11.4 - - - +
80D SER* 4.0 15.0 - - - +
214D VAL* 3.9 14.8 - - + +
216D ALA* 3.9 13.5 - - + +
217D SER 3.1 15.7 + - - +
218D GLU 3.7 1.6 - - - +
220D PHE* 1.3 86.1 - - + +
222D ASP* 1.3 63.2 + - - +
224D TYR* 3.6 2.8 - - - +
225D ASN* 2.9 42.1 + - - +
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Residues in contact with ASP 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ALA* 4.9 6.8 - - - +
14C TYR* 5.5 1.2 + - - +
218D GLU 2.9 15.8 + - - +
219D LYS* 3.5 11.2 - - - +
221D ILE* 1.3 78.7 - - - +
223D ALA* 1.3 68.7 + - - +
225D ASN* 3.3 5.8 + - - +
226D ARG* 2.7 63.4 + - - +
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU 5.4 2.7 - - - +
7C ILE 4.6 4.3 - - - +
8C ALA* 4.3 22.7 - - + +
95D MET* 3.6 19.3 - - + -
219D LYS* 3.0 9.8 + - + +
220D PHE* 2.9 11.0 + - - +
222D ASP* 1.3 84.5 + - - +
224D TYR* 1.3 57.1 + - - +
226D ARG* 2.9 27.7 + - - +
227D VAL* 3.1 14.3 + - - +
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Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D SER* 3.2 31.2 - - - -
81D VAL 2.8 19.0 + - - -
82D GLY* 3.7 3.3 - - - -
87D GLU* 4.0 5.7 + - - -
88D ILE* 3.5 30.9 - - + +
91D VAL* 3.0 37.7 - - + -
95D MET* 3.7 11.1 - - - +
214D VAL* 4.5 4.5 - - + -
220D PHE* 2.7 50.0 + + + +
221D ILE* 3.6 4.3 - - + +
223D ALA* 1.3 72.1 - - - +
225D ASN* 1.3 66.3 + - - +
227D VAL* 3.2 1.7 + - - +
228D ARG* 3.0 50.4 + - + +
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Residues in contact with ASN 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TYR* 3.7 45.2 - - + +
57D PRO* 5.6 0.6 - - - +
79D VAL 5.2 1.2 + - - -
80D SER* 2.6 27.0 + - - -
221D ILE* 2.9 38.9 + - - +
222D ASP* 3.8 6.3 - - - +
224D TYR* 1.3 74.3 - - - +
226D ARG* 1.3 62.3 + - - +
228D ARG* 2.9 37.3 + - - +
229D LEU 5.7 0.5 - - - -
230D PRO* 5.8 0.2 - - - +
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Residues in contact with ARG 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ALA 4.0 15.5 + - - +
9C LYS* 3.3 32.0 - - - +
11C ALA* 3.5 24.1 + - + +
12C TYR 3.5 20.3 + - - +
13C PRO* 3.2 41.5 - - + +
14C TYR* 4.3 5.6 - - + +
111C ILE* 5.4 5.4 - - - +
115C ALA* 3.5 14.9 - - - +
222D ASP* 2.7 60.6 + - - +
223D ALA* 2.9 10.6 + - - +
225D ASN* 1.3 78.7 - - - +
227D VAL* 1.3 63.7 + - + +
228D ARG 4.0 3.3 - - - +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE 4.3 15.9 - - - +
10C ARG* 5.8 0.4 - - - +
11C ALA* 5.5 2.7 - - + -
90C TYR* 2.6 37.6 + - - +
115C ALA* 3.5 34.0 - - - +
116C VAL* 5.1 0.2 - - - -
91D VAL* 4.3 11.2 - - + +
94D LEU* 4.6 10.5 - - + +
95D MET* 4.0 32.5 - - + -
223D ALA 3.1 15.5 + - - +
224D TYR* 3.2 5.4 + - - +
226D ARG* 1.3 79.6 - - + +
228D ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C TYR* 3.3 21.1 + - - -
90C TYR* 3.8 9.4 - - - -
112C PHE* 5.4 1.7 - - - -
115C ALA* 5.5 0.7 - - - +
57D PRO* 2.8 35.4 - - - +
80D SER* 3.8 0.6 + - - -
87D GLU* 4.9 2.9 - - - +
91D VAL* 4.1 21.3 - - + +
224D TYR* 3.0 43.4 + - + +
225D ASN* 2.9 39.5 + - - +
226D ARG 4.0 3.6 - - - +
227D VAL* 1.3 78.1 - - - +
229D LEU* 1.3 70.7 + - - +
230D PRO* 3.0 26.2 + - - +
232D ASN* 2.8 45.2 + - - +
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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