Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 5U03
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 ASP 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.8 7.3 + - - +
221A PRO 4.0 0.8 + - - -
222A LEU* 1.3 77.9 - - - +
224A THR* 1.3 63.5 + - - +
225A SER* 2.7 17.9 + - - -
226A VAL* 2.7 33.8 + - - +
227A LYS* 3.3 18.6 + - - +
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Residues in contact with THR 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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223A ASP* 1.3 75.4 + - - +
225A SER* 1.3 65.6 + - - +
227A LYS* 2.9 14.1 + - + +
228A GLU* 2.8 41.7 + - + +
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Residues in contact with SER 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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223A ASP* 2.7 28.3 + - - -
224A THR* 1.3 75.8 - - - +
226A VAL* 1.3 60.1 + - - +
228A GLU* 3.3 9.0 + - - +
229A LYS* 2.9 45.3 + - - +
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Residues in contact with VAL 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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192A GLN* 3.4 31.0 - - + +
194A THR* 3.6 25.4 - - + -
222A LEU* 3.9 20.2 - - + -
223A ASP* 2.7 29.2 + - - +
225A SER* 1.3 81.7 + - - +
227A LYS* 1.3 56.5 + - - +
229A LYS* 3.1 15.1 + - + +
230A ILE* 2.9 37.4 + - + +
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Residues in contact with LYS 227 (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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221A PRO* 6.1 1.0 - - - +
222A LEU* 3.7 41.1 + - + +
223A ASP 3.4 12.8 - - - +
224A THR* 2.9 11.6 + - + +
226A VAL* 1.3 78.1 - - - +
228A GLU* 1.3 59.9 + - - +
230A ILE* 3.3 4.2 + - - +
231A SER* 2.8 29.5 + - - -
238A PRO* 4.9 14.2 - - + +
241A VAL* 3.9 31.1 - - + +
243A CYS* 4.3 16.6 - - - +
260A GLN* 5.3 10.5 + - - +
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Residues in contact with GLU 228 (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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224A THR* 2.8 37.3 + - + +
225A SER* 3.6 8.3 - - - +
226A VAL 3.1 0.2 - - - -
227A LYS* 1.3 76.4 - - - +
229A LYS* 1.3 63.7 + - + +
231A SER* 3.3 8.9 + - - -
232A MET* 3.0 22.2 + - - +
238A PRO* 4.0 24.2 - - - +
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Residues in contact with LYS 229 (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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194A THR* 5.3 7.2 - - + +
225A SER* 2.9 29.8 + - - +
226A VAL* 3.4 13.9 - - + +
228A GLU* 1.3 74.1 - - + +
230A ILE* 1.3 60.1 + - + +
232A MET* 3.1 9.5 + - + +
233A PHE* 2.8 53.2 + - + -
54B GLU* 5.3 7.9 + - - -
602B UTP 5.1 17.9 + - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A VAL* 5.1 4.5 - - + -
194A THR* 3.7 24.9 - - + -
197A THR* 5.3 9.2 - - + -
198A GLN* 6.2 0.4 - - + -
214A VAL* 5.9 4.0 - - + -
216A CYS* 4.6 11.4 - - - -
222A LEU* 3.7 29.4 - - + -
226A VAL* 2.9 25.6 + - + +
227A LYS 3.6 5.6 - - - +
229A LYS* 1.3 73.5 - - - +
231A SER* 1.3 64.2 + - - +
233A PHE* 3.0 8.5 + - - +
234A CYS* 2.8 43.6 + - + +
236A VAL* 5.0 0.4 - - + -
241A VAL* 3.7 26.0 - - + -
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Residues in contact with SER 231 (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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227A LYS 2.8 14.3 + - - -
228A GLU* 3.3 18.0 + - - -
230A ILE* 1.3 75.5 - - - +
232A MET* 1.3 52.7 + - - +
235A HIS* 2.6 31.5 + - - -
236A VAL* 2.6 38.9 + - - +
238A PRO* 3.9 21.1 - - - +
241A VAL* 4.0 1.1 - - - +
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Residues in contact with MET 232 (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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228A GLU 3.0 12.5 + - - +
229A LYS* 3.1 9.4 + - + +
231A SER* 1.3 76.6 - - - +
233A PHE* 1.3 104.5 + - + +
235A HIS* 3.1 27.3 + - + +
114D VAL* 5.4 3.8 - - - -
115D PRO* 4.1 36.6 - - + -
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Residues in contact with PHE 233 (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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194A THR* 4.4 5.2 - - - -
198A GLN* 3.4 46.4 - - + -
205A ARG* 3.1 16.7 + - - -
229A LYS* 2.8 50.6 + - + +
230A ILE* 3.0 7.4 + - - +
232A MET* 1.3 98.2 - - + +
234A CYS* 1.3 59.1 + - - +
235A HIS* 3.3 11.3 - - - -
602B UTP 3.3 24.7 - - - -
112D GLN* 5.0 11.4 - - - -
114D VAL* 5.2 15.9 - - + +
115D PRO* 5.3 1.1 - - + -
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Residues in contact with CYS 234 (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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197A THR* 4.8 6.3 - - - -
198A GLN* 5.3 6.3 - - - -
201A VAL* 4.1 34.5 - - + -
205A ARG* 2.9 23.5 + - - +
214A VAL* 5.3 5.8 - - + -
230A ILE* 2.8 34.6 + - - +
233A PHE* 1.3 76.3 - - - +
235A HIS* 1.3 72.4 + - - +
236A VAL* 3.4 27.4 - - + +
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Residues in contact with HIS 235 (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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205A ARG* 3.0 23.1 + - - +
231A SER 2.6 17.9 + - - -
232A MET* 3.1 15.9 + - + +
233A PHE 3.3 16.8 - - - -
234A CYS* 1.3 74.6 - - - +
236A VAL* 1.3 58.1 + - - +
114D VAL* 5.0 14.4 - - + +
115D PRO* 6.3 0.8 - - - +
161D GLU* 4.1 7.9 + - - -
164D ARG* 3.7 15.9 - - - -
165D GLN* 3.3 39.9 + - + +
169D LYS* 6.2 0.7 - - - -
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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