Contacts of the strand formed by residues 229 - 237 (chain C) in PDB entry 5HMG
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 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C TYR* 4.4 1.1 - - - -
99C PRO* 3.3 29.4 - - + +
100C TYR 4.7 5.2 - - - +
101C ASP* 4.1 13.9 - - + +
183C HIS* 4.0 1.6 - - - -
184C HIS* 2.9 32.8 + - + +
220C ARG* 3.6 28.6 - - - +
221C PRO 2.7 30.9 + - - -
223C VAL* 3.2 21.0 - - - +
226C LEU 3.4 13.1 + - - -
227C SER 3.8 3.2 - - - -
228C SER* 1.3 102.8 + - - +
230C ILE* 1.3 66.3 + - - +
206E THR 4.0 10.5 + - - -
207E ARG* 3.8 15.2 + - - +
209E SER 5.3 3.6 + - - +
210E GLN* 3.3 24.0 - - + +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR* 4.2 11.4 - - + -
99C PRO 3.0 7.4 + - - +
100C TYR* 2.9 21.2 - - + +
101C ASP* 2.8 25.1 + - - +
147C PHE* 3.8 18.8 - - + -
148C PHE* 3.5 31.4 - - + -
151C LEU* 4.8 1.8 - - + -
181C GLY* 5.9 0.2 - - - -
182C ILE 3.3 9.0 - - - +
183C HIS* 3.7 31.2 - - + -
184C HIS* 4.6 0.2 - - - -
229C ARG* 1.3 80.6 - - - +
231C SER* 1.3 62.8 + - - +
232C ILE* 4.6 11.9 - - + -
252C ILE* 4.3 15.7 - - + -
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASP* 3.0 29.9 + - - -
103C PRO* 4.3 3.6 - - - -
181C GLY* 3.2 23.6 - - - -
182C ILE* 3.1 11.2 + - - -
184C HIS* 2.8 28.2 + - - -
230C ILE* 1.3 73.0 - - - +
232C ILE* 1.3 60.4 + - - +
233C TYR* 3.6 26.7 - - - -
210E GLN* 4.5 1.9 + - - -
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LEU* 3.8 26.7 - - + -
100C TYR* 3.9 33.7 - - + -
101C ASP 2.8 6.9 + - - -
102C VAL* 3.7 17.1 - - + +
103C PRO* 3.3 21.3 - - - +
108C LEU* 4.0 21.8 - - + -
151C LEU* 3.9 17.5 - - + -
179C ILE* 3.6 23.3 - - + -
180C TRP 3.6 7.0 - - - +
181C GLY* 4.9 2.5 - - - -
230C ILE* 4.6 8.7 - - + -
231C SER* 1.3 76.6 - - - +
233C TYR* 1.3 67.9 + - - +
234C TRP* 5.6 0.2 - - - -
252C ILE* 5.8 0.2 - - + -
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C PRO* 3.6 31.4 - - + +
179C ILE* 3.4 8.1 - - - +
180C TRP* 2.8 69.6 + + + +
181C GLY* 4.3 0.9 - - - -
182C ILE* 4.0 9.0 - - + -
184C HIS* 5.7 0.5 + - - -
211C GLN* 4.4 9.9 - - - +
213C ILE* 3.5 40.0 - - + +
231C SER* 3.6 32.2 - - - -
232C ILE* 1.3 77.0 - - - +
234C TRP* 1.3 65.5 + - - +
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Residues in contact with TRP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 5.5 3.1 - - - -
73B VAL 3.5 19.5 - - - -
74B GLU* 4.3 12.8 - - - -
102C VAL* 5.6 2.5 - - + -
103C PRO 5.5 4.0 + - - -
104C ASP* 4.9 8.9 + - - +
107C SER* 4.9 5.8 - - - -
108C LEU* 3.7 31.6 - - + +
111C LEU* 3.6 23.3 - - + -
177C LEU* 3.9 10.3 - - + -
178C TYR 3.3 5.6 - - - -
179C ILE* 3.6 20.6 - - + -
180C TRP* 4.1 0.4 - - - +
211C GLN* 3.7 12.5 + - - +
232C ILE 5.6 0.7 - - - -
233C TYR* 1.3 81.1 - - - +
235C THR* 1.3 65.0 + - - +
236C ILE* 3.7 40.4 - - + -
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Residues in contact with THR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C LYS 3.8 0.3 - - - +
177C LEU* 3.6 0.7 - - - -
178C TYR* 2.8 36.2 + - - +
180C TRP* 2.9 25.0 + - - -
204C VAL* 3.5 9.1 - - + +
205C SER 5.6 0.9 - - - -
206C THR* 4.0 13.5 - - + -
209C SER* 5.2 5.2 - - - +
211C GLN* 3.2 22.8 + - - +
234C TRP* 1.3 71.4 - - - +
236C ILE* 1.3 72.6 + - - +
237C VAL* 3.9 2.4 + - + -
243C LEU* 3.9 24.2 - - + -
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 4.6 10.4 - - - +
73B VAL* 3.7 28.3 - - + +
111C LEU* 4.5 2.5 - - + -
175C ASP* 4.0 30.3 - - + +
176C LYS 3.3 8.1 - - - +
177C LEU* 3.9 12.1 - - + -
206C THR* 4.4 5.0 + - - +
234C TRP* 3.7 30.8 - - + -
235C THR* 1.3 78.7 - - - +
237C VAL* 1.3 64.8 + - - +
238C LYS* 4.1 10.6 + - + +
260C MET* 3.4 32.1 - - + -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C MET 5.1 0.9 - - - +
170C ASN* 2.9 28.6 + - + +
176C LYS* 2.8 24.9 + - + +
178C TYR* 3.5 36.3 - - + -
206C THR* 3.7 18.6 - - + -
235C THR* 4.0 2.5 - - + -
236C ILE* 1.3 76.6 - - - +
238C LYS* 1.3 63.0 + - - +
241C ASP* 3.7 31.4 - - + -
242C VAL 4.1 11.0 - - - +
243C LEU* 4.0 13.7 - - + +
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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