Contacts of the helix formed by residues 189 - 200 (chain H) in PDB entry 2OME
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 GLY 189 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187H GLY 3.6 3.8 + - - -
188H PHE* 1.3 75.1 - - - +
190H ARG* 1.3 61.1 + - - -
191H THR 3.4 2.2 - - - -
192H GLY 4.3 2.8 - - - +
193H GLN* 3.0 38.7 + - - -
213H LEU* 5.4 0.7 - - - -
242H HIS 4.9 0.6 + - - -
901H NAD 3.4 31.3 + - - -
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Residues in contact with ARG 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E GLN* 3.2 43.2 + - - +
215E ASP 2.9 29.3 + - - -
216E GLY* 3.8 13.9 - - - -
217E ILE* 4.9 4.1 - - + +
220E SER* 2.8 29.3 + - - +
106H SER* 5.9 0.4 - - - -
125H ASN* 5.6 1.2 - - - +
127H PRO* 3.3 42.7 + - - +
131H VAL* 3.4 18.8 - - + +
189H GLY* 1.3 72.0 - - - +
191H THR* 1.3 61.5 + - + +
193H GLN* 4.7 1.3 - - - -
194H ALA 3.2 11.8 + - - -
355H ASN* 5.2 1.0 + - - -
901H NAD 2.8 50.6 + - - +
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Residues in contact with THR 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H VAL* 4.3 16.8 - - + -
134H THR* 4.4 24.0 - - + -
135H ALA* 4.5 2.6 - - - +
190H ARG* 1.3 71.8 - - + +
192H GLY* 1.3 62.4 + - - +
194H ALA* 3.1 8.1 + - - +
195H VAL* 2.8 33.3 + - - +
242H HIS* 3.3 28.4 + - - +
901H NAD 2.8 54.0 + - + +
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Residues in contact with GLY 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H LEU* 3.1 16.1 - - - +
187H GLY 3.8 21.1 - - - -
188H PHE* 3.8 7.6 - - - -
189H GLY 3.6 5.7 + - - +
190H ARG 3.4 0.4 - - - -
191H THR* 1.3 82.6 + - - +
193H GLN* 1.3 62.1 + - - +
195H VAL* 3.1 2.8 + - - -
196H ALA* 3.0 19.1 + - - +
242H HIS* 3.9 13.0 - - - +
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Residues in contact with GLN 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E GLN* 5.6 1.9 - - - +
217E ILE* 5.0 11.1 - - - +
220E SER* 4.3 17.2 + - - -
221E LEU* 4.6 7.6 - - + +
188H PHE* 2.9 51.6 + - + -
189H GLY* 3.0 21.4 + - - +
190H ARG* 4.2 2.8 - - - +
192H GLY* 1.3 74.3 - - - +
194H ALA* 1.3 62.7 + - - +
196H ALA* 3.3 2.3 + - - +
197H VAL* 3.1 29.0 + - - +
213H LEU* 5.9 0.2 - - - +
217H ILE* 3.7 28.3 - - - +
221H LEU* 3.7 13.2 - - + +
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Residues in contact with ALA 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ARG 5.3 0.2 - - - +
220E SER* 4.0 15.0 - - - -
131H VAL* 3.8 16.4 - - + -
132H GLU* 5.3 0.7 - - - -
135H ALA* 3.5 19.3 - - + -
190H ARG 3.2 16.7 + - - +
191H THR 3.1 5.9 + - - +
193H GLN* 1.3 80.1 - - - +
195H VAL* 1.3 62.5 + - - +
197H VAL 3.5 0.7 + - - -
198H ARG* 2.7 40.9 + - - +
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H ALA* 4.0 13.5 - - - +
138H THR* 4.0 20.6 - - + -
139H ILE* 3.9 18.4 - - + -
142H ILE* 4.8 2.2 - - + -
183H LEU* 4.2 19.3 - - + -
185H LEU* 4.3 11.0 - - + -
191H THR 2.8 19.1 + - - +
192H GLY 3.1 7.1 + - - +
194H ALA* 1.3 74.4 - - - +
196H ALA* 1.3 65.7 + - - +
198H ARG* 3.0 7.6 + - - +
199H ALA* 2.8 19.8 + - - +
242H HIS* 3.6 27.1 - - + +
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Residues in contact with ALA 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H LEU* 4.1 4.6 - - + +
188H PHE* 3.8 22.4 - - + -
192H GLY 3.0 11.4 + - - +
193H GLN 3.4 9.6 - - - +
195H VAL* 1.3 76.1 - - - +
197H VAL* 1.3 66.0 + - + +
199H ALA* 3.0 17.6 + - - +
200H LYS* 3.3 20.2 + - - +
206H VAL* 4.3 18.9 - - + +
221H LEU* 5.3 2.2 - - + -
223H VAL* 4.7 9.4 - - + -
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Residues in contact with VAL 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E LYS* 4.9 15.5 - - - +
220E SER 4.6 6.5 - - - +
221E LEU* 4.2 24.9 - - + +
201G ALA* 3.5 26.1 - - + +
193H GLN 3.1 16.4 + - - +
194H ALA* 3.7 5.4 - - - +
195H VAL 3.2 0.2 - - - -
196H ALA* 1.3 80.1 - - + +
198H ARG* 1.3 71.9 + - - +
200H LYS* 4.3 19.9 + - - +
201H ALA* 5.1 1.4 + - - +
221H LEU* 4.7 9.6 - - + -
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Residues in contact with ARG 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ARG 5.0 0.6 + - - -
220E SER 4.2 4.9 + - - -
179G ARG* 4.7 0.6 - - - +
198G ARG 5.5 0.9 - - - +
201G ALA* 3.7 31.3 + - + +
202G PHE* 3.8 32.2 + - + +
132H GLU* 2.7 39.4 + - - +
135H ALA* 3.8 19.4 - - - +
136H ASP* 3.1 25.9 + - - -
139H ILE* 3.8 18.6 - - + -
194H ALA* 2.7 42.7 + - - +
195H VAL 3.0 6.6 + - - +
197H VAL* 1.3 88.8 - - - +
199H ALA* 1.3 63.6 + - - +
200H LYS 3.3 0.6 + - - -
201H ALA* 3.9 7.8 + - - +
202H PHE* 3.2 21.5 - - - -
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Residues in contact with ALA 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H ILE* 4.3 6.7 - - + -
183H LEU* 3.7 28.5 - - + -
195H VAL 2.8 16.0 + - - +
196H ALA 3.0 4.9 + - - +
198H ARG* 1.3 76.5 - - - +
200H LYS* 1.3 66.3 + - - +
202H PHE* 3.1 26.0 + - - +
204H PHE* 3.6 20.0 + - + +
206H VAL* 3.9 11.4 - - + -
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Residues in contact with LYS 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E VAL* 6.0 4.7 - - - -
179F ARG* 5.1 3.2 - - - +
179H ARG* 4.5 4.5 + - - -
196H ALA* 3.3 15.3 + - - +
197H VAL* 4.5 16.8 - - - +
198H ARG 3.3 1.0 - - - -
199H ALA* 1.3 77.0 - - - +
201H ALA* 1.3 58.0 + - - +
203H GLY* 2.9 21.7 + - - -
204H PHE 4.1 10.2 + - - +
206H VAL* 4.8 8.3 - - + +
221H LEU* 3.1 20.1 + - - -
222H GLY* 3.0 29.3 + - - -
223H VAL* 3.9 10.5 - - + +
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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