Contacts of the helix formed by residues 175 - 189 (chain p) in PDB entry 5OOM
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 LEU 175 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174p LYS* 1.3 78.7 - - - +
176p HIS* 1.3 57.4 + - - +
178p ILE* 3.2 16.4 + - + +
179p ARG* 2.9 63.9 + - + +
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Residues in contact with HIS 176 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P PHE* 5.4 2.9 - + - -
171P VAL* 6.1 0.6 - - - +
175P PRO* 5.8 5.8 - - + -
174p LYS 3.2 7.4 - - - +
175p LEU* 1.3 77.1 - - - +
177p ARG* 1.3 66.2 - - - +
179p ARG* 3.2 32.3 + - + +
180p ILE* 3.0 52.1 + - + +
183p MET* 6.1 1.3 - - + -
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Residues in contact with ARG 177 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3226 ARG* 5.2 0.7 - - - +
54P ARG* 5.1 2.4 - - - +
57P GLU 2.9 25.7 + - - -
58P LEU* 3.2 37.0 + - - +
60P SER* 3.7 24.8 - - - -
78P TRP* 4.2 8.9 - - - -
143P PHE* 3.8 30.8 - - + +
175P PRO* 3.3 38.9 - - + +
174p LYS* 3.7 21.3 + - + +
175p LEU 3.3 0.4 - - - -
176p HIS* 1.3 79.2 - - - +
178p ILE* 1.3 59.7 + - + +
180p ILE* 3.3 1.9 + - - +
181p GLU* 2.9 57.8 + - - +
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Residues in contact with ILE 178 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3226 ARG* 3.9 25.1 - - - +
174p LYS* 3.6 29.6 - - + +
175p LEU* 3.2 16.7 + - + +
177p ARG* 1.3 77.2 - - + +
179p ARG* 1.3 64.4 + - - +
181p GLU* 4.2 6.2 - - + +
182p ASN* 2.8 49.8 + - - +
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Residues in contact with ARG 179 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175p LEU* 2.9 52.0 + - + +
176p HIS* 3.2 31.9 + - - +
178p ILE* 1.3 76.1 - - - +
180p ILE* 1.3 56.9 + - - +
182p ASN* 3.8 5.4 - - - +
183p MET* 3.0 44.2 + - + +
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Residues in contact with ILE 180 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P ASN* 4.5 7.9 - - + +
143P PHE* 3.6 36.8 - - + -
169P GLY 5.0 1.3 - - - +
171P VAL* 3.8 26.9 - - + -
176p HIS* 3.0 43.6 + - + +
177p ARG 3.9 3.6 - - - +
179p ARG* 1.3 75.5 - - - +
181p GLU* 1.3 58.6 + - - +
183p MET* 3.2 19.8 + - + +
184p ASN* 2.9 48.0 + - - +
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Residues in contact with GLU 181 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1926 GLU* 5.4 16.1 - - + +
3226 ARG* 2.4 35.3 + - - -
58P LEU* 3.6 16.4 - - - +
142P ASN* 3.5 26.3 - - - +
143P PHE* 4.0 7.9 - - + -
177p ARG* 2.9 52.1 + - - +
178p ILE* 4.2 4.7 - - + +
179p ARG 3.4 0.2 - - - -
180p ILE* 1.3 75.7 - - - +
182p ASN* 1.3 60.1 + - - +
184p ASN* 4.0 2.5 - - - +
185p ARG* 3.0 28.2 + - - +
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Residues in contact with ASN 182 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178p ILE* 2.8 43.5 + - - +
179p ARG* 3.8 5.2 - - - +
181p GLU* 1.3 78.5 - - - +
183p MET* 1.3 59.9 + - + +
185p ARG* 2.9 41.2 + - - +
186p GLU* 2.9 36.9 + - - +
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Residues in contact with MET 183 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176p HIS* 6.1 0.9 - - + -
179p ARG* 3.0 39.8 + - + +
180p ILE* 3.7 20.4 - - + +
182p ASN* 1.3 76.5 - - + +
184p ASN* 1.3 63.0 + - - +
186p GLU* 3.3 12.4 + - - +
187p ARG* 3.0 46.3 + - - +
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Residues in contact with ASN 184 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P LEU* 3.4 13.0 - - + +
142P ASN* 3.4 26.3 + - - +
169P GLY* 2.7 41.8 + - - +
180p ILE* 2.9 36.5 + - - +
181p GLU 4.3 1.8 - - - +
183p MET* 1.3 75.4 - - - +
185p ARG* 1.3 60.5 + - - +
187p ARG* 3.2 19.5 + - - +
188p LEU* 3.0 34.1 + - + +
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Residues in contact with ARG 185 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856 MET* 3.5 21.6 - - + +
1916 ASN* 5.4 1.3 - - - +
1926 GLU* 3.4 37.6 - - + +
1936 VAL 5.6 0.2 - - - -
1946 THR* 3.3 34.7 - - - +
1976 GLU* 4.3 12.7 + - - +
181p GLU 3.0 19.3 + - - +
182p ASN* 2.9 40.5 + - - +
184p ASN* 1.3 78.8 - - - +
186p GLU* 1.3 63.6 + - - +
188p LEU* 3.4 4.1 + - - +
189p ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 186 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182p ASN* 2.9 22.8 + - - +
183p MET* 3.7 11.7 - - - +
184p ASN 3.2 0.4 - - - -
185p ARG* 1.3 81.5 + - + +
187p ARG* 1.3 64.5 + - + +
189p ARG* 3.3 48.6 + - - +
190p GLN* 3.5 14.1 + - - +
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Residues in contact with ARG 187 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P LEU* 4.8 8.7 - - + -
166P THR 4.9 4.8 + - - -
167P GLU 5.0 4.6 + - - -
168P GLY 4.4 10.5 + - - -
169P GLY* 3.4 25.9 + - - +
183p MET* 3.0 33.5 + - - +
184p ASN* 3.2 24.5 + - - +
186p GLU* 1.3 78.3 - - - +
188p LEU* 1.3 64.8 + - - +
190p GLN* 3.7 31.9 - - - +
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Residues in contact with LEU 188 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856 MET* 3.7 16.2 - - + -
1866 PRO* 3.3 26.5 - - + +
1886 TYR* 4.7 13.2 - - + -
1916 ASN* 3.3 30.7 - - - +
134P GLN* 5.3 9.4 - - + +
137P LEU* 3.3 49.8 - - + +
138P GLU* 4.0 7.2 - - + +
184p ASN 3.0 19.0 + - - +
185p ARG* 5.2 0.9 - - - -
186p GLU 3.2 0.2 - - - -
187p ARG* 1.3 79.0 - - - +
189p ARG* 1.3 59.5 + - - +
190p GLN 3.1 7.5 + - - +
191p LYS* 4.2 3.5 - - - +
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Residues in contact with ARG 189 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1796 VAL* 4.4 22.9 - - + +
1836 ASP* 2.6 46.7 + - - +
1846 LEU 4.2 1.4 - - - +
1856 MET* 3.8 17.5 - - - +
1866 PRO* 4.7 1.6 - - - -
1976 GLU* 4.6 11.0 - - - -
185p ARG 3.0 17.3 + - - +
186p GLU* 3.3 42.2 + - - +
188p LEU* 1.3 74.6 - - - +
190p GLN* 1.3 51.0 + - - +
191p LYS* 2.6 26.5 + - - +
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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