Contacts of the helix formed by residues 175 - 185 (chain O) in PDB entry 5C7O
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 175 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O TYR 3.6 0.2 - - - -
174O LEU* 1.3 80.2 - - - +
176O ILE* 1.3 65.3 + - - +
177O GLN* 3.6 8.8 + - - +
178O ALA* 3.0 23.7 + - - +
179O ALA* 2.9 26.3 + - - +
192O ILE* 4.7 1.3 - - - -
196O SER* 4.0 0.4 - - - -
197O PRO* 4.2 13.2 - - - -
198O ASP* 3.6 14.1 - - - -
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Residues in contact with ILE 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O SER* 1.3 71.8 - - - +
177O GLN* 1.3 59.1 + - - +
180O SER* 2.9 35.6 + - - -
196O SER* 4.4 0.2 + - - -
198O ASP* 2.9 51.0 + - + +
199O ALA* 3.6 18.4 - - + -
200O PRO* 4.6 6.7 - - + -
218O ILE* 3.6 27.4 - - + +
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Residues in contact with GLN 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O SER* 3.2 8.3 + - - +
176O ILE* 1.3 81.7 - - - +
178O ALA* 1.3 61.3 + - - +
180O SER* 2.6 23.6 + - - +
181O ASP* 3.8 8.7 + - - +
198O ASP* 5.0 1.0 + - - -
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Residues in contact with ALA 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153O PRO* 4.3 11.3 - - - +
172O VAL 5.2 0.4 - - - +
173O TYR* 3.9 37.3 - - + -
174O LEU 4.4 0.2 - - - +
175O SER* 3.0 21.9 + - - +
177O GLN* 1.3 79.1 - - - +
179O ALA* 1.3 62.6 + - - +
181O ASP* 3.5 18.9 + - - +
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Residues in contact with ALA 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLU* 5.2 0.7 - - + -
173O TYR* 4.2 9.6 + - - +
175O SER 2.9 17.7 + - - +
176O ILE 4.1 0.2 - - - +
178O ALA* 1.3 73.0 - - - +
180O SER* 1.3 59.4 + - - +
181O ASP 3.1 2.7 - - - -
182O HIS* 3.0 37.8 + - + +
183O ILE 4.0 0.2 + - - -
190O VAL* 3.7 17.4 - - + +
192O ILE* 4.0 11.2 - - + -
218O ILE* 3.8 26.5 - - + -
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Residues in contact with SER 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176O ILE* 2.9 19.2 + - - -
177O GLN* 2.6 26.7 + - - +
179O ALA* 1.3 74.6 - - - +
181O ASP* 1.3 67.2 + - - +
182O HIS 3.1 0.2 - - - -
183O ILE* 3.0 19.8 + - - +
184O SER* 3.1 11.8 + - - -
217O ASN* 5.9 0.9 - - - -
218O ILE* 3.5 17.5 - - - -
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Residues in contact with ASP 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O PRO* 3.9 6.6 - - + +
154O LYS* 3.7 40.2 + - - +
177O GLN* 4.0 7.8 - - - +
178O ALA* 3.5 15.9 + - - +
179O ALA 3.1 0.4 - - - -
180O SER* 1.3 81.2 + - - +
182O HIS* 1.3 59.8 + - - +
184O SER* 2.8 26.5 + - - -
185O ALA* 3.0 11.6 + - - +
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Residues in contact with HIS 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O ASN* 3.5 23.8 - - + -
153O PRO* 3.5 26.1 - - + +
156O ILE* 3.8 10.1 - - + -
158O TRP* 3.0 23.9 + - - +
166O VAL* 4.0 9.8 - - + +
168O GLU* 2.8 26.1 + - + +
173O TYR* 5.8 0.2 - - + -
179O ALA* 3.0 28.8 + - - +
181O ASP* 1.3 77.6 - - - +
183O ILE* 1.3 61.2 + - - +
185O ALA* 3.0 12.4 + - - +
186O GLY 3.1 1.0 + - - -
187O ALA* 3.0 28.7 + - + +
190O VAL* 3.5 26.5 - - + -
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Residues in contact with ILE 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O ARG* 4.7 1.9 + - - -
180O SER* 3.0 14.1 + - - +
182O HIS* 1.3 76.2 - - - +
184O SER* 1.3 63.0 + - - +
186O GLY* 3.0 15.4 + - - -
187O ALA 3.3 24.3 - - - +
188O GLN 3.7 20.9 - - - +
189O ARG* 3.9 15.3 - - - +
190O VAL* 4.1 6.7 - - + -
217O ASN* 3.5 33.9 - - + +
218O ILE* 4.3 11.0 - - + -
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Residues in contact with SER 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154O LYS* 4.6 7.3 + - - +
159O ARG* 2.8 26.7 + - - +
180O SER 3.1 11.2 + - - -
181O ASP* 2.8 26.1 + - - +
183O ILE* 1.3 76.6 - - - +
185O ALA* 1.3 56.9 + - - +
186O GLY 3.2 0.2 - - - -
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Residues in contact with ALA 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O PRO 3.5 13.9 - - - +
154O LYS* 3.9 12.8 - - - +
156O ILE 3.3 21.1 - - - +
157O PRO* 4.4 0.9 - - - +
158O TRP* 3.5 23.5 + - + -
159O ARG* 3.5 18.1 + - - +
181O ASP 3.0 14.8 + - - +
182O HIS 3.0 7.4 + - - +
184O SER* 1.3 78.8 + - - +
186O GLY* 1.3 55.9 + - - +
187O ALA 3.7 0.2 - - - -
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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